0s autopkgtest [14:45:36]: starting date: 2024-03-19
  0s autopkgtest [14:45:36]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline
  0s autopkgtest [14:45:36]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3ga4evvu/out --timeout-copy=6000 --setup-commands 'sed -i "s/ports.ubuntu.com/ftpmaster.internal/; s/ubuntu-ports/ubuntu/" /etc/apt/sources.list `ls /etc/apt/sources.list.d/*.list 2>/dev/null || true`; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3.12/3.12.2-4build3 db5.3/5.3.28+dfsg2-5build1 openssl/3.0.13-0ubuntu2 readline/8.2-3.1' -- lxd -r lxd-armhf-10.44.124.223 lxd-armhf-10.44.124.223:autopkgtest/ubuntu/noble/armhf
 58s autopkgtest [14:46:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 61s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 63s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 63s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB]
 63s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [486 kB]
 63s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3777 kB]
 64s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [588 kB]
 64s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B]
 64s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B]
 64s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B]
 64s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3664 kB]
 65s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B]
 65s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [35.6 kB]
 65s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B]
 76s Fetched 8738 kB in 5s (1794 kB/s)
 77s Reading package lists...
 91s tee: /proc/self/fd/2: Permission denied
122s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
122s Hit:2 http://ports.ubuntu.com/ubuntu-ports noble InRelease
122s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
122s Hit:4 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease
122s Hit:5 http://ftpmaster.internal/ubuntu noble-security InRelease
122s Hit:6 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease
122s Hit:7 http://ftpmaster.internal/ubuntu noble-proposed InRelease
122s Hit:8 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease
129s Reading package lists...
129s Reading package lists...
130s Building dependency tree...
130s Reading state information...
132s Calculating upgrade...
134s The following packages were automatically installed and are no longer required:
134s   libatasmart4 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3
134s   libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3
134s   libblockdev-utils3 libblockdev3 libbytesize-common libbytesize1 libnspr4
134s   libnss3 libnvme1t64 libpolkit-agent-1-0 libvolume-key1
134s   linux-headers-6.8.0-11 python3-lib2to3
134s Use 'apt autoremove' to remove them.
135s The following packages will be REMOVED:
135s   libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1
135s   libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11
135s   libhogweed6 libmagic1 libnetplan0 libnettle8 libnpth0 libnvme1 libparted2
135s   libpcap0.8 libperl5.38 libpng16-16 libpsl5 libreadline8 libreiserfscore0
135s   libssl3 libtirpc3 libudisks2-0 libuv1 linux-headers-6.8.0-11-generic
135s   linux-headers-generic python3-distutils udisks2
135s The following NEW packages will be installed:
135s   libapt-pkg6.0t64 libarchive13t64 libatm1t64 libcurl3t64-gnutls libcurl4t64
135s   libdb5.3t64 libelf1t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64
135s   libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 libmagic1t64
135s   libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64
135s   libpcap0.8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64
135s   libreiserfscore0t64 libssl3t64 libtirpc3t64 libuv1t64 xdg-user-dirs
135s The following packages have been kept back:
135s   multipath-tools
135s The following packages will be upgraded:
135s   apparmor apt apt-utils bind9-dnsutils bind9-host bind9-libs bolt
135s   bsdextrautils bsdutils btrfs-progs coreutils cryptsetup-bin curl dbus
135s   dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common
135s   dbus-user-session debianutils dhcpcd-base dirmngr dmsetup dpkg dpkg-dev
135s   e2fsprogs e2fsprogs-l10n eject fdisk file ftp fwupd gawk gcc-13-base
135s   gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnupg gnupg-l10n
135s   gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv groff-base
135s   ibverbs-providers inetutils-telnet info initramfs-tools initramfs-tools-bin
135s   initramfs-tools-core install-info iproute2 jq keyboxd kmod kpartx
135s   krb5-locales libapparmor1 libaudit-common libaudit1 libblkid1
135s   libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3
135s   libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3
135s   libblockdev3 libbpf1 libbrotli1 libbsd0 libc-bin libc6 libcap-ng0
135s   libcom-err2 libcryptsetup12 libdbus-1-3 libdebconfclient0 libdevmapper1.02.1
135s   libdpkg-perl libevent-core-2.1-7 libexpat1 libfdisk1 libfido2-1 libftdi1-2
135s   libfwupd2 libgcc-s1 libgirepository-1.0-1 libglib2.0-data libgssapi-krb5-2
135s   libgudev-1.0-0 libgusb2 libibverbs1 libjcat1 libjq1 libjson-glib-1.0-0
135s   libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 libkrb5support0
135s   libldap-common libldap2 liblocale-gettext-perl liblzma5 libmagic-mgc
135s   libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 libnsl2
135s   libnss-systemd libpam-modules libpam-modules-bin libpam-runtime
135s   libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0
135s   libpolkit-gobject-1-0 libpython3-stdlib libpython3.11-minimal
135s   libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libqmi-glib5
135s   libqmi-proxy libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules
135s   libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2
135s   libslang2 libsmartcols1 libsqlite3-0 libss2 libssh-4 libstdc++6
135s   libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl
135s   libtirpc-common libudev1 libusb-1.0-0 libuuid1 libvolume-key1 libxml2
135s   libxmlb2 libxmuu1 locales logsave lshw lsof man-db mount mtr-tiny
135s   netplan-generator netplan.io openssh-client openssh-server
135s   openssh-sftp-server openssl parted perl perl-base perl-modules-5.38
135s   pinentry-curses plymouth plymouth-theme-ubuntu-text psmisc python-apt-common
135s   python3 python3-apt python3-cryptography python3-dbus python3-gdbm
135s   python3-gi python3-lib2to3 python3-markupsafe python3-minimal
135s   python3-netplan python3-openssl python3-pkg-resources python3-pyrsistent
135s   python3-setuptools python3-typing-extensions python3-yaml python3.11
135s   python3.11-minimal python3.12 python3.12-minimal readline-common rsync
135s   shared-mime-info sudo systemd systemd-dev systemd-resolved systemd-sysv
135s   systemd-timesyncd tcpdump telnet tnftp ubuntu-minimal ubuntu-pro-client
135s   ubuntu-pro-client-l10n ubuntu-standard udev usb.ids util-linux uuid-runtime
135s   vim-common vim-tiny wget xxd xz-utils zlib1g
135s 228 upgraded, 30 newly installed, 34 to remove and 1 not upgraded.
135s Need to get 87.4 MB of archives.
135s After this operation, 8988 kB disk space will be freed.
135s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu2 [102 kB]
136s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB]
136s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB]
136s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB]
136s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu6 [2827 kB]
136s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu2 [975 kB]
136s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu1 [49.2 kB]
136s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build6 [51.3 kB]
136s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12 armhf 3.12.2-4build3 [645 kB]
136s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1 armhf 2.6.1-2 [65.9 kB]
137s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-minimal armhf 3.12.2-4build3 [1942 kB]
137s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-stdlib armhf 3.12.2-4build3 [1906 kB]
137s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-minimal armhf 3.12.2-4build3 [816 kB]
137s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf parted armhf 3.6-3.1build2 [39.4 kB]
137s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu2 [160 kB]
137s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2build3 [70.5 kB]
137s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu5 [103 kB]
137s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-timesyncd armhf 255.4-1ubuntu5 [36.0 kB]
137s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB]
137s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B]
137s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build1 [13.5 kB]
137s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1 [44.3 kB]
137s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu3 [62.0 kB]
137s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.0-0.2 [117 kB]
137s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB]
137s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0t64 armhf 2.79.3-3ubuntu5 [1414 kB]
137s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libvolume-key1 armhf 0.3.12-7build1 [38.4 kB]
137s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpgme11t64 armhf 1.18.0-4.1ubuntu3 [120 kB]
137s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjcat1 armhf 0.2.0-2build2 [30.4 kB]
137s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libarchive13t64 armhf 3.7.2-1.1ubuntu1 [330 kB]
137s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fwupd armhf 1.9.15-1 [4349 kB]
138s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client-l10n armhf 31.2 [19.4 kB]
138s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client armhf 31.2 [216 kB]
138s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11 armhf 3.11.8-1build4 [589 kB]
138s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11-minimal armhf 3.11.8-1build4 [1795 kB]
138s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-minimal armhf 3.11.8-1build4 [826 kB]
138s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4ubuntu4 [19.2 kB]
138s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build2 [12.7 kB]
138s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build2 [8962 B]
138s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2 [1671 kB]
139s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu3 [15.0 kB]
139s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
139s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gdbm armhf 3.12.2-3ubuntu2 [17.1 kB]
139s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-3build4 [1196 kB]
139s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1 [30.3 kB]
139s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1 [6208 B]
139s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2 [4101 kB]
140s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2 [231 kB]
140s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-5build1 [661 kB]
140s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-stdlib armhf 3.11.8-1build4 [1810 kB]
140s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf keyboxd armhf 2.4.4-2ubuntu15 [111 kB]
140s Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1 [6940 B]
140s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu15 [224 kB]
140s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu15 [524 kB]
140s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-wks-client armhf 2.4.4-2ubuntu15 [87.4 kB]
140s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-utils armhf 2.4.4-2ubuntu15 [158 kB]
140s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu15 [235 kB]
140s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgsm armhf 2.4.4-2ubuntu15 [241 kB]
140s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-3.1 [129 kB]
140s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gawk armhf 1:5.2.1-2build2 [415 kB]
140s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fdisk armhf 2.39.3-9ubuntu2 [135 kB]
140s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu15 [115 kB]
140s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dirmngr armhf 2.4.4-2ubuntu15 [346 kB]
140s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg all 2.4.4-2ubuntu15 [359 kB]
140s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-apt armhf 2.7.6build1 [162 kB]
140s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.13ubuntu1 [210 kB]
140s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.13ubuntu1 [986 kB]
140s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2 [187 kB]
140s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2 [187 kB]
140s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu2 [1046 kB]
141s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.13ubuntu1 [1367 kB]
141s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu7 [290 kB]
141s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfwupd2 armhf 1.9.15-1 [123 kB]
141s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.7 kB]
141s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf wget armhf 1.21.4-1ubuntu2 [317 kB]
141s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tnftp armhf 20230507-2build1 [98.6 kB]
141s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcap0.8t64 armhf 1.10.4-4.1ubuntu1 [137 kB]
141s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tcpdump armhf 4.99.4-3ubuntu2 [425 kB]
141s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB]
141s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-resolved armhf 255.4-1ubuntu5 [289 kB]
141s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sudo armhf 1.9.15p5-3ubuntu3 [936 kB]
141s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsync armhf 3.2.7-1build1 [413 kB]
141s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cryptography armhf 41.0.7-4build2 [788 kB]
142s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu10 [35.5 kB]
142s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-client armhf 1:9.6p1-3ubuntu10 [890 kB]
142s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-server armhf 1:9.6p1-3ubuntu10 [503 kB]
142s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu2 [1558 kB]
142s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB]
142s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB]
142s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udev armhf 255.4-1ubuntu5 [1852 kB]
142s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB]
142s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnss-systemd armhf 255.4-1ubuntu5 [148 kB]
142s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-systemd armhf 255.4-1ubuntu5 [216 kB]
142s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB]
143s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu3 [47.0 kB]
143s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu3 [261 kB]
143s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB]
143s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-user-session armhf 1.14.10-4ubuntu2 [9962 B]
143s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu2 [45.0 kB]
143s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-bin armhf 1.14.10-4ubuntu2 [37.1 kB]
143s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB]
143s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus armhf 1.14.10-4ubuntu2 [28.1 kB]
143s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-daemon armhf 1.14.10-4ubuntu2 [109 kB]
143s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu2 [190 kB]
143s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kmod armhf 31+20240202-2ubuntu4 [91.8 kB]
143s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu4 [44.9 kB]
143s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu2 [171 kB]
143s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu2 [49.5 kB]
143s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu2 [34.4 kB]
143s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu2 [238 kB]
143s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu2 [196 kB]
143s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu2 [134 kB]
143s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu2 [135 kB]
143s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libparted2t64 armhf 3.6-3.1build2 [143 kB]
143s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu1 [599 kB]
143s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB]
143s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu2 [117 kB]
143s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-3.1 [56.4 kB]
143s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-yaml armhf 6.0.1-2build1 [117 kB]
143s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python-apt-common all 2.7.6build1 [19.8 kB]
143s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB]
143s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB]
143s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu4 [1229 kB]
144s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.12.2-0ubuntu1 [27.1 kB]
144s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.12.2-0ubuntu1 [24.1 kB]
144s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.12.2-0ubuntu1 [9802 B]
144s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu2 [78.7 kB]
144s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build1 [946 kB]
144s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4ubuntu4 [49.7 kB]
144s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-common all 1.8.0-2build1 [4210 B]
144s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-0 armhf 1.8.0-2build1 [61.2 kB]
144s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu2 [595 kB]
144s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgudev-1.0-0 armhf 1:238-3ubuntu2 [13.6 kB]
144s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libusb-1.0-0 armhf 2:1.0.27-1 [48.7 kB]
144s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgusb2 armhf 0.4.8-1build1 [34.6 kB]
144s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-proxy armhf 1.31.2-0ubuntu2 [5748 B]
144s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-glib4 armhf 1.31.2-0ubuntu2 [216 kB]
144s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmm-glib0 armhf 1.23.4-0ubuntu1 [214 kB]
144s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-agent-1-0 armhf 124-1ubuntu1 [15.3 kB]
144s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-gobject-1-0 armhf 124-1ubuntu1 [44.1 kB]
144s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-proxy armhf 1.35.2-0ubuntu1 [5732 B]
144s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqrtr-glib0 armhf 1.2.2-1ubuntu3 [15.4 kB]
144s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-glib5 armhf 1.35.2-0ubuntu1 [908 kB]
144s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmlb2 armhf 0.3.15-1build1 [57.0 kB]
144s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf shared-mime-info armhf 2.4-1build1 [470 kB]
144s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB]
144s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-5.1build3 [119 kB]
144s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-5.1build3 [321 kB]
144s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-5.1build3 [31.4 kB]
144s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-5.1build3 [78.6 kB]
144s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB]
144s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build1 [68.1 kB]
144s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB]
144s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libibverbs1 armhf 50.0-2build1 [57.9 kB]
144s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfido2-1 armhf 1.14.0-1build1 [75.8 kB]
144s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu3 [1280 kB]
144s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debianutils armhf 5.17 [88.9 kB]
144s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu2 [1216 kB]
144s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu6 [530 kB]
144s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf curl armhf 8.5.0-2ubuntu7 [219 kB]
144s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4t64 armhf 8.5.0-2ubuntu7 [296 kB]
144s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbpf1 armhf 1:1.3.0-2build1 [146 kB]
144s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf iproute2 armhf 6.1.0-1ubuntu5 [1060 kB]
144s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build2 [49.9 kB]
144s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lsof armhf 4.95.0-1build2 [248 kB]
144s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build2 [36.5 kB]
144s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B]
144s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1 [73.2 kB]
145s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-utils3 armhf 3.1.0-1build1 [16.9 kB]
145s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-fs3 armhf 3.1.0-1build1 [34.4 kB]
145s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB]
145s Get:172 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-minimal armhf 1.536build1 [10.7 kB]
145s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools all 0.142ubuntu22 [9056 B]
145s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-core all 0.142ubuntu22 [50.0 kB]
145s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B]
145s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu2 [201 kB]
145s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu2 [571 kB]
145s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf btrfs-progs armhf 6.6.3-1.1build1 [852 kB]
145s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dhcpcd-base armhf 1:10.0.6-1ubuntu2 [186 kB]
145s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf eject armhf 2.39.3-9ubuntu2 [43.2 kB]
145s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf locales all 2.39-0ubuntu6 [4232 kB]
145s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnetplan1 armhf 1.0-1 [113 kB]
145s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-netplan armhf 1.0-1 [22.5 kB]
145s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan-generator armhf 1.0-1 [58.7 kB]
145s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dbus armhf 1.3.2-5build2 [94.7 kB]
145s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan.io armhf 1.0-1 [64.3 kB]
145s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-tiny armhf 2:9.1.0016-1ubuntu5 [665 kB]
145s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-common all 2:9.1.0016-1ubuntu5 [385 kB]
145s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-bin armhf 0.142ubuntu22 [20.1 kB]
145s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreiserfscore0t64 armhf 1:3.6.27-7.1 [66.2 kB]
145s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3 [21.1 kB]
145s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3 [307 kB]
145s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3 [81.4 kB]
145s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-nvme3 armhf 3.1.0-1build1 [17.5 kB]
145s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnvme1t64 armhf 1.8-3 [67.5 kB]
145s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libplymouth5 armhf 24.004.60-1ubuntu5 [140 kB]
145s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-3 [166 kB]
145s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-host armhf 1:9.18.24-0ubuntu3 [47.4 kB]
145s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu3 [149 kB]
145s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-libs armhf 1:9.18.24-0ubuntu3 [1148 kB]
145s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuv1t64 armhf 1.48.0-1.1 [82.9 kB]
145s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu2 [41.7 kB]
145s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu2 [10.8 kB]
145s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build4 [10.1 kB]
145s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB]
146s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf install-info armhf 7.1-3build1 [60.5 kB]
146s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-19ubuntu1 [47.7 kB]
146s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu2 [14.7 kB]
146s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dmsetup armhf 2:1.02.185-3ubuntu2 [81.1 kB]
146s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-girepository-2.0 armhf 1.79.1-1ubuntu6 [24.8 kB]
146s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-glib-2.0 armhf 2.79.3-3ubuntu5 [182 kB]
146s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgirepository-1.0-1 armhf 1.79.1-1ubuntu6 [106 kB]
146s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-5.1build3 [13.8 kB]
146s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbsd0 armhf 0.12.1-1 [36.6 kB]
146s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
146s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libslang2 armhf 2.3.3-3build1 [478 kB]
146s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gi armhf 3.47.0-3build1 [219 kB]
146s Get:218 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB]
146s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xxd armhf 2:9.1.0016-1ubuntu5 [62.4 kB]
146s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apparmor armhf 4.0.0-beta3-0ubuntu2 [562 kB]
147s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ftp all 20230507-2build1 [4724 B]
147s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf inetutils-telnet armhf 2:2.5-3ubuntu3 [90.7 kB]
147s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf info armhf 7.1-3build1 [127 kB]
147s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmuu1 armhf 2:1.1.3-3build1 [8004 B]
147s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2build2 [310 kB]
147s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mtr-tiny armhf 0.95-1.1build1 [51.7 kB]
147s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu5 [9826 B]
147s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth armhf 24.004.60-1ubuntu5 [143 kB]
147s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1 [176 kB]
147s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main armhf telnet all 0.17+2.5-3ubuntu3 [3682 B]
147s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.0-0.2 [271 kB]
147s Get:232 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-standard armhf 1.536build1 [10.7 kB]
147s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main armhf usb.ids all 2024.03.18-1 [223 kB]
147s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bolt armhf 0.9.6-2build1 [138 kB]
147s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu2 [214 kB]
147s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu4 [1074 kB]
148s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu4 [268 kB]
148s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB]
148s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ibverbs-providers armhf 50.0-2build1 [27.4 kB]
148s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main armhf jq armhf 1.7.1-3 [65.2 kB]
148s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjq1 armhf 1.7.1-3 [156 kB]
148s Get:242 http://ftpmaster.internal/ubuntu noble/main armhf libatm1t64 armhf 1:2.5.1-5.1 [20.0 kB]
148s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-crypto3 armhf 3.1.0-1build1 [20.3 kB]
148s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-loop3 armhf 3.1.0-1build1 [6502 B]
148s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-mdraid3 armhf 3.1.0-1build1 [13.3 kB]
148s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-part3 armhf 3.1.0-1build1 [16.4 kB]
148s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-swap3 armhf 3.1.0-1build1 [8894 B]
148s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev3 armhf 3.1.0-1build1 [42.9 kB]
148s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB]
148s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libftdi1-2 armhf 1.5-6build4 [25.7 kB]
148s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB]
148s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules armhf 2.1.28+dfsg1-4ubuntu4 [61.4 kB]
148s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lib2to3 all 3.12.2-3ubuntu2 [79.3 kB]
148s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-markupsafe armhf 2.1.5-1build1 [12.1 kB]
148s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-openssl all 24.0.0-4 [47.9 kB]
148s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyrsistent armhf 0.20.0-1build1 [53.0 kB]
148s Get:257 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-typing-extensions all 4.10.0-1 [60.7 kB]
148s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kpartx armhf 0.9.4-5ubuntu4 [31.4 kB]
152s Preconfiguring packages ...
153s Fetched 87.4 MB in 13s (6755 kB/s)
154s (Reading database ... 
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(Reading database ... 58620 files and directories currently installed.)
154s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_armhf.deb ...
154s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ...
154s Setting up bsdutils (1:2.39.3-9ubuntu2) ...
154s (Reading database ... 
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(Reading database ... 58620 files and directories currently installed.)
154s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ...
154s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
154s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ...
154s (Reading database ... 
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(Reading database ... 58620 files and directories currently installed.)
154s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ...
154s Unpacking libgcc-s1:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
154s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ...
155s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 58620 files and directories currently installed.)
155s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ...
155s Unpacking libstdc++6:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
155s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ...
155s (Reading database ... 
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155s Preparing to unpack .../libc6_2.39-0ubuntu6_armhf.deb ...
156s Unpacking libc6:armhf (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
157s Setting up libc6:armhf (2.39-0ubuntu6) ...
158s (Reading database ... 
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158s Preparing to unpack .../openssl_3.0.13-0ubuntu2_armhf.deb ...
158s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
159s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ...
159s Unpacking zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ...
159s Setting up zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) ...
159s (Reading database ... 
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159s Preparing to unpack .../0-librtmp1_2.4+20151223.gitfa8646d.1-2build6_armhf.deb ...
159s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ...
159s Preparing to unpack .../1-python3.12_3.12.2-4build3_armhf.deb ...
159s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ...
160s Preparing to unpack .../2-libexpat1_2.6.1-2_armhf.deb ...
160s Unpacking libexpat1:armhf (2.6.1-2) over (2.6.0-1) ...
160s Preparing to unpack .../3-python3.12-minimal_3.12.2-4build3_armhf.deb ...
160s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ...
160s Preparing to unpack .../4-libpython3.12-stdlib_3.12.2-4build3_armhf.deb ...
160s Unpacking libpython3.12-stdlib:armhf (3.12.2-4build3) over (3.12.2-1) ...
161s Preparing to unpack .../5-libpython3.12-minimal_3.12.2-4build3_armhf.deb ...
162s Unpacking libpython3.12-minimal:armhf (3.12.2-4build3) over (3.12.2-1) ...
162s Preparing to unpack .../6-parted_3.6-3.1build2_armhf.deb ...
163s Unpacking parted (3.6-3.1build2) over (3.6-3) ...
163s (Reading database ... 
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163s Removing libparted2:armhf (3.6-3) ...
163s (Reading database ... 
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163s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_armhf.deb ...
163s Unpacking libblkid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
163s Setting up libblkid1:armhf (2.39.3-9ubuntu2) ...
163s (Reading database ... 
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164s Preparing to unpack .../libselinux1_3.5-2build3_armhf.deb ...
164s Unpacking libselinux1:armhf (3.5-2build3) over (3.5-2build1) ...
164s Setting up libselinux1:armhf (3.5-2build3) ...
164s (Reading database ... 
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164s Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ...
164s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
164s Preparing to unpack .../systemd-timesyncd_255.4-1ubuntu5_armhf.deb ...
164s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
164s Preparing to unpack .../dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ...
164s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
164s Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ...
164s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ...
165s Setting up libaudit-common (1:3.1.2-2.1) ...
165s (Reading database ... 
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165s Preparing to unpack .../libcap-ng0_0.8.4-2build1_armhf.deb ...
165s Unpacking libcap-ng0:armhf (0.8.4-2build1) over (0.8.4-2) ...
165s Setting up libcap-ng0:armhf (0.8.4-2build1) ...
165s (Reading database ... 
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165s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_armhf.deb ...
165s Unpacking libaudit1:armhf (1:3.1.2-2.1) over (1:3.1.2-2) ...
165s Setting up libaudit1:armhf (1:3.1.2-2.1) ...
165s (Reading database ... 
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165s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_armhf.deb ...
165s Unpacking libpam0g:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
166s Setting up libpam0g:armhf (1.5.3-5ubuntu3) ...
166s (Reading database ... 
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166s Preparing to unpack .../liblzma5_5.6.0-0.2_armhf.deb ...
166s Unpacking liblzma5:armhf (5.6.0-0.2) over (5.4.5-0.3) ...
166s Setting up liblzma5:armhf (5.6.0-0.2) ...
166s (Reading database ... 
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166s Preparing to unpack .../libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ...
166s Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
167s (Reading database ... 
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167s Removing udisks2 (2.10.1-1ubuntu2) ...
168s dpkg: libglib2.0-0:armhf: dependency problems, but removing anyway as you requested:
168s  shared-mime-info depends on libglib2.0-0 (>= 2.75.3).
168s  python3-gi depends on libglib2.0-0 (>= 2.77.0).
168s  python3-dbus depends on libglib2.0-0 (>= 2.16.0).
168s  netplan.io depends on libglib2.0-0 (>= 2.70.0).
168s  netplan-generator depends on libglib2.0-0 (>= 2.70.0).
168s  libxmlb2:armhf depends on libglib2.0-0 (>= 2.54.0).
168s  libvolume-key1:armhf depends on libglib2.0-0 (>= 2.18.0).
168s  libudisks2-0:armhf depends on libglib2.0-0 (>= 2.75.3).
168s  libqrtr-glib0:armhf depends on libglib2.0-0 (>= 2.56).
168s  libqmi-proxy depends on libglib2.0-0 (>= 2.30.0).
168s  libqmi-glib5:armhf depends on libglib2.0-0 (>= 2.54.0).
168s  libpolkit-gobject-1-0:armhf depends on libglib2.0-0 (>= 2.38.0).
168s  libpolkit-agent-1-0:armhf depends on libglib2.0-0 (>= 2.38.0).
168s  libnetplan0:armhf depends on libglib2.0-0 (>= 2.75.3).
168s  libmm-glib0:armhf depends on libglib2.0-0 (>= 2.62.0).
168s  libmbim-proxy depends on libglib2.0-0 (>= 2.56).
168s  libmbim-glib4:armhf depends on libglib2.0-0 (>= 2.56).
168s  libjson-glib-1.0-0:armhf depends on libglib2.0-0 (>= 2.75.3).
168s  libjcat1:armhf depends on libglib2.0-0 (>= 2.75.3).
168s  libgusb2:armhf depends on libglib2.0-0 (>= 2.75.3).
168s  libgudev-1.0-0:armhf depends on libglib2.0-0 (>= 2.38.0).
168s  libgirepository-1.0-1:armhf depends on libglib2.0-0 (>= 2.79.0).
168s  libfwupd2:armhf depends on libglib2.0-0 (>= 2.79.0).
168s  libblockdev3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  libblockdev-utils3:armhf depends on libglib2.0-0 (>= 2.75.3).
168s  libblockdev-swap3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  libblockdev-part3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  libblockdev-nvme3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  libblockdev-mdraid3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  libblockdev-loop3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  libblockdev-fs3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  libblockdev-crypto3:armhf depends on libglib2.0-0 (>= 2.42.2).
168s  gir1.2-glib-2.0:armhf depends on libglib2.0-0 (= 2.79.2-1~ubuntu1).
168s  fwupd depends on libglib2.0-0 (>= 2.79.0).
168s  bolt depends on libglib2.0-0 (>= 2.56.0).
168s 
168s Removing libglib2.0-0:armhf (2.79.2-1~ubuntu1) ...
168s Selecting previously unselected package libglib2.0-0t64:armhf.
168s (Reading database ... 
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168s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_armhf.deb ...
168s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:armhf.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
168s removed '/var/lib/dpkg/info/libglib2.0-0:armhf.postrm'
168s Unpacking libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ...
169s Preparing to unpack .../libvolume-key1_0.3.12-7build1_armhf.deb ...
169s Unpacking libvolume-key1:armhf (0.3.12-7build1) over (0.3.12-5build2) ...
169s dpkg: libgpgme11:armhf: dependency problems, but removing anyway as you requested:
169s  libjcat1:armhf depends on libgpgme11 (>= 1.2.0).
169s 
169s (Reading database ... 
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169s Removing libgpgme11:armhf (1.18.0-4ubuntu1) ...
169s Selecting previously unselected package libgpgme11t64:armhf.
169s (Reading database ... 
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169s Preparing to unpack .../libgpgme11t64_1.18.0-4.1ubuntu3_armhf.deb ...
169s Unpacking libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ...
169s Preparing to unpack .../libjcat1_0.2.0-2build2_armhf.deb ...
169s Unpacking libjcat1:armhf (0.2.0-2build2) over (0.2.0-2) ...
169s dpkg: libarchive13:armhf: dependency problems, but removing anyway as you requested:
169s  fwupd depends on libarchive13 (>= 3.2.1).
169s 
169s (Reading database ... 
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169s Removing libarchive13:armhf (3.7.2-1ubuntu2) ...
170s Selecting previously unselected package libarchive13t64:armhf.
170s (Reading database ... 
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170s Preparing to unpack .../00-libarchive13t64_3.7.2-1.1ubuntu1_armhf.deb ...
170s Unpacking libarchive13t64:armhf (3.7.2-1.1ubuntu1) ...
170s Preparing to unpack .../01-fwupd_1.9.15-1_armhf.deb ...
170s Unpacking fwupd (1.9.15-1) over (1.9.14-1) ...
171s Preparing to unpack .../02-ubuntu-pro-client-l10n_31.2_armhf.deb ...
171s Unpacking ubuntu-pro-client-l10n (31.2) over (31.1) ...
171s Preparing to unpack .../03-ubuntu-pro-client_31.2_armhf.deb ...
173s Unpacking ubuntu-pro-client (31.2) over (31.1) ...
173s Preparing to unpack .../04-python3.11_3.11.8-1build4_armhf.deb ...
173s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ...
174s Preparing to unpack .../05-python3.11-minimal_3.11.8-1build4_armhf.deb ...
174s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ...
174s Preparing to unpack .../06-libpython3.11-minimal_3.11.8-1build4_armhf.deb ...
174s Unpacking libpython3.11-minimal:armhf (3.11.8-1build4) over (3.11.8-1) ...
175s Preparing to unpack .../07-libsasl2-modules-db_2.1.28+dfsg1-4ubuntu4_armhf.deb ...
175s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-4ubuntu4) over (2.1.28+dfsg1-4) ...
175s Preparing to unpack .../08-libtext-iconv-perl_1.7-8build2_armhf.deb ...
175s Unpacking libtext-iconv-perl:armhf (1.7-8build2) over (1.7-8build1) ...
176s Preparing to unpack .../09-libtext-charwidth-perl_0.04-11build2_armhf.deb ...
176s Unpacking libtext-charwidth-perl:armhf (0.04-11build2) over (0.04-11build1) ...
176s Preparing to unpack .../10-perl-base_5.38.2-3.2_armhf.deb ...
176s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
177s Setting up perl-base (5.38.2-3.2) ...
178s (Reading database ... 
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178s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu3_armhf.deb ...
178s Unpacking liblocale-gettext-perl (1.07-6ubuntu3) over (1.07-6build1) ...
178s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
178s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
181s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu2_armhf.deb ...
181s Unpacking python3-gdbm:armhf (3.12.2-3ubuntu2) over (3.11.5-1) ...
181s Preparing to unpack .../man-db_2.12.0-3build4_armhf.deb ...
181s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ...
181s dpkg: libgdbm-compat4:armhf: dependency problems, but removing anyway as you requested:
181s  libperl5.38:armhf depends on libgdbm-compat4 (>= 1.18-3).
181s 
182s (Reading database ... 
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182s Removing libgdbm-compat4:armhf (1.23-5) ...
182s dpkg: libgdbm6:armhf: dependency problems, but removing anyway as you requested:
182s  libperl5.38:armhf depends on libgdbm6 (>= 1.21).
182s 
182s Removing libgdbm6:armhf (1.23-5) ...
182s Selecting previously unselected package libgdbm6t64:armhf.
182s (Reading database ... 
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182s Preparing to unpack .../libgdbm6t64_1.23-5.1_armhf.deb ...
182s Unpacking libgdbm6t64:armhf (1.23-5.1) ...
182s Selecting previously unselected package libgdbm-compat4t64:armhf.
182s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_armhf.deb ...
182s Unpacking libgdbm-compat4t64:armhf (1.23-5.1) ...
182s dpkg: libperl5.38:armhf: dependency problems, but removing anyway as you requested:
182s  perl depends on libperl5.38 (= 5.38.2-3).
182s 
182s (Reading database ... 
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182s Removing libperl5.38:armhf (5.38.2-3) ...
183s Selecting previously unselected package libperl5.38t64:armhf.
183s (Reading database ... 
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183s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_armhf.deb ...
183s Unpacking libperl5.38t64:armhf (5.38.2-3.2) ...
184s Preparing to unpack .../perl_5.38.2-3.2_armhf.deb ...
184s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ...
184s dpkg: libdb5.3:armhf: dependency problems, but removing anyway as you requested:
184s  libpython3.11-stdlib:armhf depends on libdb5.3.
184s  libpam-modules:armhf depends on libdb5.3.
184s  iproute2 depends on libdb5.3.
184s  apt-utils depends on libdb5.3.
184s 
184s (Reading database ... 
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184s Removing libdb5.3:armhf (5.3.28+dfsg2-4) ...
184s Selecting previously unselected package libdb5.3t64:armhf.
184s (Reading database ... 
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184s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_armhf.deb ...
184s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-5build1) ...
185s Preparing to unpack .../libpython3.11-stdlib_3.11.8-1build4_armhf.deb ...
185s Unpacking libpython3.11-stdlib:armhf (3.11.8-1build4) over (3.11.8-1) ...
186s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_armhf.deb ...
186s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
186s dpkg: libnpth0:armhf: dependency problems, but removing anyway as you requested:
186s  gpgv depends on libnpth0 (>= 0.90).
186s  gpgsm depends on libnpth0 (>= 0.90).
186s  gpg-agent depends on libnpth0 (>= 0.90).
186s  gpg depends on libnpth0 (>= 0.90).
186s  dirmngr depends on libnpth0 (>= 0.90).
186s 
186s (Reading database ... 
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186s Removing libnpth0:armhf (1.6-3build2) ...
186s Selecting previously unselected package libnpth0t64:armhf.
186s (Reading database ... 
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186s Preparing to unpack .../libnpth0t64_1.6-3.1_armhf.deb ...
186s Unpacking libnpth0t64:armhf (1.6-3.1) ...
186s Setting up libnpth0t64:armhf (1.6-3.1) ...
187s (Reading database ... 
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187s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_armhf.deb ...
187s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
187s Setting up gpgv (2.4.4-2ubuntu15) ...
187s (Reading database ... 
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187s Preparing to unpack .../gpg_2.4.4-2ubuntu15_armhf.deb ...
187s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
187s Preparing to unpack .../gpg-wks-client_2.4.4-2ubuntu15_armhf.deb ...
187s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
187s Preparing to unpack .../gnupg-utils_2.4.4-2ubuntu15_armhf.deb ...
187s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
187s Preparing to unpack .../gpg-agent_2.4.4-2ubuntu15_armhf.deb ...
187s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
188s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_armhf.deb ...
188s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
188s dpkg: libreadline8:armhf: dependency problems, but removing anyway as you requested:
188s  gpgconf depends on libreadline8 (>= 6.0).
188s  gawk depends on libreadline8 (>= 6.0).
188s  fdisk depends on libreadline8 (>= 6.0).
188s 
188s (Reading database ... 
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188s Removing libreadline8:armhf (8.2-3) ...
188s Selecting previously unselected package libreadline8t64:armhf.
188s (Reading database ... 
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188s Preparing to unpack .../libreadline8t64_8.2-3.1_armhf.deb ...
188s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
188s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
188s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
188s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
188s Unpacking libreadline8t64:armhf (8.2-3.1) ...
188s Setting up libreadline8t64:armhf (8.2-3.1) ...
189s (Reading database ... 
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189s Preparing to unpack .../0-gawk_1%3a5.2.1-2build2_armhf.deb ...
189s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ...
189s Preparing to unpack .../1-fdisk_2.39.3-9ubuntu2_armhf.deb ...
189s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
189s Preparing to unpack .../2-gpgconf_2.4.4-2ubuntu15_armhf.deb ...
189s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
189s Preparing to unpack .../3-dirmngr_2.4.4-2ubuntu15_armhf.deb ...
189s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
190s Preparing to unpack .../4-gnupg_2.4.4-2ubuntu15_all.deb ...
190s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
190s Preparing to unpack .../5-python3-apt_2.7.6build1_armhf.deb ...
190s Unpacking python3-apt (2.7.6build1) over (2.7.6) ...
190s Preparing to unpack .../6-apt-utils_2.7.13ubuntu1_armhf.deb ...
190s Unpacking apt-utils (2.7.13ubuntu1) over (2.7.12) ...
191s dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested:
191s  apt depends on libapt-pkg6.0 (>= 2.7.12).
191s 
191s (Reading database ... 
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191s Removing libapt-pkg6.0:armhf (2.7.12) ...
191s dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested:
191s  libhogweed6:armhf depends on libnettle8.
191s  libgnutls30:armhf depends on libnettle8 (>= 3.9~).
191s  libcurl3-gnutls:armhf depends on libnettle8.
191s 
191s Removing libnettle8:armhf (3.9.1-2) ...
191s Selecting previously unselected package libapt-pkg6.0t64:armhf.
191s (Reading database ... 
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191s Preparing to unpack .../libapt-pkg6.0t64_2.7.13ubuntu1_armhf.deb ...
191s Unpacking libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ...
191s Setting up libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ...
192s Selecting previously unselected package libnettle8t64:armhf.
192s (Reading database ... 
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192s Preparing to unpack .../libnettle8t64_3.9.1-2.2_armhf.deb ...
192s Unpacking libnettle8t64:armhf (3.9.1-2.2) ...
192s Setting up libnettle8t64:armhf (3.9.1-2.2) ...
192s dpkg: libhogweed6:armhf: dependency problems, but removing anyway as you requested:
192s  libgnutls30:armhf depends on libhogweed6 (>= 3.6).
192s 
192s (Reading database ... 
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192s Removing libhogweed6:armhf (3.9.1-2) ...
192s Selecting previously unselected package libhogweed6t64:armhf.
192s (Reading database ... 
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192s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_armhf.deb ...
192s Unpacking libhogweed6t64:armhf (3.9.1-2.2) ...
192s Setting up libhogweed6t64:armhf (3.9.1-2.2) ...
192s dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested:
192s  libcurl3-gnutls:armhf depends on libgnutls30 (>= 3.8.2).
192s  apt depends on libgnutls30 (>= 3.8.1).
192s 
192s (Reading database ... 
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192s Removing libgnutls30:armhf (3.8.3-1ubuntu1) ...
193s Selecting previously unselected package libgnutls30t64:armhf.
193s (Reading database ... 
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193s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_armhf.deb ...
193s Unpacking libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ...
193s Setting up libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ...
193s (Reading database ... 
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193s Preparing to unpack .../apt_2.7.13ubuntu1_armhf.deb ...
193s Unpacking apt (2.7.13ubuntu1) over (2.7.12) ...
194s Setting up apt (2.7.13ubuntu1) ...
196s dpkg: libcurl3-gnutls:armhf: dependency problems, but removing anyway as you requested:
196s  libfwupd2:armhf depends on libcurl3-gnutls (>= 7.63.0).
196s 
196s (Reading database ... 
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196s Removing libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ...
196s Selecting previously unselected package libcurl3t64-gnutls:armhf.
196s (Reading database ... 
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196s Preparing to unpack .../libcurl3t64-gnutls_8.5.0-2ubuntu7_armhf.deb ...
196s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ...
196s Preparing to unpack .../libfwupd2_1.9.15-1_armhf.deb ...
197s Unpacking libfwupd2:armhf (1.9.15-1) over (1.9.14-1) ...
197s dpkg: libpsl5:armhf: dependency problems, but removing anyway as you requested:
197s  wget depends on libpsl5 (>= 0.16.0).
197s  libcurl4:armhf depends on libpsl5 (>= 0.16.0).
197s 
197s (Reading database ... 
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197s Removing libpsl5:armhf (0.21.2-1build1) ...
197s Selecting previously unselected package libpsl5t64:armhf.
197s (Reading database ... 
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197s Preparing to unpack .../libpsl5t64_0.21.2-1.1_armhf.deb ...
197s Unpacking libpsl5t64:armhf (0.21.2-1.1) ...
197s Preparing to unpack .../wget_1.21.4-1ubuntu2_armhf.deb ...
197s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ...
197s Preparing to unpack .../tnftp_20230507-2build1_armhf.deb ...
197s Unpacking tnftp (20230507-2build1) over (20230507-2) ...
198s dpkg: libpcap0.8:armhf: dependency problems, but removing anyway as you requested:
198s  tcpdump depends on libpcap0.8 (>= 1.9.1).
198s 
198s (Reading database ... 
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198s Removing libpcap0.8:armhf (1.10.4-4ubuntu3) ...
198s Selecting previously unselected package libpcap0.8t64:armhf.
198s (Reading database ... 
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198s Preparing to unpack .../0-libpcap0.8t64_1.10.4-4.1ubuntu1_armhf.deb ...
198s Unpacking libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ...
198s Preparing to unpack .../1-tcpdump_4.99.4-3ubuntu2_armhf.deb ...
198s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ...
198s Preparing to unpack .../2-libsystemd-shared_255.4-1ubuntu5_armhf.deb ...
198s Unpacking libsystemd-shared:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
198s Preparing to unpack .../3-systemd-resolved_255.4-1ubuntu5_armhf.deb ...
198s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Preparing to unpack .../4-sudo_1.9.15p5-3ubuntu3_armhf.deb ...
199s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ...
199s Preparing to unpack .../5-rsync_3.2.7-1build1_armhf.deb ...
199s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ...
199s Preparing to unpack .../6-python3-cryptography_41.0.7-4build2_armhf.deb ...
200s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ...
200s Preparing to unpack .../7-openssh-sftp-server_1%3a9.6p1-3ubuntu10_armhf.deb ...
200s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu10) over (1:9.6p1-3ubuntu2) ...
200s Preparing to unpack .../8-openssh-client_1%3a9.6p1-3ubuntu10_armhf.deb ...
200s Unpacking openssh-client (1:9.6p1-3ubuntu10) over (1:9.6p1-3ubuntu2) ...
201s Preparing to unpack .../9-openssh-server_1%3a9.6p1-3ubuntu10_armhf.deb ...
201s Unpacking openssh-server (1:9.6p1-3ubuntu10) over (1:9.6p1-3ubuntu2) ...
202s (Reading database ... 
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202s Removing linux-headers-generic (6.8.0-11.11+1) ...
202s Removing linux-headers-6.8.0-11-generic (6.8.0-11.11) ...
204s dpkg: libssl3:armhf: dependency problems, but removing anyway as you requested:
204s  systemd depends on libssl3 (>= 3.0.0).
204s  libssh-4:armhf depends on libssl3 (>= 3.0.0).
204s  libsasl2-modules:armhf depends on libssl3 (>= 3.0.0).
204s  libsasl2-2:armhf depends on libssl3 (>= 3.0.0).
204s  libnvme1 depends on libssl3 (>= 3.0.0).
204s  libkrb5-3:armhf depends on libssl3 (>= 3.0.0).
204s  libkmod2:armhf depends on libssl3 (>= 3.0.0).
204s  libfido2-1:armhf depends on libssl3 (>= 3.0.0).
204s  libcurl4:armhf depends on libssl3 (>= 3.0.0).
204s  libcryptsetup12:armhf depends on libssl3 (>= 3.0.0).
204s  kmod depends on libssl3 (>= 3.0.0).
204s  dhcpcd-base depends on libssl3 (>= 3.0.0).
204s  bind9-libs:armhf depends on libssl3 (>= 3.0.0).
204s 
204s Removing libssl3:armhf (3.0.10-1ubuntu4) ...
204s Selecting previously unselected package libssl3t64:armhf.
204s (Reading database ... 
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204s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_armhf.deb ...
204s Unpacking libssl3t64:armhf (3.0.13-0ubuntu2) ...
205s Setting up libssl3t64:armhf (3.0.13-0ubuntu2) ...
205s (Reading database ... 
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205s Preparing to unpack .../libudev1_255.4-1ubuntu5_armhf.deb ...
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205s Setting up libudev1:armhf (255.4-1ubuntu5) ...
205s (Reading database ... 
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205s Preparing to unpack .../systemd_255.4-1ubuntu5_armhf.deb ...
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207s Preparing to unpack .../udev_255.4-1ubuntu5_armhf.deb ...
207s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
208s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_armhf.deb ...
208s Unpacking libsystemd0:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
208s Setting up libsystemd0:armhf (255.4-1ubuntu5) ...
208s Setting up libsystemd-shared:armhf (255.4-1ubuntu5) ...
208s Setting up systemd-dev (255.4-1ubuntu5) ...
208s Setting up systemd (255.4-1ubuntu5) ...
210s (Reading database ... 
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210s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_armhf.deb ...
210s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
210s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_armhf.deb ...
210s Unpacking libnss-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
211s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_armhf.deb ...
211s Unpacking libpam-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
211s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_armhf.deb ...
211s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
211s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ...
212s pam_namespace.service is a disabled or a static unit not running, not starting it.
212s (Reading database ... 
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212s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_armhf.deb ...
212s Unpacking libpam-modules:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
213s Setting up libpam-modules:armhf (1.5.3-5ubuntu3) ...
213s Installing new version of config file /etc/security/namespace.init ...
213s (Reading database ... 
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213s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu3_all.deb ...
213s Unpacking libpam-runtime (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
213s Setting up libpam-runtime (1.5.3-5ubuntu3) ...
214s (Reading database ... 
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214s Preparing to unpack .../0-dbus-user-session_1.14.10-4ubuntu2_armhf.deb ...
214s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
214s Preparing to unpack .../1-libapparmor1_4.0.0-beta3-0ubuntu2_armhf.deb ...
214s Unpacking libapparmor1:armhf (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ...
214s Preparing to unpack .../2-dbus-bin_1.14.10-4ubuntu2_armhf.deb ...
214s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
214s Preparing to unpack .../3-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ...
214s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
214s Preparing to unpack .../4-dbus_1.14.10-4ubuntu2_armhf.deb ...
214s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
214s Preparing to unpack .../5-dbus-daemon_1.14.10-4ubuntu2_armhf.deb ...
214s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
214s Preparing to unpack .../6-libdbus-1-3_1.14.10-4ubuntu2_armhf.deb ...
214s Unpacking libdbus-1-3:armhf (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
215s Preparing to unpack .../7-kmod_31+20240202-2ubuntu4_armhf.deb ...
215s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
215s dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty
215s Preparing to unpack .../8-libkmod2_31+20240202-2ubuntu4_armhf.deb ...
215s Unpacking libkmod2:armhf (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
215s Preparing to unpack .../9-libmount1_2.39.3-9ubuntu2_armhf.deb ...
215s Unpacking libmount1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
215s Setting up libmount1:armhf (2.39.3-9ubuntu2) ...
215s (Reading database ... 
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215s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu2_armhf.deb ...
215s Unpacking libseccomp2:armhf (2.5.5-1ubuntu2) over (2.5.5-1ubuntu1) ...
215s Setting up libseccomp2:armhf (2.5.5-1ubuntu2) ...
215s (Reading database ... 
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215s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_armhf.deb ...
215s Unpacking libuuid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
216s Setting up libuuid1:armhf (2.39.3-9ubuntu2) ...
216s (Reading database ... 
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216s Preparing to unpack .../0-libcryptsetup12_2%3a2.7.0-1ubuntu2_armhf.deb ...
216s Unpacking libcryptsetup12:armhf (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ...
216s Preparing to unpack .../1-libfdisk1_2.39.3-9ubuntu2_armhf.deb ...
216s Unpacking libfdisk1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
216s Preparing to unpack .../2-mount_2.39.3-9ubuntu2_armhf.deb ...
216s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
216s Preparing to unpack .../3-libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_armhf.deb ...
216s Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ...
216s Selecting previously unselected package libparted2t64:armhf.
216s Preparing to unpack .../4-libparted2t64_3.6-3.1build2_armhf.deb ...
216s Unpacking libparted2t64:armhf (3.6-3.1build2) ...
217s Preparing to unpack .../5-libsqlite3-0_3.45.1-1ubuntu1_armhf.deb ...
217s Unpacking libsqlite3-0:armhf (3.45.1-1ubuntu1) over (3.45.1-1) ...
217s Preparing to unpack .../6-pinentry-curses_1.2.1-3ubuntu4_armhf.deb ...
217s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ...
217s Preparing to unpack .../7-libsmartcols1_2.39.3-9ubuntu2_armhf.deb ...
217s Unpacking libsmartcols1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
217s Setting up libsmartcols1:armhf (2.39.3-9ubuntu2) ...
217s (Reading database ... 
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217s Preparing to unpack .../0-readline-common_8.2-3.1_all.deb ...
217s Unpacking readline-common (8.2-3.1) over (8.2-3) ...
217s Preparing to unpack .../1-python3-yaml_6.0.1-2build1_armhf.deb ...
218s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ...
218s Preparing to unpack .../2-python-apt-common_2.7.6build1_all.deb ...
218s Unpacking python-apt-common (2.7.6build1) over (2.7.6) ...
218s Preparing to unpack .../3-python3-setuptools_68.1.2-2ubuntu1_all.deb ...
219s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ...
219s Preparing to unpack .../4-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ...
219s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ...
220s Preparing to unpack .../5-dpkg_1.22.6ubuntu4_armhf.deb ...
220s Unpacking dpkg (1.22.6ubuntu4) over (1.22.4ubuntu5) ...
220s Setting up dpkg (1.22.6ubuntu4) ...
221s Setting up libpython3.12-minimal:armhf (3.12.2-4build3) ...
221s Setting up libexpat1:armhf (2.6.1-2) ...
221s Setting up python3.12-minimal (3.12.2-4build3) ...
224s (Reading database ... 
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224s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_armhf.deb ...
224s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
224s Setting up python3-minimal (3.12.2-0ubuntu1) ...
225s (Reading database ... 
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225s Preparing to unpack .../00-python3_3.12.2-0ubuntu1_armhf.deb ...
225s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
225s Preparing to unpack .../01-libpython3-stdlib_3.12.2-0ubuntu1_armhf.deb ...
225s Unpacking libpython3-stdlib:armhf (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
225s Preparing to unpack .../02-bsdextrautils_2.39.3-9ubuntu2_armhf.deb ...
225s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
226s Preparing to unpack .../03-groff-base_1.23.0-3build1_armhf.deb ...
226s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ...
226s Preparing to unpack .../04-libsasl2-2_2.1.28+dfsg1-4ubuntu4_armhf.deb ...
226s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-4ubuntu4) over (2.1.28+dfsg1-4) ...
226s Preparing to unpack .../05-libjson-glib-1.0-common_1.8.0-2build1_all.deb ...
226s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ...
226s Preparing to unpack .../06-libjson-glib-1.0-0_1.8.0-2build1_armhf.deb ...
226s Unpacking libjson-glib-1.0-0:armhf (1.8.0-2build1) over (1.8.0-2) ...
227s Preparing to unpack .../07-libxml2_2.9.14+dfsg-1.3ubuntu2_armhf.deb ...
227s Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ...
227s Preparing to unpack .../08-libgudev-1.0-0_1%3a238-3ubuntu2_armhf.deb ...
227s Unpacking libgudev-1.0-0:armhf (1:238-3ubuntu2) over (1:238-3) ...
227s Preparing to unpack .../09-libusb-1.0-0_2%3a1.0.27-1_armhf.deb ...
227s Unpacking libusb-1.0-0:armhf (2:1.0.27-1) over (2:1.0.26-1) ...
227s Preparing to unpack .../10-libgusb2_0.4.8-1build1_armhf.deb ...
227s Unpacking libgusb2:armhf (0.4.8-1build1) over (0.4.8-1) ...
227s Preparing to unpack .../11-libmbim-proxy_1.31.2-0ubuntu2_armhf.deb ...
227s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ...
227s Preparing to unpack .../12-libmbim-glib4_1.31.2-0ubuntu2_armhf.deb ...
227s Unpacking libmbim-glib4:armhf (1.31.2-0ubuntu2) over (1.30.0-1) ...
227s Preparing to unpack .../13-libmm-glib0_1.23.4-0ubuntu1_armhf.deb ...
227s Unpacking libmm-glib0:armhf (1.23.4-0ubuntu1) over (1.22.0-3) ...
228s Preparing to unpack .../14-libpolkit-agent-1-0_124-1ubuntu1_armhf.deb ...
228s Unpacking libpolkit-agent-1-0:armhf (124-1ubuntu1) over (124-1) ...
228s Preparing to unpack .../15-libpolkit-gobject-1-0_124-1ubuntu1_armhf.deb ...
228s Unpacking libpolkit-gobject-1-0:armhf (124-1ubuntu1) over (124-1) ...
228s Preparing to unpack .../16-libqmi-proxy_1.35.2-0ubuntu1_armhf.deb ...
228s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ...
228s Preparing to unpack .../17-libqrtr-glib0_1.2.2-1ubuntu3_armhf.deb ...
228s Unpacking libqrtr-glib0:armhf (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ...
228s Preparing to unpack .../18-libqmi-glib5_1.35.2-0ubuntu1_armhf.deb ...
228s Unpacking libqmi-glib5:armhf (1.35.2-0ubuntu1) over (1.34.0-2) ...
228s Preparing to unpack .../19-libxmlb2_0.3.15-1build1_armhf.deb ...
228s Unpacking libxmlb2:armhf (0.3.15-1build1) over (0.3.15-1) ...
228s Preparing to unpack .../20-shared-mime-info_2.4-1build1_armhf.deb ...
228s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ...
228s Preparing to unpack .../21-libbrotli1_1.1.0-2build1_armhf.deb ...
228s Unpacking libbrotli1:armhf (1.1.0-2build1) over (1.1.0-2) ...
229s Preparing to unpack .../22-libgssapi-krb5-2_1.20.1-5.1build3_armhf.deb ...
229s Unpacking libgssapi-krb5-2:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ...
229s Preparing to unpack .../23-libkrb5-3_1.20.1-5.1build3_armhf.deb ...
229s Unpacking libkrb5-3:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ...
229s Preparing to unpack .../24-libkrb5support0_1.20.1-5.1build3_armhf.deb ...
229s Unpacking libkrb5support0:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ...
229s Preparing to unpack .../25-libk5crypto3_1.20.1-5.1build3_armhf.deb ...
229s Unpacking libk5crypto3:armhf (1.20.1-5.1build3) over (1.20.1-5build1) ...
229s Preparing to unpack .../26-libcom-err2_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
229s Unpacking libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
229s Preparing to unpack .../27-libnghttp2-14_1.59.0-1build1_armhf.deb ...
229s Unpacking libnghttp2-14:armhf (1.59.0-1build1) over (1.59.0-1) ...
229s Preparing to unpack .../28-libssh-4_0.10.6-2build1_armhf.deb ...
229s Unpacking libssh-4:armhf (0.10.6-2build1) over (0.10.6-2) ...
230s Preparing to unpack .../29-libibverbs1_50.0-2build1_armhf.deb ...
230s Unpacking libibverbs1:armhf (50.0-2build1) over (50.0-2) ...
230s Preparing to unpack .../30-libfido2-1_1.14.0-1build1_armhf.deb ...
230s Unpacking libfido2-1:armhf (1.14.0-1build1) over (1.14.0-1) ...
230s Preparing to unpack .../31-coreutils_9.4-3ubuntu3_armhf.deb ...
230s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ...
230s Setting up coreutils (9.4-3ubuntu3) ...
231s (Reading database ... 
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231s Preparing to unpack .../debianutils_5.17_armhf.deb ...
231s Unpacking debianutils (5.17) over (5.16) ...
231s Setting up debianutils (5.17) ...
231s (Reading database ... 
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231s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_armhf.deb ...
231s Unpacking util-linux (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
232s Setting up util-linux (2.39.3-9ubuntu2) ...
234s fstrim.service is a disabled or a static unit not running, not starting it.
234s (Reading database ... 
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234s Preparing to unpack .../libc-bin_2.39-0ubuntu6_armhf.deb ...
234s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
234s Setting up libc-bin (2.39-0ubuntu6) ...
235s (Reading database ... 
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235s Removing libatm1:armhf (1:2.5.1-5) ...
235s (Reading database ... 
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235s Preparing to unpack .../curl_8.5.0-2ubuntu7_armhf.deb ...
235s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ...
235s (Reading database ... 
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235s Removing libcurl4:armhf (8.5.0-2ubuntu2) ...
235s Selecting previously unselected package libcurl4t64:armhf.
235s (Reading database ... 
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235s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_armhf.deb ...
235s Unpacking libcurl4t64:armhf (8.5.0-2ubuntu7) ...
235s Preparing to unpack .../libbpf1_1%3a1.3.0-2build1_armhf.deb ...
236s Unpacking libbpf1:armhf (1:1.3.0-2build1) over (1:1.3.0-2) ...
236s Preparing to unpack .../iproute2_6.1.0-1ubuntu5_armhf.deb ...
236s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ...
236s (Reading database ... 
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236s Removing libelf1:armhf (0.190-1) ...
236s Selecting previously unselected package libelf1t64:armhf.
236s (Reading database ... 
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236s Preparing to unpack .../libelf1t64_0.190-1.1build2_armhf.deb ...
236s Unpacking libelf1t64:armhf (0.190-1.1build2) ...
236s Preparing to unpack .../lsof_4.95.0-1build2_armhf.deb ...
236s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ...
237s Preparing to unpack .../libnsl2_1.3.0-3build2_armhf.deb ...
237s Unpacking libnsl2:armhf (1.3.0-3build2) over (1.3.0-3) ...
237s (Reading database ... 
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237s Removing libtirpc3:armhf (1.3.4+ds-1build1) ...
237s (Reading database ... 
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237s Preparing to unpack .../0-libtirpc-common_1.3.4+ds-1.1_all.deb ...
237s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ...
237s Selecting previously unselected package libtirpc3t64:armhf.
237s Preparing to unpack .../1-libtirpc3t64_1.3.4+ds-1.1_armhf.deb ...
237s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64'
237s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
237s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1) ...
238s Preparing to unpack .../2-libblockdev-utils3_3.1.0-1build1_armhf.deb ...
238s Unpacking libblockdev-utils3:armhf (3.1.0-1build1) over (3.1.0-1) ...
238s Preparing to unpack .../3-libblockdev-fs3_3.1.0-1build1_armhf.deb ...
238s Unpacking libblockdev-fs3:armhf (3.1.0-1build1) over (3.1.0-1) ...
238s Preparing to unpack .../4-logsave_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
238s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
238s Preparing to unpack .../5-ubuntu-minimal_1.536build1_armhf.deb ...
238s Unpacking ubuntu-minimal (1.536build1) over (1.536) ...
238s Preparing to unpack .../6-initramfs-tools_0.142ubuntu22_all.deb ...
239s Unpacking initramfs-tools (0.142ubuntu22) over (0.142ubuntu20) ...
239s Preparing to unpack .../7-initramfs-tools-core_0.142ubuntu22_all.deb ...
239s Unpacking initramfs-tools-core (0.142ubuntu22) over (0.142ubuntu20) ...
239s Preparing to unpack .../8-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ...
239s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
239s dpkg: libext2fs2:armhf: dependency problems, but removing anyway as you requested:
239s  e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1).
239s  btrfs-progs depends on libext2fs2 (>= 1.42).
239s 
239s (Reading database ... 
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239s Removing libext2fs2:armhf (1.47.0-2ubuntu1) ...
239s Selecting previously unselected package libext2fs2t64:armhf.
239s (Reading database ... 
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239s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
239s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64'
239s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64'
240s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64'
240s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64'
240s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ...
240s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) ...
240s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ...
240s (Reading database ... 
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240s Preparing to unpack .../00-e2fsprogs_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
240s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
240s Preparing to unpack .../01-btrfs-progs_6.6.3-1.1build1_armhf.deb ...
240s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ...
241s Preparing to unpack .../02-dhcpcd-base_1%3a10.0.6-1ubuntu2_armhf.deb ...
241s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ...
241s Preparing to unpack .../03-eject_2.39.3-9ubuntu2_armhf.deb ...
241s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
241s Preparing to unpack .../04-locales_2.39-0ubuntu6_all.deb ...
241s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
242s Selecting previously unselected package libnetplan1:armhf.
242s Preparing to unpack .../05-libnetplan1_1.0-1_armhf.deb ...
242s Unpacking libnetplan1:armhf (1.0-1) ...
243s Preparing to unpack .../06-python3-netplan_1.0-1_armhf.deb ...
243s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ...
243s Preparing to unpack .../07-netplan-generator_1.0-1_armhf.deb ...
243s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
243s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ...
243s Preparing to unpack .../08-python3-dbus_1.3.2-5build2_armhf.deb ...
243s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ...
243s Preparing to unpack .../09-netplan.io_1.0-1_armhf.deb ...
243s Unpacking netplan.io (1.0-1) over (0.107.1-3) ...
244s Preparing to unpack .../10-vim-tiny_2%3a9.1.0016-1ubuntu5_armhf.deb ...
244s Unpacking vim-tiny (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ...
244s Preparing to unpack .../11-vim-common_2%3a9.1.0016-1ubuntu5_all.deb ...
244s Unpacking vim-common (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ...
244s Preparing to unpack .../12-initramfs-tools-bin_0.142ubuntu22_armhf.deb ...
244s Unpacking initramfs-tools-bin (0.142ubuntu22) over (0.142ubuntu20) ...
244s (Reading database ... 
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244s Removing libreiserfscore0 (1:3.6.27-7) ...
244s Selecting previously unselected package libreiserfscore0t64.
244s (Reading database ... 
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244s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_armhf.deb ...
244s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ...
245s Preparing to unpack .../file_1%3a5.45-3_armhf.deb ...
245s Unpacking file (1:5.45-3) over (1:5.45-2) ...
245s (Reading database ... 
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245s Removing libmagic1:armhf (1:5.45-2) ...
245s (Reading database ... 
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245s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_armhf.deb ...
245s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ...
245s Selecting previously unselected package libmagic1t64:armhf.
245s Preparing to unpack .../libmagic1t64_1%3a5.45-3_armhf.deb ...
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245s Removing libnetplan0:armhf (0.107.1-3) ...
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246s Preparing to unpack .../libblockdev-nvme3_3.1.0-1build1_armhf.deb ...
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246s Removing libnvme1 (1.8-2) ...
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246s Preparing to unpack .../libnvme1t64_1.8-3_armhf.deb ...
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246s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu5_armhf.deb ...
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246s Removing libpng16-16:armhf (1.6.43-1) ...
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247s Preparing to unpack .../libpng16-16t64_1.6.43-3_armhf.deb ...
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247s Removing libudisks2-0:armhf (2.10.1-1ubuntu2) ...
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247s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_armhf.deb ...
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247s Removing libuv1:armhf (1.48.0-1) ...
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247s Preparing to unpack .../libuv1t64_1.48.0-1.1_armhf.deb ...
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247s Removing python3-distutils (3.11.5-1) ...
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248s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_armhf.deb ...
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248s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_armhf.deb ...
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248s Setting up libdebconfclient0:armhf (0.271ubuntu2) ...
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248s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ...
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248s Setting up libsemanage-common (3.5-1build4) ...
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248s Preparing to unpack .../libsemanage2_3.5-1build4_armhf.deb ...
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248s Setting up libsemanage2:armhf (3.5-1build4) ...
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248s Preparing to unpack .../install-info_7.1-3build1_armhf.deb ...
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249s Setting up install-info (7.1-3build1) ...
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249s Preparing to unpack .../00-gcc-13-base_13.2.0-19ubuntu1_armhf.deb ...
249s Unpacking gcc-13-base:armhf (13.2.0-19ubuntu1) over (13.2.0-17ubuntu2) ...
249s Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
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249s Preparing to unpack .../02-dmsetup_2%3a1.02.185-3ubuntu2_armhf.deb ...
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249s Preparing to unpack .../03-gir1.2-girepository-2.0_1.79.1-1ubuntu6_armhf.deb ...
249s Unpacking gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ...
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250s Preparing to unpack .../05-libgirepository-1.0-1_1.79.1-1ubuntu6_armhf.deb ...
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250s Preparing to unpack .../06-krb5-locales_1.20.1-5.1build3_all.deb ...
250s Unpacking krb5-locales (1.20.1-5.1build3) over (1.20.1-5build1) ...
250s Preparing to unpack .../07-libbsd0_0.12.1-1_armhf.deb ...
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250s Preparing to unpack .../09-libslang2_2.3.3-3build1_armhf.deb ...
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250s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ...
250s Selecting previously unselected package xdg-user-dirs.
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251s Unpacking xxd (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ...
251s Preparing to unpack .../13-apparmor_4.0.0-beta3-0ubuntu2_armhf.deb ...
253s Unpacking apparmor (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ...
254s Preparing to unpack .../14-ftp_20230507-2build1_all.deb ...
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254s Preparing to unpack .../15-inetutils-telnet_2%3a2.5-3ubuntu3_armhf.deb ...
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254s Preparing to unpack .../16-info_7.1-3build1_armhf.deb ...
254s Unpacking info (7.1-3build1) over (7.1-3) ...
254s Preparing to unpack .../17-libxmuu1_2%3a1.1.3-3build1_armhf.deb ...
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254s Preparing to unpack .../18-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_armhf.deb ...
254s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ...
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255s Preparing to unpack .../20-plymouth-theme-ubuntu-text_24.004.60-1ubuntu5_armhf.deb ...
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255s Preparing to unpack .../22-psmisc_23.7-1_armhf.deb ...
255s Unpacking psmisc (23.7-1) over (23.6-2) ...
256s Preparing to unpack .../23-telnet_0.17+2.5-3ubuntu3_all.deb ...
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256s Preparing to unpack .../24-xz-utils_5.6.0-0.2_armhf.deb ...
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256s Preparing to unpack .../25-ubuntu-standard_1.536build1_armhf.deb ...
256s Unpacking ubuntu-standard (1.536build1) over (1.536) ...
256s Preparing to unpack .../26-usb.ids_2024.03.18-1_all.deb ...
256s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ...
256s Preparing to unpack .../27-bolt_0.9.6-2build1_armhf.deb ...
256s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ...
256s Preparing to unpack .../28-cryptsetup-bin_2%3a2.7.0-1ubuntu2_armhf.deb ...
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257s Preparing to unpack .../29-dpkg-dev_1.22.6ubuntu4_all.deb ...
257s Unpacking dpkg-dev (1.22.6ubuntu4) over (1.22.4ubuntu5) ...
257s Preparing to unpack .../30-libdpkg-perl_1.22.6ubuntu4_all.deb ...
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257s Preparing to unpack .../31-gnupg-l10n_2.4.4-2ubuntu15_all.deb ...
257s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
257s Preparing to unpack .../32-ibverbs-providers_50.0-2build1_armhf.deb ...
258s Unpacking ibverbs-providers:armhf (50.0-2build1) over (50.0-2) ...
258s Preparing to unpack .../33-jq_1.7.1-3_armhf.deb ...
258s Unpacking jq (1.7.1-3) over (1.7.1-2) ...
258s Preparing to unpack .../34-libjq1_1.7.1-3_armhf.deb ...
258s Unpacking libjq1:armhf (1.7.1-3) over (1.7.1-2) ...
258s Selecting previously unselected package libatm1t64:armhf.
258s Preparing to unpack .../35-libatm1t64_1%3a2.5.1-5.1_armhf.deb ...
258s Unpacking libatm1t64:armhf (1:2.5.1-5.1) ...
258s Preparing to unpack .../36-libblockdev-crypto3_3.1.0-1build1_armhf.deb ...
258s Unpacking libblockdev-crypto3:armhf (3.1.0-1build1) over (3.1.0-1) ...
258s Preparing to unpack .../37-libblockdev-loop3_3.1.0-1build1_armhf.deb ...
258s Unpacking libblockdev-loop3:armhf (3.1.0-1build1) over (3.1.0-1) ...
258s Preparing to unpack .../38-libblockdev-mdraid3_3.1.0-1build1_armhf.deb ...
258s Unpacking libblockdev-mdraid3:armhf (3.1.0-1build1) over (3.1.0-1) ...
258s Preparing to unpack .../39-libblockdev-part3_3.1.0-1build1_armhf.deb ...
258s Unpacking libblockdev-part3:armhf (3.1.0-1build1) over (3.1.0-1) ...
258s Preparing to unpack .../40-libblockdev-swap3_3.1.0-1build1_armhf.deb ...
258s Unpacking libblockdev-swap3:armhf (3.1.0-1build1) over (3.1.0-1) ...
258s Preparing to unpack .../41-libblockdev3_3.1.0-1build1_armhf.deb ...
258s Unpacking libblockdev3:armhf (3.1.0-1build1) over (3.1.0-1) ...
259s Preparing to unpack .../42-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ...
259s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ...
259s Preparing to unpack .../43-libftdi1-2_1.5-6build4_armhf.deb ...
259s Unpacking libftdi1-2:armhf (1.5-6build4) over (1.5-6build3) ...
259s Preparing to unpack .../44-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ...
259s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
259s Preparing to unpack .../45-libsasl2-modules_2.1.28+dfsg1-4ubuntu4_armhf.deb ...
259s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-4ubuntu4) over (2.1.28+dfsg1-4) ...
259s Preparing to unpack .../46-python3-lib2to3_3.12.2-3ubuntu2_all.deb ...
260s Unpacking python3-lib2to3 (3.12.2-3ubuntu2) over (3.11.5-1) ...
260s Preparing to unpack .../47-python3-markupsafe_2.1.5-1build1_armhf.deb ...
260s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ...
260s Preparing to unpack .../48-python3-openssl_24.0.0-4_all.deb ...
261s Unpacking python3-openssl (24.0.0-4) over (23.2.0-1) ...
261s Preparing to unpack .../49-python3-pyrsistent_0.20.0-1build1_armhf.deb ...
261s Unpacking python3-pyrsistent:armhf (0.20.0-1build1) over (0.20.0-1) ...
261s Preparing to unpack .../50-python3-typing-extensions_4.10.0-1_all.deb ...
261s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ...
261s Preparing to unpack .../51-kpartx_0.9.4-5ubuntu4_armhf.deb ...
261s Unpacking kpartx (0.9.4-5ubuntu4) over (0.9.4-5ubuntu3) ...
262s Setting up pinentry-curses (1.2.1-3ubuntu4) ...
262s Setting up libtext-iconv-perl:armhf (1.7-8build2) ...
262s Setting up libtext-charwidth-perl:armhf (0.04-11build2) ...
262s Setting up libibverbs1:armhf (50.0-2build1) ...
262s Setting up systemd-sysv (255.4-1ubuntu5) ...
262s Setting up libapparmor1:armhf (4.0.0-beta3-0ubuntu2) ...
262s Setting up libatm1t64:armhf (1:2.5.1-5.1) ...
262s Setting up libgdbm6t64:armhf (1.23-5.1) ...
262s Setting up bsdextrautils (2.39.3-9ubuntu2) ...
262s Setting up libgdbm-compat4t64:armhf (1.23-5.1) ...
262s Setting up xdg-user-dirs (0.18-1) ...
262s Setting up ibverbs-providers:armhf (50.0-2build1) ...
262s Setting up libmagic-mgc (1:5.45-3) ...
262s Setting up gawk (1:5.2.1-2build2) ...
262s Setting up psmisc (23.7-1) ...
262s Setting up libjq1:armhf (1.7.1-3) ...
262s Setting up libtirpc-common (1.3.4+ds-1.1) ...
262s Setting up libbrotli1:armhf (1.1.0-2build1) ...
262s Setting up libsqlite3-0:armhf (3.45.1-1ubuntu1) ...
262s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-4ubuntu4) ...
262s Setting up libuv1t64:armhf (1.48.0-1.1) ...
262s Setting up libmagic1t64:armhf (1:5.45-3) ...
262s Setting up libpsl5t64:armhf (0.21.2-1.1) ...
262s Setting up libnghttp2-14:armhf (1.59.0-1build1) ...
262s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ...
262s Setting up libnss-systemd:armhf (255.4-1ubuntu5) ...
262s Setting up krb5-locales (1.20.1-5.1build3) ...
262s Setting up file (1:5.45-3) ...
262s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ...
262s Setting up locales (2.39-0ubuntu6) ...
264s Generating locales (this might take a while)...
272s   en_US.UTF-8... done
272s Generation complete.
272s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ...
272s Setting up xxd (2:9.1.0016-1ubuntu5) ...
272s Setting up libelf1t64:armhf (0.190-1.1build2) ...
272s Setting up libkrb5support0:armhf (1.20.1-5.1build3) ...
272s Setting up eject (2.39.3-9ubuntu2) ...
272s Setting up apparmor (4.0.0-beta3-0ubuntu2) ...
272s Installing new version of config file /etc/apparmor.d/abstractions/authentication ...
272s Installing new version of config file /etc/apparmor.d/abstractions/crypto ...
272s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ...
272s Installing new version of config file /etc/apparmor.d/abstractions/openssl ...
272s Installing new version of config file /etc/apparmor.d/code ...
272s Installing new version of config file /etc/apparmor.d/firefox ...
272s apparmor_parser: Unable to replace "lsb_release".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
272s 
272s apparmor_parser: Unable to replace "kmod".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
272s 
272s apparmor_parser: Unable to replace "nvidia_modprobe".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
272s 
275s sysctl: cannot stat /proc/sys/kernel/apparmor_restrict_unprivileged_userns: No such file or directory
275s Reloading AppArmor profiles 
275s /sbin/apparmor_parser: Unable to replace "1password".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "Discord".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "MongoDB Compass".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "brave".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "cam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "buildah".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "chrome".  /sbin/apparmor_parser: Unable to replace "ch-checkns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "ch-run".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "busybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "vscode".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "crun".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "devhelp".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "element-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "epiphany".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "evolution".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "flatpak".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "firefox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "geary".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "github-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "goldendict".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "kchmviewer".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "ipa_verify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "keybase".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "libcamerify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lc-compliance".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "loupe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "linux-sandbox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lxc-attach".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lxc-create".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lxc-destroy".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lxc-stop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lxc-execute".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lxc-unshare".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "mmdebstrap".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "msedge".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "nautilus".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "notepadqq".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "lsb_release".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "opam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "opera".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "pageedit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "obsidian".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "podman".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "polypane".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "qmapshack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "qutebrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "qcam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "rssguard".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "privacybrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-abort".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "rpm".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-apt".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-adduser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "runc".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "rootlesskit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-shell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-update".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "scide".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "signal-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "slack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "slirp4netns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-hold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "stress-ng".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "steam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "surfshark".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "systemd-coredump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-clean".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "plasmashell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "sbuild-unhold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "thunderbird".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "toybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "trinity".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "tup".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "userbindmount".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "unprivileged_userns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "kmod".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "uwsgi-core".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "vdens".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "vivaldi-bin".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "virtiofsd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "vpnns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "wpcom".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "/usr/bin/man".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "unix-chkpwd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
275s /sbin/apparmor_parser: Unable to replace "rsyslogd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
275s 
276s /sbin/apparmor_parser: Unable to replace "tcpdump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
276s 
276s Error: At least one profile failed to load
276s Setting up libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ...
276s No schema files found: doing nothing.
276s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
276s Setting up vim-common (2:9.1.0016-1ubuntu5) ...
276s Setting up gcc-13-base:armhf (13.2.0-19ubuntu1) ...
276s Setting up libqrtr-glib0:armhf (1.2.2-1ubuntu3) ...
276s Setting up libslang2:armhf (2.3.3-3build1) ...
276s Setting up libnvme1t64 (1.8-3) ...
276s Setting up mtr-tiny (0.95-1.1build1) ...
276s Setting up gnupg-l10n (2.4.4-2ubuntu15) ...
276s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) ...
276s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu2) ...
276s Setting up xz-utils (5.6.0-0.2) ...
276s Setting up perl-modules-5.38 (5.38.2-3.2) ...
276s Setting up libpng16-16t64:armhf (1.6.43-3) ...
276s Setting up systemd-timesyncd (255.4-1ubuntu5) ...
277s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ...
277s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu2) ...
277s Setting up usb.ids (2024.03.18-1) ...
277s Setting up sudo (1.9.15p5-3ubuntu3) ...
277s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ...
277s Setting up gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) ...
277s Setting up libk5crypto3:armhf (1.20.1-5.1build3) ...
277s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ...
277s Setting up libfdisk1:armhf (2.39.3-9ubuntu2) ...
277s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-5build1) ...
277s Setting up libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) ...
277s Setting up python-apt-common (2.7.6build1) ...
277s Setting up mount (2.39.3-9ubuntu2) ...
277s Setting up dmsetup (2:1.02.185-3ubuntu2) ...
277s Setting up uuid-runtime (2.39.3-9ubuntu2) ...
279s uuidd.service is a disabled or a static unit not running, not starting it.
280s Setting up libmm-glib0:armhf (1.23.4-0ubuntu1) ...
280s Setting up groff-base (1.23.0-3build1) ...
280s Setting up libplymouth5:armhf (24.004.60-1ubuntu5) ...
280s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ...
280s Setting up jq (1.7.1-3) ...
280s Setting up gpgconf (2.4.4-2ubuntu15) ...
280s Setting up libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ...
280s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu2) ...
280s Setting up libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) ...
280s Setting up libjson-glib-1.0-common (1.8.0-2build1) ...
280s Setting up libkrb5-3:armhf (1.20.1-5.1build3) ...
280s Setting up libpython3.11-minimal:armhf (3.11.8-1build4) ...
280s Setting up libusb-1.0-0:armhf (2:1.0.27-1) ...
280s Setting up libperl5.38t64:armhf (5.38.2-3.2) ...
280s Setting up tnftp (20230507-2build1) ...
280s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ...
280s Setting up libfido2-1:armhf (1.14.0-1build1) ...
280s Setting up openssl (3.0.13-0ubuntu2) ...
280s Setting up libbsd0:armhf (0.12.1-1) ...
280s Setting up readline-common (8.2-3.1) ...
280s Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) ...
280s Setting up libxmuu1:armhf (2:1.1.3-3build1) ...
280s Setting up dbus-bin (1.14.10-4ubuntu2) ...
280s Setting up info (7.1-3build1) ...
280s Setting up liblocale-gettext-perl (1.07-6ubuntu3) ...
280s Setting up gpg (2.4.4-2ubuntu15) ...
280s Setting up libgudev-1.0-0:armhf (1:238-3ubuntu2) ...
280s Setting up libpolkit-gobject-1-0:armhf (124-1ubuntu1) ...
280s Setting up libbpf1:armhf (1:1.3.0-2build1) ...
280s Setting up libmbim-glib4:armhf (1.31.2-0ubuntu2) ...
280s Setting up rsync (3.2.7-1build1) ...
282s rsync.service is a disabled or a static unit not running, not starting it.
282s Setting up libkmod2:armhf (31+20240202-2ubuntu4) ...
282s Setting up bolt (0.9.6-2build1) ...
283s bolt.service is a disabled or a static unit not running, not starting it.
283s Setting up gnupg-utils (2.4.4-2ubuntu15) ...
283s Setting up initramfs-tools-bin (0.142ubuntu22) ...
283s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ...
283s Setting up python3.11-minimal (3.11.8-1build4) ...
286s Setting up tcpdump (4.99.4-3ubuntu2) ...
286s apparmor_parser: Unable to replace "tcpdump".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
286s 
286s Setting up apt-utils (2.7.13ubuntu1) ...
286s Setting up gpg-agent (2.4.4-2ubuntu15) ...
288s Setting up libpython3.12-stdlib:armhf (3.12.2-4build3) ...
288s Setting up wget (1.21.4-1ubuntu2) ...
288s Setting up libxmlb2:armhf (0.3.15-1build1) ...
288s Setting up btrfs-progs (6.6.3-1.1build1) ...
288s Setting up libpython3.11-stdlib:armhf (3.11.8-1build4) ...
288s Setting up python3.12 (3.12.2-4build3) ...
292s Setting up gpgsm (2.4.4-2ubuntu15) ...
292s Setting up inetutils-telnet (2:2.5-3ubuntu3) ...
292s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ...
292s update-initramfs: deferring update (trigger activated)
293s e2scrub_all.service is a disabled or a static unit not running, not starting it.
294s Setting up libparted2t64:armhf (3.6-3.1build2) ...
294s Setting up dbus-daemon (1.14.10-4ubuntu2) ...
294s Setting up libmbim-proxy (1.31.2-0ubuntu2) ...
294s Setting up vim-tiny (2:9.1.0016-1ubuntu5) ...
294s Setting up kmod (31+20240202-2ubuntu4) ...
295s Setting up libnetplan1:armhf (1.0-1) ...
295s Setting up man-db (2.12.0-3build4) ...
295s Updating database of manual pages ...
300s apparmor_parser: Unable to replace "/usr/bin/man".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
300s 
301s man-db.service is a disabled or a static unit not running, not starting it.
301s Setting up fdisk (2.39.3-9ubuntu2) ...
301s Setting up libjson-glib-1.0-0:armhf (1.8.0-2build1) ...
301s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4ubuntu4) ...
301s Setting up libftdi1-2:armhf (1.5-6build4) ...
301s Setting up perl (5.38.2-3.2) ...
301s Setting up gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) ...
301s Setting up dbus (1.14.10-4ubuntu2) ...
301s A reboot is required to replace the running dbus-daemon.
301s Please reboot the system when convenient.
302s Setting up shared-mime-info (2.4-1build1) ...
304s Setting up libblockdev-utils3:armhf (3.1.0-1build1) ...
304s Setting up libgssapi-krb5-2:armhf (1.20.1-5.1build3) ...
304s Setting up udev (255.4-1ubuntu5) ...
306s Setting up ftp (20230507-2build1) ...
306s Setting up keyboxd (2.4.4-2ubuntu15) ...
307s Setting up libdpkg-perl (1.22.6ubuntu4) ...
307s Setting up libsasl2-2:armhf (2.1.28+dfsg1-4ubuntu4) ...
307s Setting up libssh-4:armhf (0.10.6-2build1) ...
307s Setting up libblockdev-nvme3:armhf (3.1.0-1build1) ...
307s Setting up libblockdev-fs3:armhf (3.1.0-1build1) ...
307s Setting up kpartx (0.9.4-5ubuntu4) ...
307s Setting up libpam-systemd:armhf (255.4-1ubuntu5) ...
307s Setting up libpolkit-agent-1-0:armhf (124-1ubuntu1) ...
307s Setting up libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ...
307s Setting up netplan-generator (1.0-1) ...
307s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
307s Setting up initramfs-tools-core (0.142ubuntu22) ...
307s Setting up libarchive13t64:armhf (3.7.2-1.1ubuntu1) ...
307s Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ...
307s Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu1) ...
307s Setting up systemd-resolved (255.4-1ubuntu5) ...
309s Setting up python3.11 (3.11.8-1build4) ...
312s Setting up telnet (0.17+2.5-3ubuntu3) ...
312s Setting up initramfs-tools (0.142ubuntu22) ...
312s update-initramfs: deferring update (trigger activated)
312s Setting up libblockdev-mdraid3:armhf (3.1.0-1build1) ...
312s Setting up libcurl4t64:armhf (8.5.0-2ubuntu7) ...
312s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu3) ...
312s Setting up libtirpc3t64:armhf (1.3.4+ds-1.1) ...
312s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ...
312s Setting up libblockdev-swap3:armhf (3.1.0-1build1) ...
312s Setting up plymouth (24.004.60-1ubuntu5) ...
312s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
313s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
314s Setting up iproute2 (6.1.0-1ubuntu5) ...
314s Setting up openssh-client (1:9.6p1-3ubuntu10) ...
314s Setting up libgusb2:armhf (0.4.8-1build1) ...
314s Setting up libblockdev-loop3:armhf (3.1.0-1build1) ...
314s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ...
314s Setting up parted (3.6-3.1build2) ...
315s Setting up libqmi-glib5:armhf (1.35.2-0ubuntu1) ...
315s Setting up python3 (3.12.2-0ubuntu1) ...
316s Setting up python3-markupsafe (2.1.5-1build1) ...
316s Setting up libblockdev3:armhf (3.1.0-1build1) ...
316s Setting up libjcat1:armhf (0.2.0-2build2) ...
316s Setting up dpkg-dev (1.22.6ubuntu4) ...
316s Setting up libblockdev-part3:armhf (3.1.0-1build1) ...
316s Setting up dirmngr (2.4.4-2ubuntu15) ...
317s Setting up dbus-user-session (1.14.10-4ubuntu2) ...
317s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu5) ...
317s update-initramfs: deferring update (trigger activated)
317s Setting up python3-cryptography (41.0.7-4build2) ...
318s Setting up python3-gi (3.47.0-3build1) ...
319s Setting up python3-typing-extensions (4.10.0-1) ...
319s Setting up lsof (4.95.0-1build2) ...
319s Setting up python3-pyrsistent:armhf (0.20.0-1build1) ...
320s Setting up libnsl2:armhf (1.3.0-3build2) ...
320s Setting up gnupg (2.4.4-2ubuntu15) ...
320s Setting up python3-netplan (1.0-1) ...
320s Setting up curl (8.5.0-2ubuntu7) ...
320s Setting up libvolume-key1:armhf (0.3.12-7build1) ...
320s Setting up bind9-host (1:9.18.24-0ubuntu3) ...
320s Setting up python3-lib2to3 (3.12.2-3ubuntu2) ...
320s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ...
321s Setting up openssh-sftp-server (1:9.6p1-3ubuntu10) ...
321s Setting up python3-dbus (1.3.2-5build2) ...
322s Setting up python3-setuptools (68.1.2-2ubuntu1) ...
325s Setting up gpg-wks-client (2.4.4-2ubuntu15) ...
325s Setting up openssh-server (1:9.6p1-3ubuntu10) ...
326s Replacing config file /etc/ssh/sshd_config with new version
330s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket.

335s Setting up libblockdev-crypto3:armhf (3.1.0-1build1) ...
335s Setting up python3-gdbm:armhf (3.12.2-3ubuntu2) ...
335s Setting up python3-apt (2.7.6build1) ...
335s Setting up python3-openssl (24.0.0-4) ...
336s Setting up libfwupd2:armhf (1.9.15-1) ...
336s Setting up python3-yaml (6.0.1-2build1) ...
337s Setting up libqmi-proxy (1.35.2-0ubuntu1) ...
337s Setting up netplan.io (1.0-1) ...
337s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ...
337s Setting up ubuntu-pro-client (31.2) ...
337s apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
337s 
342s Setting up fwupd (1.9.15-1) ...
344s fwupd-offline-update.service is a disabled or a static unit not running, not starting it.
344s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
344s fwupd.service is a disabled or a static unit not running, not starting it.
344s Setting up ubuntu-pro-client-l10n (31.2) ...
344s Setting up ubuntu-minimal (1.536build1) ...
344s Setting up ubuntu-standard (1.536build1) ...
344s Processing triggers for libc-bin (2.39-0ubuntu6) ...
345s Processing triggers for ufw (0.36.2-5) ...
346s Processing triggers for install-info (7.1-3build1) ...
346s Processing triggers for initramfs-tools (0.142ubuntu22) ...
351s Reading package lists...
352s Building dependency tree...
352s Reading state information...
354s The following packages will be REMOVED:
354s   libatasmart4* libblockdev-crypto3* libblockdev-fs3* libblockdev-loop3*
354s   libblockdev-mdraid3* libblockdev-nvme3* libblockdev-part3*
354s   libblockdev-swap3* libblockdev-utils3* libblockdev3* libbytesize-common*
354s   libbytesize1* libnspr4* libnss3* libnvme1t64* libpolkit-agent-1-0*
354s   libvolume-key1* linux-headers-6.8.0-11* python3-lib2to3*
355s 0 upgraded, 0 newly installed, 19 to remove and 1 not upgraded.
355s After this operation, 89.7 MB disk space will be freed.
355s (Reading database ... 
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(Reading database ... 47405 files and directories currently installed.)
355s Removing libatasmart4:armhf (0.19-5build2) ...
356s Removing libblockdev-crypto3:armhf (3.1.0-1build1) ...
356s Removing libblockdev-fs3:armhf (3.1.0-1build1) ...
356s Removing libblockdev-loop3:armhf (3.1.0-1build1) ...
356s Removing libblockdev-mdraid3:armhf (3.1.0-1build1) ...
356s Removing libblockdev-nvme3:armhf (3.1.0-1build1) ...
356s Removing libblockdev-part3:armhf (3.1.0-1build1) ...
356s Removing libblockdev-swap3:armhf (3.1.0-1build1) ...
356s Removing libblockdev3:armhf (3.1.0-1build1) ...
356s Removing libblockdev-utils3:armhf (3.1.0-1build1) ...
356s Removing libbytesize1:armhf (2.10-1ubuntu1) ...
356s Removing libbytesize-common (2.10-1ubuntu1) ...
356s Removing libvolume-key1:armhf (0.3.12-7build1) ...
356s Removing libnss3:armhf (2:3.98-1) ...
356s Removing libnspr4:armhf (2:4.35-1.1) ...
356s Removing libnvme1t64 (1.8-3) ...
356s Removing libpolkit-agent-1-0:armhf (124-1ubuntu1) ...
356s Removing linux-headers-6.8.0-11 (6.8.0-11.11) ...
360s Removing python3-lib2to3 (3.12.2-3ubuntu2) ...
361s Processing triggers for libc-bin (2.39-0ubuntu6) ...
362s (Reading database ... 
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(Reading database ... 27134 files and directories currently installed.)
362s Purging configuration files for libblockdev3:armhf (3.1.0-1build1) ...
365s autopkgtest [14:51:41]: rebooting testbed after setup commands that affected boot
402s autopkgtest [14:52:18]: testbed running kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024
407s autopkgtest [14:52:23]: testbed dpkg architecture: armhf
423s autopkgtest [14:52:39]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs
451s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe apbs 3.4.1-5.1build1 (dsc) [2705 B]
451s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe apbs 3.4.1-5.1build1 (tar) [85.8 MB]
451s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe apbs 3.4.1-5.1build1 (diff) [20.4 MB]
452s gpgv: Signature made Sat Mar  2 20:23:58 2024 UTC
452s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
452s gpgv: Can't check signature: No public key
452s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-5.1build1.dsc: no acceptable signature found
462s autopkgtest [14:53:18]: testing package apbs version 3.4.1-5.1build1
462s autopkgtest [14:53:18]: build not needed
683s autopkgtest [14:56:59]: test test-apbs: preparing testbed
699s Reading package lists...
700s Building dependency tree...
700s Reading state information...
701s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
701s Starting 2 pkgProblemResolver with broken count: 0
701s Done
702s  Done
703s Starting pkgProblemResolver with broken count: 0
703s Starting 2 pkgProblemResolver with broken count: 0
703s Done
705s The following additional packages will be installed:
705s   apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax libamd3
705s   libapbs-dev libapbs3t64 libarpack2t64 libblas3 libcamd3 libccolamd3
705s   libcholmod5 libcolamd3 libevent-pthreads-2.1-7 libfabric1 libfetk-dev
705s   libfetk1.9t64 libgfortran5 libgomp1 libhwloc-plugins libhwloc15 libjs-jquery
705s   libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 libmaloc-dev
705s   libmaloc1 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64
705s   libpython3.12t64 librdmacm1t64 libspqr4 libsuitesparseconfig7 libsuperlu6
705s   libumfpack6 libxnvctrl0 ocl-icd-libopencl1 python3-apbslib
705s   sphinx-rtd-theme-common
705s Suggested packages:
705s   fonts-mathjax-extras fonts-stix libjs-mathjax-doc opencl-icd
705s Recommended packages:
705s   javascript-common
705s The following NEW packages will be installed:
705s   apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax libamd3
705s   libapbs-dev libapbs3t64 libarpack2t64 libblas3 libcamd3 libccolamd3
705s   libcholmod5 libcolamd3 libevent-pthreads-2.1-7 libfabric1 libfetk-dev
705s   libfetk1.9t64 libgfortran5 libgomp1 libhwloc-plugins libhwloc15 libjs-jquery
705s   libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 libmaloc-dev
705s   libmaloc1 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64
705s   libpython3.12t64 librdmacm1t64 libspqr4 libsuitesparseconfig7 libsuperlu6
705s   libumfpack6 libxnvctrl0 ocl-icd-libopencl1 python3-apbslib
705s   sphinx-rtd-theme-common
705s 0 upgraded, 44 newly installed, 0 to remove and 1 not upgraded.
705s 1 not fully installed or removed.
705s Need to get 31.4 MB of archives.
705s After this operation, 117 MB of additional disk space will be used.
705s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf apbs-data all 3.4.1-5.1build1 [1765 kB]
706s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmaloc1 armhf 1.5-1build1 [79.6 kB]
706s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.12.0-3 [123 kB]
706s Get:4 http://ftpmaster.internal/ubuntu noble/universe armhf libsuperlu6 armhf 6.0.1+dfsg1-1 [154 kB]
706s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 14-20240315-1ubuntu1 [125 kB]
706s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libsuitesparseconfig7 armhf 1:7.6.1+dfsg-1 [12.0 kB]
706s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf libamd3 armhf 1:7.6.1+dfsg-1 [28.1 kB]
706s Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf libcamd3 armhf 1:7.6.1+dfsg-1 [26.1 kB]
706s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf libccolamd3 armhf 1:7.6.1+dfsg-1 [28.3 kB]
706s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libcolamd3 armhf 1:7.6.1+dfsg-1 [20.1 kB]
706s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgfortran5 armhf 14-20240315-1ubuntu1 [312 kB]
706s Get:12 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3 [2085 kB]
707s Get:13 http://ftpmaster.internal/ubuntu noble/universe armhf libcholmod5 armhf 1:7.6.1+dfsg-1 [665 kB]
707s Get:14 http://ftpmaster.internal/ubuntu noble/universe armhf libumfpack6 armhf 1:7.6.1+dfsg-1 [284 kB]
707s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfetk1.9t64 armhf 3.4.1-5.1build1 [535 kB]
707s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libapbs3t64 armhf 3.4.1-5.1build1 [254 kB]
707s Get:17 http://ftpmaster.internal/ubuntu noble/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
707s Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
708s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libarpack2t64 armhf 3.9.1-1.1build1 [88.3 kB]
708s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-9build1 [7370 B]
708s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librdmacm1t64 armhf 50.0-2build1 [63.0 kB]
708s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfabric1 armhf 1.17.0-3build1 [419 kB]
708s Get:23 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB]
708s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmunge2 armhf 0.5.15-4 [17.1 kB]
708s Get:25 http://ftpmaster.internal/ubuntu noble/main armhf libpciaccess0 armhf 0.17-3 [16.3 kB]
708s Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu1 [10.4 kB]
708s Get:27 http://ftpmaster.internal/ubuntu noble/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1 [34.4 kB]
708s Get:28 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-plugins armhf 2.10.0-1 [13.7 kB]
708s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpmix2t64 armhf 5.0.1-4.1 [616 kB]
708s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu1 [2041 kB]
708s Get:31 http://ftpmaster.internal/ubuntu noble/universe armhf libspqr4 armhf 1:7.6.1+dfsg-1 [127 kB]
708s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf apbs armhf 3.4.1-5.1build1 [73.7 kB]
708s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12t64 armhf 3.12.2-4build3 [2056 kB]
708s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-apbslib armhf 3.4.1-5.1build1 [211 kB]
708s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libapbs-dev armhf 3.4.1-5.1build1 [99.5 kB]
708s Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
708s Get:37 http://ftpmaster.internal/ubuntu noble/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
708s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjs-sphinxdoc all 7.2.6-5 [149 kB]
708s Get:39 http://ftpmaster.internal/ubuntu noble/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
708s Get:40 http://ftpmaster.internal/ubuntu noble/main armhf fonts-lato all 2.015-1 [2781 kB]
708s Get:41 http://ftpmaster.internal/ubuntu noble/main armhf sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB]
708s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf apbs-doc all 3.4.1-5.1build1 [5848 kB]
709s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmaloc-dev armhf 1.5-1build1 [120 kB]
709s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfetk-dev armhf 3.4.1-5.1build1 [144 kB]
711s Fetched 31.4 MB in 4s (8671 kB/s)
711s Selecting previously unselected package apbs-data.
711s (Reading database ... 
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(Reading database ... 27130 files and directories currently installed.)
711s Preparing to unpack .../00-apbs-data_3.4.1-5.1build1_all.deb ...
711s Unpacking apbs-data (3.4.1-5.1build1) ...
712s Selecting previously unselected package libmaloc1.
712s Preparing to unpack .../01-libmaloc1_1.5-1build1_armhf.deb ...
712s Unpacking libmaloc1 (1.5-1build1) ...
712s Selecting previously unselected package libblas3:armhf.
712s Preparing to unpack .../02-libblas3_3.12.0-3_armhf.deb ...
712s Unpacking libblas3:armhf (3.12.0-3) ...
712s Selecting previously unselected package libsuperlu6:armhf.
712s Preparing to unpack .../03-libsuperlu6_6.0.1+dfsg1-1_armhf.deb ...
712s Unpacking libsuperlu6:armhf (6.0.1+dfsg1-1) ...
712s Selecting previously unselected package libgomp1:armhf.
712s Preparing to unpack .../04-libgomp1_14-20240315-1ubuntu1_armhf.deb ...
712s Unpacking libgomp1:armhf (14-20240315-1ubuntu1) ...
713s Selecting previously unselected package libsuitesparseconfig7:armhf.
713s Preparing to unpack .../05-libsuitesparseconfig7_1%3a7.6.1+dfsg-1_armhf.deb ...
713s Unpacking libsuitesparseconfig7:armhf (1:7.6.1+dfsg-1) ...
713s Selecting previously unselected package libamd3:armhf.
713s Preparing to unpack .../06-libamd3_1%3a7.6.1+dfsg-1_armhf.deb ...
713s Unpacking libamd3:armhf (1:7.6.1+dfsg-1) ...
713s Selecting previously unselected package libcamd3:armhf.
713s Preparing to unpack .../07-libcamd3_1%3a7.6.1+dfsg-1_armhf.deb ...
713s Unpacking libcamd3:armhf (1:7.6.1+dfsg-1) ...
713s Selecting previously unselected package libccolamd3:armhf.
713s Preparing to unpack .../08-libccolamd3_1%3a7.6.1+dfsg-1_armhf.deb ...
713s Unpacking libccolamd3:armhf (1:7.6.1+dfsg-1) ...
713s Selecting previously unselected package libcolamd3:armhf.
713s Preparing to unpack .../09-libcolamd3_1%3a7.6.1+dfsg-1_armhf.deb ...
713s Unpacking libcolamd3:armhf (1:7.6.1+dfsg-1) ...
714s Selecting previously unselected package libgfortran5:armhf.
714s Preparing to unpack .../10-libgfortran5_14-20240315-1ubuntu1_armhf.deb ...
714s Unpacking libgfortran5:armhf (14-20240315-1ubuntu1) ...
714s Selecting previously unselected package liblapack3:armhf.
714s Preparing to unpack .../11-liblapack3_3.12.0-3_armhf.deb ...
714s Unpacking liblapack3:armhf (3.12.0-3) ...
714s Selecting previously unselected package libcholmod5:armhf.
714s Preparing to unpack .../12-libcholmod5_1%3a7.6.1+dfsg-1_armhf.deb ...
714s Unpacking libcholmod5:armhf (1:7.6.1+dfsg-1) ...
714s Selecting previously unselected package libumfpack6:armhf.
714s Preparing to unpack .../13-libumfpack6_1%3a7.6.1+dfsg-1_armhf.deb ...
714s Unpacking libumfpack6:armhf (1:7.6.1+dfsg-1) ...
714s Selecting previously unselected package libfetk1.9t64:armhf.
714s Preparing to unpack .../14-libfetk1.9t64_3.4.1-5.1build1_armhf.deb ...
714s Unpacking libfetk1.9t64:armhf (3.4.1-5.1build1) ...
715s Selecting previously unselected package libapbs3t64:armhf.
715s Preparing to unpack .../15-libapbs3t64_3.4.1-5.1build1_armhf.deb ...
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725s Selecting previously unselected package libmaloc-dev.
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725s Unpacking libmaloc-dev (1.5-1build1) ...
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726s Unpacking libfetk-dev:armhf (3.4.1-5.1build1) ...
726s Setting up libmaloc1 (1.5-1build1) ...
726s Setting up libpciaccess0:armhf (0.17-3) ...
726s Setting up fonts-lato (2.015-1) ...
726s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
726s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
726s Setting up apbs-data (3.4.1-5.1build1) ...
726s Setting up libgomp1:armhf (14-20240315-1ubuntu1) ...
726s Setting up libxnvctrl0:armhf (510.47.03-0ubuntu1) ...
726s Setting up libpython3.12t64:armhf (3.12.2-4build3) ...
726s Setting up libblas3:armhf (3.12.0-3) ...
726s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
726s Setting up libmunge2:armhf (0.5.15-4) ...
726s Setting up libhwloc15:armhf (2.10.0-1) ...
726s Setting up libgfortran5:armhf (14-20240315-1ubuntu1) ...
726s Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ...
726s Setting up libsuitesparseconfig7:armhf (1:7.6.1+dfsg-1) ...
726s Setting up librdmacm1t64:armhf (50.0-2build1) ...
726s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
726s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
726s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ...
726s Setting up libmaloc-dev (1.5-1build1) ...
726s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
726s Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ...
726s Setting up libfabric1:armhf (1.17.0-3build1) ...
726s Setting up liblapack3:armhf (3.12.0-3) ...
726s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
726s Setting up libarpack2t64:armhf (3.9.1-1.1build1) ...
726s Setting up libamd3:armhf (1:7.6.1+dfsg-1) ...
726s Setting up libcolamd3:armhf (1:7.6.1+dfsg-1) ...
726s Setting up libsuperlu6:armhf (6.0.1+dfsg1-1) ...
726s Setting up libhwloc-plugins:armhf (2.10.0-1) ...
726s Setting up libcamd3:armhf (1:7.6.1+dfsg-1) ...
726s Setting up libpmix2t64:armhf (5.0.1-4.1) ...
726s Setting up libjs-sphinxdoc (7.2.6-5) ...
726s Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu1) ...
726s Setting up libccolamd3:armhf (1:7.6.1+dfsg-1) ...
726s Setting up libcholmod5:armhf (1:7.6.1+dfsg-1) ...
726s Setting up libspqr4:armhf (1:7.6.1+dfsg-1) ...
726s Setting up apbs-doc (3.4.1-5.1build1) ...
726s Setting up libumfpack6:armhf (1:7.6.1+dfsg-1) ...
726s Setting up libfetk1.9t64:armhf (3.4.1-5.1build1) ...
726s Setting up libapbs3t64:armhf (3.4.1-5.1build1) ...
726s Setting up libfetk-dev:armhf (3.4.1-5.1build1) ...
726s Setting up libapbs-dev:armhf (3.4.1-5.1build1) ...
726s Setting up apbs (3.4.1-5.1build1) ...
726s Setting up python3-apbslib (3.4.1-5.1build1) ...
727s Setting up autopkgtest-satdep (0) ...
727s Processing triggers for man-db (2.12.0-3build4) ...
728s Processing triggers for libc-bin (2.39-0ubuntu6) ...
770s (Reading database ... 33076 files and directories currently installed.)
770s Removing autopkgtest-satdep (0) ...
783s autopkgtest [14:58:39]: test test-apbs: [-----------------------
787s TESTING WITH BINARY_NAME:apbs
787s START_DIR:/tmp/autopkgtest.zK81Ye/autopkgtest_tmp/build
787s --------------------------------------------------------------------------------
787s Testing forces from apbs-forces.in
787s 
787s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.008254 seconds
787s --------------------------------------------------------------------------------
787s --------------------------------------------------------------------------------
787s Testing input file apbs-mol-auto.in
787s 
812s CHECKING:/usr/local/sbin/apbs
812s CHECKING:/usr/local/bin/apbs
812s CHECKING:/usr/sbin/apbs
812s CHECKING:/usr/bin/apbs
812s NOTE: Using apbs binary:/usr/bin/apbs
812s Testing all sections
812s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv
812s ================================================================================
812s Running tests for born section
812s BINARY:  /usr/bin/apbs
812s INPUT:   apbs-mol-auto.in
812s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in']
812s asc_getToken: Error occurred (bailing out).
812s Vio_scanf: Format problem with input.
812s 
812s 
812s ----------------------------------------------------------------------
812s     APBS -- Adaptive Poisson-Boltzmann Solver
812s     Version APBS 3.4.1
812s     
812s     Nathan A. Baker (nathan.baker@pnnl.gov)
812s     Pacific Northwest National Laboratory
812s     
812s     Additional contributing authors listed in the code documentation.
812s     
812s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
812s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
812s     Northwest Division for the U.S. Department of Energy.
812s     
812s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
812s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
812s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
812s     Portions Copyright (c) 1995, Michael Holst.
812s     All rights reserved.
812s     
812s     Redistribution and use in source and binary forms, with or without
812s     modification, are permitted provided that the following conditions are met:
812s     
812s     * Redistributions of source code must retain the above copyright notice, this
812s       list of conditions and the following disclaimer.
812s     
812s     * Redistributions in binary form must reproduce the above copyright notice,
812s       this list of conditions and the following disclaimer in the documentation
812s       and/or other materials provided with the distribution.
812s     
812s     * Neither the name of the developer nor the names of its contributors may be
812s       used to endorse or promote products derived from this software without
812s       specific prior written permission.
812s     
812s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
812s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
812s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
812s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
812s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
812s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
812s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
812s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
812s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
812s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
812s ----------------------------------------------------------------------
812s     APBS uses FETK (the Finite Element ToolKit) to solve the
812s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
812s     of finite element modeling class libraries developed by the Michael Holst
812s     research group and written in an object-oriented form of C.  FEtk is
812s     designed to solve general coupled systems of nonlinear partial differential
812s     equations using adaptive finite element methods, inexact Newton methods,
812s     and algebraic multilevel methods.  More information about FEtk may be found
812s     at <http://www.FEtk.ORG>.
812s ----------------------------------------------------------------------
812s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
812s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
812s     which has been modified by Patrice Koehl
812s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
812s     memory usage when solving the Poisson-Boltzmann equation.
812s ----------------------------------------------------------------------
812s     Please cite your use of APBS as:
812s 
812s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
812s     nanosystems: application to microtubules and the ribosome. Proc.
812s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
812s     
812s 
812s This executable compiled on Mar  2 2024 at 20:11:10
812s 
812s Parsing input file apbs-mol-auto.in...
812s rank 0 size 1...
812s Parsed input file.
812s Got paths for 1 molecules
812s Reading PQR-format atom data from ion.pqr.
812s   1 atoms
812s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
812s   Net charge 1.00e+00 e
812s Preparing to run 6 PBE calculations.
812s ----------------------------------------
812s CALCULATION #1 (solvated): MULTIGRID
812s   Setting up problem...
812s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
812s   Debye length:  0 A
812s   Current memory usage:  61.262 MB total, 61.262 MB high water
812s   Using cubic spline charge discretization.
812s   Grid dimensions: 65 x 65 x 65
812s   Grid spacings: 0.781 x 0.781 x 0.781
812s   Grid lengths: 50.000 x 50.000 x 50.000
812s   Grid center: (0.000, 0.000, 0.000)
812s   Multigrid levels: 5
812s   Molecule ID: 1
812s   Linearized traditional PBE
812s   Multiple Debye-Huckel sphere boundary conditions
812s   0 ion species (0.000 M ionic strength):
812s   Solute dielectric: 1.000
812s   Solvent dielectric: 78.540
812s   Using "molecular" surface definition; no smoothing
812s   Solvent probe radius: 1.400 A
812s   Temperature:  298.150 K
812s   Electrostatic energies will be calculated
812s   Total electrostatic energy = 9.607073836227E+02 kJ/mol
812s   Calculating forces...
812s ----------------------------------------
812s CALCULATION #2 (solvated): MULTIGRID
812s   Setting up problem...
812s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
812s   Debye length:  0 A
812s   Current memory usage:  61.262 MB total, 122.067 MB high water
812s   Using cubic spline charge discretization.
812s   Grid dimensions: 65 x 65 x 65
812s   Grid spacings: 0.383 x 0.383 x 0.383
812s   Grid lengths: 24.495 x 24.495 x 24.495
812s   Grid center: (0.000, 0.000, 0.000)
812s   Multigrid levels: 5
812s   Molecule ID: 1
812s   Linearized traditional PBE
812s   Boundary conditions from focusing
812s   0 ion species (0.000 M ionic strength):
812s   Solute dielectric: 1.000
812s   Solvent dielectric: 78.540
812s   Using "molecular" surface definition; no smoothing
812s   Solvent probe radius: 1.400 A
812s   Temperature:  298.150 K
812s   Electrostatic energies will be calculated
812s   Total electrostatic energy = 2.200266567971E+03 kJ/mol
812s   Calculating forces...
812s ----------------------------------------
812s CALCULATION #3 (solvated): MULTIGRID
812s   Setting up problem...
812s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
812s   Debye length:  0 A
812s   Current memory usage:  61.262 MB total, 122.067 MB high water
812s   Using cubic spline charge discretization.
812s   Grid dimensions: 65 x 65 x 65
812s   Grid spacings: 0.188 x 0.188 x 0.188
812s   Grid lengths: 12.000 x 12.000 x 12.000
812s   Grid center: (0.000, 0.000, 0.000)
812s   Multigrid levels: 5
812s   Molecule ID: 1
812s   Linearized traditional PBE
812s   Boundary conditions from focusing
812s   0 ion species (0.000 M ionic strength):
812s   Solute dielectric: 1.000
812s   Solvent dielectric: 78.540
812s   Using "molecular" surface definition; no smoothing
812s   Solvent probe radius: 1.400 A
812s   Temperature:  298.150 K
812s   Electrostatic energies will be calculated
812s   Potential to be written to potential.dx.gz
812s   Total electrostatic energy = 4.732245131587E+03 kJ/mol
812s   Calculating forces...
812s   Writing potential to potential-PE0.dx.gz
812s ----------------------------------------
812s CALCULATION #4 (reference): MULTIGRID
812s   Setting up problem...
812s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
812s   Debye length:  0 A
812s   Current memory usage:  61.189 MB total, 122.067 MB high water
812s   Using cubic spline charge discretization.
812s   Grid dimensions: 65 x 65 x 65
812s   Grid spacings: 0.781 x 0.781 x 0.781
812s   Grid lengths: 50.000 x 50.000 x 50.000
812s   Grid center: (0.000, 0.000, 0.000)
812s   Multigrid levels: 5
812s   Molecule ID: 1
812s   Linearized traditional PBE
812s   Multiple Debye-Huckel sphere boundary conditions
812s   0 ion species (0.000 M ionic strength):
812s   Solute dielectric: 1.000
812s   Solvent dielectric: 1.000
812s   Using "molecular" surface definition; no smoothing
812s   Solvent probe radius: 1.400 A
812s   Temperature:  298.150 K
812s   Electrostatic energies will be calculated
812s   Total electrostatic energy = 1.190871482831E+03 kJ/mol
812s   Calculating forces...
812s ----------------------------------------
812s CALCULATION #5 (reference): MULTIGRID
812s   Setting up problem...
812s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
812s   Debye length:  0 A
812s   Current memory usage:  61.189 MB total, 122.067 MB high water
812s   Using cubic spline charge discretization.
812s   Grid dimensions: 65 x 65 x 65
812s   Grid spacings: 0.383 x 0.383 x 0.383
812s   Grid lengths: 24.495 x 24.495 x 24.495
812s   Grid center: (0.000, 0.000, 0.000)
812s   Multigrid levels: 5
812s   Molecule ID: 1
812s   Linearized traditional PBE
812s   Boundary conditions from focusing
812s   0 ion species (0.000 M ionic strength):
812s   Solute dielectric: 1.000
812s   Solvent dielectric: 1.000
812s   Using "molecular" surface definition; no smoothing
812s   Solvent probe radius: 1.400 A
812s   Temperature:  298.150 K
812s   Electrostatic energies will be calculated
812s   Total electrostatic energy = 2.430874049735E+03 kJ/mol
812s   Calculating forces...
812s [focusFillBound()]: WARNING:
812s     Unusually large potential values
812s     detected on the focusing boundary!
812s     Convergence not guaranteed for NPBE/NRPBE calculations!
812s 
812s ----------------------------------------
812s CALCULATION #6 (reference): MULTIGRID
812s   Setting up problem...
812s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
812s   Debye length:  0 A
812s   Current memory usage:  61.189 MB total, 122.067 MB high water
812s   Using cubic spline charge discretization.
812s   Grid dimensions: 65 x 65 x 65
812s   Grid spacings: 0.188 x 0.188 x 0.188
812s   Grid lengths: 12.000 x 12.000 x 12.000
812s   Grid center: (0.000, 0.000, 0.000)
812s   Multigrid levels: 5
812s   Molecule ID: 1
812s   Linearized traditional PBE
812s   Boundary conditions from focusing
812s   0 ion species (0.000 M ionic strength):
812s   Solute dielectric: 1.000
812s   Solvent dielectric: 1.000
812s   Using "molecular" surface definition; no smoothing
812s   Solvent probe radius: 1.400 A
812s   Temperature:  298.150 K
812s   Electrostatic energies will be calculated
812s   Total electrostatic energy = 4.962018684215E+03 kJ/mol
812s   Calculating forces...
812s ----------------------------------------
812s PRINT STATEMENTS
812s 
812s print energy 1 (solvated) - 2 (reference) end
812s   Local net energy (PE 0) = -2.297735526282E+02 kJ/mol
812s   Global net ELEC energy = -2.297735526282E+02 kJ/mol
812s ----------------------------------------
812s CLEANING UP AND SHUTTING DOWN...
812s Destroying force arrays.
812s No energy arrays to destroy.
812s Destroying multigrid structures.
812s Destroying finite element structures.
812s Destroying 1 molecules
812s Final memory usage:  0.001 MB total, 122.067 MB high water
812s 
812s 
812s Thanks for using APBS!
812s 
812s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02)
812s *** PASSED ***
812s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03)
812s *** PASSED ***
812s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03)
812s *** PASSED ***
812s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
812s *** PASSED ***
812s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03)
812s *** PASSED ***
812s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03)
812s *** PASSED ***
812s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02)
812s *** PASSED ***
812s Elapsed time: 24.805449 seconds
812s --------------------------------------------------------------------------------
812s --------------------------------------------------------------------------------
812s Testing input file apbs-smol-auto.in
812s 
832s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02)
832s *** PASSED ***
832s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03)
832s *** PASSED ***
832s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03)
832s *** PASSED ***
832s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
832s *** PASSED ***
832s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03)
832s *** PASSED ***
832s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03)
832s *** PASSED ***
832s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02)
832s *** PASSED ***
832s Elapsed time: 20.231338 seconds
832s --------------------------------------------------------------------------------
832s --------------------------------------------------------------------------------
832s Testing input file apbs-mol-parallel.in
832s 
832s Checking for intermediate energies in input file apbs-mol-auto.out
832s EXPECTED COMPUTED: 7
832s EXPECTED EXPECTED: 7
832s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282]
832s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02']
832s COMPUTED RESULT 960.7073836227
832s COMPUTED RESULT 2200.266567971
832s COMPUTED RESULT 4732.245131587
832s COMPUTED RESULT 1190.871482831
832s COMPUTED RESULT 2430.874049735
832s COMPUTED RESULT 4962.018684215
832s COMPUTED RESULT -229.7735526282
832s BINARY:  /usr/bin/apbs
832s INPUT:   apbs-smol-auto.in
832s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in']
832s asc_getToken: Error occurred (bailing out).
832s Vio_scanf: Format problem with input.
832s 
832s 
832s ----------------------------------------------------------------------
832s     APBS -- Adaptive Poisson-Boltzmann Solver
832s     Version APBS 3.4.1
832s     
832s     Nathan A. Baker (nathan.baker@pnnl.gov)
832s     Pacific Northwest National Laboratory
832s     
832s     Additional contributing authors listed in the code documentation.
832s     
832s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
832s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
832s     Northwest Division for the U.S. Department of Energy.
832s     
832s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
832s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
832s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
832s     Portions Copyright (c) 1995, Michael Holst.
832s     All rights reserved.
832s     
832s     Redistribution and use in source and binary forms, with or without
832s     modification, are permitted provided that the following conditions are met:
832s     
832s     * Redistributions of source code must retain the above copyright notice, this
832s       list of conditions and the following disclaimer.
832s     
832s     * Redistributions in binary form must reproduce the above copyright notice,
832s       this list of conditions and the following disclaimer in the documentation
832s       and/or other materials provided with the distribution.
832s     
832s     * Neither the name of the developer nor the names of its contributors may be
832s       used to endorse or promote products derived from this software without
832s       specific prior written permission.
832s     
832s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
832s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
832s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
832s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
832s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
832s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
832s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
832s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
832s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
832s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
832s ----------------------------------------------------------------------
832s     APBS uses FETK (the Finite Element ToolKit) to solve the
832s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
832s     of finite element modeling class libraries developed by the Michael Holst
832s     research group and written in an object-oriented form of C.  FEtk is
832s     designed to solve general coupled systems of nonlinear partial differential
832s     equations using adaptive finite element methods, inexact Newton methods,
832s     and algebraic multilevel methods.  More information about FEtk may be found
832s     at <http://www.FEtk.ORG>.
832s ----------------------------------------------------------------------
832s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
832s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
832s     which has been modified by Patrice Koehl
832s     <http://koehllab.genomeSplitting the input file into 4 separate files using the inputgen utility
832s 
832s center.ucdavis.edu/> for improved efficiency and
832s     memory usage when solving the Poisson-Boltzmann equation.
832s ----------------------------------------------------------------------
832s     Please cite your use of APBS as:
832s 
832s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
832s     nanosystems: application to microtubules and the ribosome. Proc.
832s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
832s     
832s 
832s This executable compiled on Mar  2 2024 at 20:11:10
832s 
832s Parsing input file apbs-smol-auto.in...
832s rank 0 size 1...
832s Parsed input file.
832s Got paths for 1 molecules
832s Reading PQR-format atom data from ion.pqr.
832s   1 atoms
832s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
832s   Net charge 1.00e+00 e
832s Preparing to run 6 PBE calculations.
832s ----------------------------------------
832s CALCULATION #1 (solvated): MULTIGRID
832s   Setting up problem...
832s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
832s   Debye length:  0 A
832s   Current memory usage:  61.262 MB total, 61.262 MB high water
832s   Using cubic spline charge discretization.
832s   Grid dimensions: 65 x 65 x 65
832s   Grid spacings: 0.781 x 0.781 x 0.781
832s   Grid lengths: 50.000 x 50.000 x 50.000
832s   Grid center: (0.000, 0.000, 0.000)
832s   Multigrid levels: 5
832s   Molecule ID: 1
832s   Linearized traditional PBE
832s   Multiple Debye-Huckel sphere boundary conditions
832s   0 ion species (0.000 M ionic strength):
832s   Solute dielectric: 1.000
832s   Solvent dielectric: 78.540
832s   Using "molecular" surface definition;harmonic average smoothing
832s   Solvent probe radius: 1.400 A
832s   Temperature:  298.150 K
832s   Electrostatic energies will be calculated
832s   Total electrostatic energy = 9.532928767450E+02 kJ/mol
832s   Calculating forces...
832s ----------------------------------------
832s CALCULATION #2 (solvated): MULTIGRID
832s   Setting up problem...
832s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
832s   Debye length:  0 A
832s   Current memory usage:  61.262 MB total, 122.067 MB high water
832s   Using cubic spline charge discretization.
832s   Grid dimensions: 65 x 65 x 65
832s   Grid spacings: 0.383 x 0.383 x 0.383
832s   Grid lengths: 24.495 x 24.495 x 24.495
832s   Grid center: (0.000, 0.000, 0.000)
832s   Multigrid levels: 5
832s   Molecule ID: 1
832s   Linearized traditional PBE
832s   Boundary conditions from focusing
832s   0 ion species (0.000 M ionic strength):
832s   Solute dielectric: 1.000
832s   Solvent dielectric: 78.540
832s   Using "molecular" surface definition;harmonic average smoothing
832s   Solvent probe radius: 1.400 A
832s   Temperature:  298.150 K
832s   Electrostatic energies will be calculated
832s   Total electrostatic energy = 2.201243880085E+03 kJ/mol
832s   Calculating forces...
832s ----------------------------------------
832s CALCULATION #3 (solvated): MULTIGRID
832s   Setting up problem...
832s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
832s   Debye length:  0 A
832s   Current memory usage:  61.262 MB total, 122.067 MB high water
832s   Using cubic spline charge discretization.
832s   Grid dimensions: 65 x 65 x 65
832s   Grid spacings: 0.188 x 0.188 x 0.188
832s   Grid lengths: 12.000 x 12.000 x 12.000
832s   Grid center: (0.000, 0.000, 0.000)
832s   Multigrid levels: 5
832s   Molecule ID: 1
832s   Linearized traditional PBE
832s   Boundary conditions from focusing
832s   0 ion species (0.000 M ionic strength):
832s   Solute dielectric: 1.000
832s   Solvent dielectric: 78.540
832s   Using "molecular" surface definition;harmonic average smoothing
832s   Solvent probe radius: 1.400 A
832s   Temperature:  298.150 K
832s   Electrostatic energies will be calculated
832s   Total electrostatic energy = 4.733006258977E+03 kJ/mol
832s   Calculating forces...
832s ----------------------------------------
832s CALCULATION #4 (reference): MULTIGRID
832s   Setting up problem...
832s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
832s   Debye length:  0 A
832s   Current memory usage:  61.189 MB total, 122.067 MB high water
832s   Using cubic spline charge discretization.
832s   Grid dimensions: 65 x 65 x 65
832s   Grid spacings: 0.781 x 0.781 x 0.781
832s   Grid lengths: 50.000 x 50.000 x 50.000
832s   Grid center: (0.000, 0.000, 0.000)
832s   Multigrid levels: 5
832s   Molecule ID: 1
832s   Linearized traditional PBE
832s   Multiple Debye-Huckel sphere boundary conditions
832s   0 ion species (0.000 M ionic strength):
832s   Solute dielectric: 1.000
832s   Solvent dielectric: 1.000
832s   Using "molecular" surface definition;harmonic average smoothing
832s   Solvent probe radius: 1.400 A
832s   Temperature:  298.150 K
832s   Electrostatic energies will be calculated
832s   Total electrostatic energy = 1.190871482831E+03 kJ/mol
832s   Calculating forces...
832s ----------------------------------------
832s CALCULATION #5 (reference): MULTIGRID
832s   Setting up problem...
832s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
832s   Debye length:  0 A
832s   Current memory usage:  61.189 MB total, 122.067 MB high water
832s   Using cubic spline charge discretization.
832s   Grid dimensions: 65 x 65 x 65
832s   Grid spacings: 0.383 x 0.383 x 0.383
832s   Grid lengths: 24.495 x 24.495 x 24.495
832s   Grid center: (0.000, 0.000, 0.000)
832s   Multigrid levels: 5
832s   Molecule ID: 1
832s   Linearized traditional PBE
832s   Boundary conditions from focusing
832s   0 ion species (0.000 M ionic strength):
832s   Solute dielectric: 1.000
832s   Solvent dielectric: 1.000
832s   Using "molecular" surface definition;harmonic average smoothing
832s   Solvent probe radius: 1.400 A
832s   Temperature:  298.150 K
832s   Electrostatic energies will be calculated
832s   Total electrostatic energy = 2.430874049735E+03 kJ/mol
832s   Calculating forces...
832s [focusFillBound()]: WARNING:
832s     Unusually large potential values
832s     detected on the focusing boundary!
832s     Convergence not guaranteed for NPBE/NRPBE calculations!
832s 
832s ----------------------------------------
832s CALCULATION #6 (reference): MULTIGRID
832s   Setting up problem...
832s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
832s   Debye length:  0 A
832s   Current memory usage:  61.189 MB total, 122.067 MB high water
832s   Using cubic spline charge discretization.
832s   Grid dimensions: 65 x 65 x 65
832s   Grid spacings: 0.188 x 0.188 x 0.188
832s   Grid lengths: 12.000 x 12.000 x 12.000
832s   Grid center: (0.000, 0.000, 0.000)
832s   Multigrid levels: 5
832s   Molecule ID: 1
832s   Linearized traditional PBE
832s   Boundary conditions from focusing
832s   0 ion species (0.000 M ionic strength):
832s   Solute dielectric: 1.000
832s   Solvent dielectric: 1.000
832s   Using "molecular" surface definition;harmonic average smoothing
832s   Solvent probe radius: 1.400 A
832s   Temperature:  298.150 K
832s   Electrostatic energies will be calculated
832s   Total electrostatic energy = 4.962018684215E+03 kJ/mol
832s   Calculating forces...
832s ----------------------------------------
832s PRINT STATEMENTS
832s 
832s print energy 1 (solvated) - 2 (reference) end
832s   Local net energy (PE 0) = -2.290124252387E+02 kJ/mol
832s   Global net ELEC energy = -2.290124252387E+02 kJ/mol
832s ----------------------------------------
832s CLEANING UP AND SHUTTING DOWN...
832s Destroying force arrays.
832s No energy arrays to destroy.
832s Destroying multigrid structures.
832s Destroying finite element structures.
832s Destroying 1 molecules
832s Final memory usage:  0.001 MB total, 122.067 MB high water
832s 
832s 
832s Thanks for using APBS!
832s 
861s Checking for intermediate energies in input file apbs-smol-auto.out
861s EXPECTED COMPUTED: 7
861s EXPECTED EXPECTED: 7
861s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387]
861s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02']
861s COMPUTED RESULT 953.292876745
861s COMPUTED RESULT 2201.243880085
861s COMPUTED RESULT 4733.006258977
861s COMPUTED RESULT 1190.871482831
861s COMPUTED RESULT 2430.874049735
861s COMPUTED RESULT 4962.018684215
861s COMPUTED RESULT -229.0124252387
861s BINARY:  /usr/bin/apbs
861s INPUT:   apbs-mol-parallel-PE0.in
861s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in']
861s asc_getToken: Error occurred (bailing out).
861s Vio_scanf: Format problem with input.
861s 
861s 
861s ----------------------------------------------------------------------
861s     APBS -- Adaptive Poisson-Boltzmann Solver
861s     Version APBS 3.4.1
861s     
861s     Nathan A. Baker (nathan.baker@pnnl.gov)
861s     Pacific Northwest National Laboratory
861s     
861s     Additional contributing authors listed in the code documentation.
861s     
861s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
861s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
861s     Northwest Division for the U.S. Department of Energy.
861s     
861s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
861s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
861s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
861s     Portions Copyright (c) 1995, Michael Holst.
861s     All rights reserved.
861s     
861s     Redistribution and use in source and binary forms, with or without
861s     modification, are permitted provided that the following conditions are met:
861s     
861s     * Redistributions of source code must retain the above copyright notice, this
861s       list of conditions and the following disclaimer.
861s     
861s     * Redistributions in binary form must reproduce the above copyright notice,
861s       this list of conditions and the following disclaimer in the documentation
861s       and/or other materials provided with the distribution.
861s     
861s     * Neither the name of the developer nor the names of its contributors may be
861s       used to endorse or promote products derived from this software without
861s       specific prior written permission.
861s     
861s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
861s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
861s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
861s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
861s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
861s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
861s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
861s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
861s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
861s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
861s ----------------------------------------------------------------------
861s     APBS uses FETK (the Finite Element ToolKit) to solve the
861s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
861s     of finite element modeling class libraries developed by the Michael Holst
861s     research group and written in an object-oriented form of C.  FEtk is
861s     designed to solve general coupled systems of nonlinear partial differential
861s     equations using adaptive finite element methods, inexact Newton methods,
861s     and algebraic multilevel methods.  More information about FEtk may be found
861s     at <http://www.FEtk.ORG>.
861s ----------------------------------------------------------------------
861s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
861s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
861s     which has been modified by Patrice Koehl
861s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
861s     memory usage when solving the Poisson-Boltzmann equation.
861s ----------------------------------------------------------------------
861s     Please cite your use of APBS as:
861s 
861s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
861s     nanosystems: application to microtubules and the ribosome. Proc.
861s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
861s     
861s 
861s This executable compiled on Mar  2 2024 at 20:11:10
861s 
861s Parsing input file apbs-mol-parallel-PE0.in...
861s rank 0 size 1...
861s Parsed input file.
861s Got paths for 1 molecules
861s Reading PQR-format atom data from ion.pqr.
861s   1 atoms
861s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
861s   Net charge 1.00e+00 e
861s Preparing to run 6 PBE calculations.
861s ----------------------------------------
861s CALCULATION #1 (solvated): MULTIGRID
861s   Setting up problem...
861s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
861s   Debye length:  0 A
861s   Current memory usage:  61.262 MB total, 61.262 MB high water
861s   Using cubic spline charge discretization.
861s   Partition overlap fraction = 0.1
861s   Processor array = 2 x 2 x 1
861s   Grid dimensions: 65 x 65 x 65
861s   Grid spacings: 0.781 x 0.781 x 0.781
861s   Grid lengths: 50.000 x 50.000 x 50.000
861s   Grid center: (0.000, 0.000, 0.000)
861s   Multigrid levels: 5
861s   Molecule ID: 1
861s   Linearized traditional PBE
861s   Multiple Debye-Huckel sphere boundary conditions
861s   0 ion species (0.000 M ionic strength):
861s   Solute dielectric: 1.000
861s   Solvent dielectric: 78.540
861s   Using "molecular" surface definition; no smoothing
861s   Solvent probe radius: 1.400 A
861s   Temperature:  298.150 K
861s   Electrostatic energies will be calculated
861s   Total electrostatic energy = 2.401768459022E+02 kJ/mol
861s   Calculating forces...
861s ----------------------------------------
861s CALCULATION #2 (solvated): MULTIGRID
861s   Setting up problem...
861s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
861s   Debye length:  0 A
861s   Current memory usage:  61.262 MB total, 122.067 MB high water
861s   Using cubic spline charge discretization.
861s   Partition overlap fraction = 0.1
861s   Processor array = 2 x 2 x 1
861s   Grid dimensions: 65 x 65 x 65
861s   Grid spacings: 0.296 x 0.296 x 0.383
861s   Grid lengths: 18.944 x 18.944 x 24.495
861s   Grid center: (-2.411, -2.411, 0.000)
861s   Multigrid levels: 5
861s   Molecule ID: 1
861s   Linearized traditional PBE
861s   Boundary conditions from focusing
861s   0 ion species (0.000 M ionic strength):
861s   Solute dielectric: 1.000
861s   Solvent dielectric: 78.540
861s   Using "molecular" surface definition; no smoothing
861s   Solvent probe radius: 1.400 A
861s   Temperature:  298.150 K
861s   Electrostatic energies will be calculated
861s   Total electrostatic energy = 8.142935592471E+02 kJ/mol
861s   Calculating forces...
861s [focusFillBound()]: WARNING:
861s     Unusually large potential values
861s     detected on the focusing boundary!
861s     Convergence not guaranteed for NPBE/NRPBE calculations!
861s 
861s ----------------------------------------
861s CALCULATION #3 (solvated): MULTIGRID
861s   Setting up problem...
861s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
861s   Debye length:  0 A
861s   Current memory usage:  61.262 MB total, 122.067 MB high water
861s   Using cubic spline charge discretization.
861s   Partition overlap fraction = 0.1
861s   Processor array = 2 x 2 x 1
861s   Grid dimensions: 65 x 65 x 65
861s   Grid spacings: 0.112 x 0.112 x 0.188
861s   Grid lengths: 7.178 x 7.178 x 12.000
861s   Grid center: (-2.411, -2.411, 0.000)
861s   Multigrid levels: 5
861s   Molecule ID: 1
861s   Linearized traditional PBE
861s   Boundary conditions from focusing
861s   0 ion species (0.000 M ionic strength):
861s   Solute dielectric: 1.000
861s   Solvent dielectric: 78.540
861s   Using "molecular" surface definition; no smoothing
861s   Solvent probe radius: 1.400 A
861s   Temperature:  298.150 K
861s   Electrostatic energies will be calculated
861s   Total electrostatic energy = 1.485255308186E+03 kJ/mol
861s   Calculating forces...
861s ----------------------------------------
861s CALCULATION #4 (reference): MULTIGRID
861s   Setting up problem...
861s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
861s   Debye length:  0 A
861s   Current memory usage:  61.189 MB total, 122.067 MB high water
861s   Using cubic spline charge discretization.
861s   Partition overlap fraction = 0.1
861s   Processor array = 2 x 2 x 1
861s   Grid dimensions: 65 x 65 x 65
861s   Grid spacings: 0.781 x 0.781 x 0.781
861s   Grid lengths: 50.000 x 50.000 x 50.000
861s   Grid center: (0.000, 0.000, 0.000)
861s   Multigrid levels: 5
861s   Molecule ID: 1
861s   Linearized traditional PBE
861s   Multiple Debye-Huckel sphere boundary conditions
861s   0 ion species (0.000 M ionic strength):
861s   Solute dielectric: 1.000
861s   Solvent dielectric: 1.000
861s   Using "molecular" surface definition; no smoothing
861s   Solvent probe radius: 1.400 A
861s   Temperature:  298.150 K
861s   Electrostatic energies will be calculated
861s   Total electrostatic energy = 2.977178707009E+02 kJ/mol
861s   Calculating forces...
861s ----------------------------------------
861s CALCULATION #5 (reference): MULTIGRID
861s   Setting up problem...
861s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
861s   Debye length:  0 A
861s   Current memory usage:  61.189 MB total, 122.067 MB high water
861s   Using cubic spline charge discretization.
861s   Partition overlap fraction = 0.1
861s   Processor array = 2 x 2 x 1
861s   Grid dimensions: 65 x 65 x 65
861s   Grid spacings: 0.296 x 0.296 x 0.383
861s   Grid lengths: 18.944 x 18.944 x 24.495
861s   Grid center: (-2.411, -2.411, 0.000)
861s   Multigrid levels: 5
861s   Molecule ID: 1
861s   Linearized traditional PBE
861s   Boundary conditions from focusing
861s   0 ion species (0.000 M ionic strength):
861s   Solute dielectric: 1.000
861s   Solvent dielectric: 1.000
861s   Using "molecular" surface definition; no smoothing
861s   Solvent probe radius: 1.400 A
861s   Temperature:  298.150 K
861s   Electrostatic energies will be calculated
861s   Total electrostatic energy = 8.799304557588E+02 kJ/mol
861s   Calculating forces...
861s [focusFillBound()]: WARNING:
861s     Unusually large potential values
861s     detected on the focusing boundary!
861s     Convergence not guaranteed for NPBE/NRPBE calculations!
861s 
861s ----------------------------------------
861s CALCULATION #6 (reference): MULTIGRID
861s   Setting up problem...
861s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
861s   Debye length:  0 A
861s   Current memory usage:  61.189 MB total, 122.067 MB high water
861s   Using cubic spline charge discretization.
861s   Partition overlap fraction = 0.1
861s   Processor array = 2 x 2 x 1
861s   Grid dimensions: 65 x 65 x 65
861s   Grid spacings: 0.112 x 0.112 x 0.188
861s   Grid lengths: 7.178 x 7.178 x 12.000
861s   Grid center: (-2.411, -2.411, 0.000)
861s   Multigrid levels: 5
861s   Molecule ID: 1
861s   Linearized traditional PBE
861s   Boundary conditions from focusing
861s   0 ion species (0.000 M ionic strength):
861s   Solute dielectric: 1.000
861s   Solvent dielectric: 1.000
861s   Using "molecular" surface definition; no smoothing
861s   Solvent probe radius: 1.400 A
861s   Temperature:  298.150 K
861s   Electrostatic energies will be calculated
861s   Total electrostatic energy = 1.542873949131E+03 kJ/mol
861s   Calculating forces...
861s ----------------------------------------
861s PRINT STATEMENTS
861s 
861s print energy 1 (solvated) - 2 (reference) end
861s   Local net energy (PE 0) = -5.761864094552E+01 kJ/mol
861s   Global net ELEC energy = -5.761864094552E+01 kJ/mol
861s ----------------------------------------
861s CLEANING UP AND SHUTTING DOWN...
861s Destroying force arrays.
861s No energy arrays to destroy.
861s Destroying multigrid structures.
861s Destroying finite element structures.
861s Destroying 1 molecules
861s Final memory usage:  0.001 MB total, 122.067 MB high water
861s 
861s 
861s Thanks for using APBS!
861s 
861s Processor 0 results:
861s   2.401768459022e+02
861s   8.142935592471e+02
861s   1.485255308186e+03
861s   2.977178707009e+02
861s   8.799304557588e+02
861s   1.542873949131e+03
861s   -5.761864094552e+01
861s 
891s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out
891s BINARY:  /usr/bin/apbs
891s INPUT:   apbs-mol-parallel-PE1.in
891s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in']
891s asc_getToken: Error occurred (bailing out).
891s Vio_scanf: Format problem with input.
891s 
891s 
891s ----------------------------------------------------------------------
891s     APBS -- Adaptive Poisson-Boltzmann Solver
891s     Version APBS 3.4.1
891s     
891s     Nathan A. Baker (nathan.baker@pnnl.gov)
891s     Pacific Northwest National Laboratory
891s     
891s     Additional contributing authors listed in the code documentation.
891s     
891s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
891s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
891s     Northwest Division for the U.S. Department of Energy.
891s     
891s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
891s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
891s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
891s     Portions Copyright (c) 1995, Michael Holst.
891s     All rights reserved.
891s     
891s     Redistribution and use in source and binary forms, with or without
891s     modification, are permitted provided that the following conditions are met:
891s     
891s     * Redistributions of source code must retain the above copyright notice, this
891s       list of conditions and the following disclaimer.
891s     
891s     * Redistributions in binary form must reproduce the above copyright notice,
891s       this list of conditions and the following disclaimer in the documentation
891s       and/or other materials provided with the distribution.
891s     
891s     * Neither the name of the developer nor the names of its contributors may be
891s       used to endorse or promote products derived from this software without
891s       specific prior written permission.
891s     
891s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
891s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
891s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
891s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
891s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
891s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
891s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
891s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
891s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
891s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
891s ----------------------------------------------------------------------
891s     APBS uses FETK (the Finite Element ToolKit) to solve the
891s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
891s     of finite element modeling class libraries developed by the Michael Holst
891s     research group and written in an object-oriented form of C.  FEtk is
891s     designed to solve general coupled systems of nonlinear partial differential
891s     equations using adaptive finite element methods, inexact Newton methods,
891s     and algebraic multilevel methods.  More information about FEtk may be found
891s     at <http://www.FEtk.ORG>.
891s ----------------------------------------------------------------------
891s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
891s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
891s     which has been modified by Patrice Koehl
891s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
891s     memory usage when solving the Poisson-Boltzmann equation.
891s ----------------------------------------------------------------------
891s     Please cite your use of APBS as:
891s 
891s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
891s     nanosystems: application to microtubules and the ribosome. Proc.
891s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
891s     
891s 
891s This executable compiled on Mar  2 2024 at 20:11:10
891s 
891s Parsing input file apbs-mol-parallel-PE1.in...
891s rank 0 size 1...
891s Parsed input file.
891s Got paths for 1 molecules
891s Reading PQR-format atom data from ion.pqr.
891s   1 atoms
891s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
891s   Net charge 1.00e+00 e
891s Preparing to run 6 PBE calculations.
891s ----------------------------------------
891s CALCULATION #1 (solvated): MULTIGRID
891s   Setting up problem...
891s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
891s   Debye length:  0 A
891s   Current memory usage:  61.262 MB total, 61.262 MB high water
891s   Using cubic spline charge discretization.
891s   Partition overlap fraction = 0.1
891s   Processor array = 2 x 2 x 1
891s   Grid dimensions: 65 x 65 x 65
891s   Grid spacings: 0.781 x 0.781 x 0.781
891s   Grid lengths: 50.000 x 50.000 x 50.000
891s   Grid center: (0.000, 0.000, 0.000)
891s   Multigrid levels: 5
891s   Molecule ID: 1
891s   Linearized traditional PBE
891s   Multiple Debye-Huckel sphere boundary conditions
891s   0 ion species (0.000 M ionic strength):
891s   Solute dielectric: 1.000
891s   Solvent dielectric: 78.540
891s   Using "molecular" surface definition; no smoothing
891s   Solvent probe radius: 1.400 A
891s   Temperature:  298.150 K
891s   Electrostatic energies will be calculated
891s   Total electrostatic energy = 2.401768459022E+02 kJ/mol
891s   Calculating forces...
891s ----------------------------------------
891s CALCULATION #2 (solvated): MULTIGRID
891s   Setting up problem...
891s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
891s   Debye length:  0 A
891s   Current memory usage:  61.262 MB total, 122.067 MB high water
891s   Using cubic spline charge discretization.
891s   Partition overlap fraction = 0.1
891s   Processor array = 2 x 2 x 1
891s   Grid dimensions: 65 x 65 x 65
891s   Grid spacings: 0.296 x 0.296 x 0.383
891s   Grid lengths: 18.944 x 18.944 x 24.495
891s   Grid center: (2.411, -2.411, 0.000)
891s   Multigrid levels: 5
891s   Molecule ID: 1
891s   Linearized traditional PBE
891s   Boundary conditions from focusing
891s   0 ion species (0.000 M ionic strength):
891s   Solute dielectric: 1.000
891s   Solvent dielectric: 78.540
891s   Using "molecular" surface definition; no smoothing
891s   Solvent probe radius: 1.400 A
891s   Temperature:  298.150 K
891s   Electrostatic energies will be calculated
891s   Total electrostatic energy = 8.142778312125E+02 kJ/mol
891s   Calculating forces...
891s [focusFillBound()]: WARNING:
891s     Unusually large potential values
891s     detected on the focusing boundary!
891s     Convergence not guaranteed for NPBE/NRPBE calculations!
891s 
891s ----------------------------------------
891s CALCULATION #3 (solvated): MULTIGRID
891s   Setting up problem...
891s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
891s   Debye length:  0 A
891s   Current memory usage:  61.262 MB total, 122.067 MB high water
891s   Using cubic spline charge discretization.
891s   Partition overlap fraction = 0.1
891s   Processor array = 2 x 2 x 1
891s   Grid dimensions: 65 x 65 x 65
891s   Grid spacings: 0.112 x 0.112 x 0.188
891s   Grid lengths: 7.178 x 7.178 x 12.000
891s   Grid center: (2.411, -2.411, 0.000)
891s   Multigrid levels: 5
891s   Molecule ID: 1
891s   Linearized traditional PBE
891s   Boundary conditions from focusing
891s   0 ion species (0.000 M ionic strength):
891s   Solute dielectric: 1.000
891s   Solvent dielectric: 78.540
891s   Using "molecular" surface definition; no smoothing
891s   Solvent probe radius: 1.400 A
891s   Temperature:  298.150 K
891s   Electrostatic energies will be calculated
891s   Total electrostatic energy = 1.485246667424E+03 kJ/mol
891s   Calculating forces...
891s ----------------------------------------
891s CALCULATION #4 (reference): MULTIGRID
891s   Setting up problem...
891s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
891s   Debye length:  0 A
891s   Current memory usage:  61.189 MB total, 122.067 MB high water
891s   Using cubic spline charge discretization.
891s   Partition overlap fraction = 0.1
891s   Processor array = 2 x 2 x 1
891s   Grid dimensions: 65 x 65 x 65
891s   Grid spacings: 0.781 x 0.781 x 0.781
891s   Grid lengths: 50.000 x 50.000 x 50.000
891s   Grid center: (0.000, 0.000, 0.000)
891s   Multigrid levels: 5
891s   Molecule ID: 1
891s   Linearized traditional PBE
891s   Multiple Debye-Huckel sphere boundary conditions
891s   0 ion species (0.000 M ionic strength):
891s   Solute dielectric: 1.000
891s   Solvent dielectric: 1.000
891s   Using "molecular" surface definition; no smoothing
891s   Solvent probe radius: 1.400 A
891s   Temperature:  298.150 K
891s   Electrostatic energies will be calculated
891s   Total electrostatic energy = 2.977178707009E+02 kJ/mol
891s   Calculating forces...
891s ----------------------------------------
891s CALCULATION #5 (reference): MULTIGRID
891s   Setting up problem...
891s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
891s   Debye length:  0 A
891s   Current memory usage:  61.189 MB total, 122.067 MB high water
891s   Using cubic spline charge discretization.
891s   Partition overlap fraction = 0.1
891s   Processor array = 2 x 2 x 1
891s   Grid dimensions: 65 x 65 x 65
891s   Grid spacings: 0.296 x 0.296 x 0.383
891s   Grid lengths: 18.944 x 18.944 x 24.495
891s   Grid center: (2.411, -2.411, 0.000)
891s   Multigrid levels: 5
891s   Molecule ID: 1
891s   Linearized traditional PBE
891s   Boundary conditions from focusing
891s   0 ion species (0.000 M ionic strength):
891s   Solute dielectric: 1.000
891s   Solvent dielectric: 1.000
891s   Using "molecular" surface definition; no smoothing
891s   Solvent probe radius: 1.400 A
891s   Temperature:  298.150 K
891s   Electrostatic energies will be calculated
891s   Total electrostatic energy = 8.799304557588E+02 kJ/mol
891s   Calculating forces...
891s [focusFillBound()]: WARNING:
891s     Unusually large potential values
891s     detected on the focusing boundary!
891s     Convergence not guaranteed for NPBE/NRPBE calculations!
891s 
891s ----------------------------------------
891s CALCULATION #6 (reference): MULTIGRID
891s   Setting up problem...
891s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
891s   Debye length:  0 A
891s   Current memory usage:  61.189 MB total, 122.067 MB high water
891s   Using cubic spline charge discretization.
891s   Partition overlap fraction = 0.1
891s   Processor array = 2 x 2 x 1
891s   Grid dimensions: 65 x 65 x 65
891s   Grid spacings: 0.112 x 0.112 x 0.188
891s   Grid lengths: 7.178 x 7.178 x 12.000
891s   Grid center: (2.411, -2.411, 0.000)
891s   Multigrid levels: 5
891s   Molecule ID: 1
891s   Linearized traditional PBE
891s   Boundary conditions from focusing
891s   0 ion species (0.000 M ionic strength):
891s   Solute dielectric: 1.000
891s   Solvent dielectric: 1.000
891s   Using "molecular" surface definition; no smoothing
891s   Solvent probe radius: 1.400 A
891s   Temperature:  298.150 K
891s   Electrostatic energies will be calculated
891s   Total electrostatic energy = 1.542873949131E+03 kJ/mol
891s   Calculating forces...
891s ----------------------------------------
891s PRINT STATEMENTS
891s 
891s print energy 1 (solvated) - 2 (reference) end
891s   Local net energy (PE 0) = -5.762728170718E+01 kJ/mol
891s   Global net ELEC energy = -5.762728170718E+01 kJ/mol
891s ----------------------------------------
891s CLEANING UP AND SHUTTING DOWN...
891s Destroying force arrays.
891s No energy arrays to destroy.
891s Destroying multigrid structures.
891s Destroying finite element structures.
891s Destroying 1 molecules
891s Final memory usage:  0.001 MB total, 122.067 MB high water
891s 
891s 
891s Thanks for using APBS!
891s 
891s Processor 1 results:
891s   2.401768459022e+02
891s   8.142778312125e+02
891s   1.485246667424e+03
891s   2.977178707009e+02
891s   8.799304557588e+02
891s   1.542873949131e+03
891s   -5.762728170718e+01
891s 
920s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out
920s BINARY:  /usr/bin/apbs
920s INPUT:   apbs-mol-parallel-PE2.in
920s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in']
920s asc_getToken: Error occurred (bailing out).
920s Vio_scanf: Format problem with input.
920s 
920s 
920s ----------------------------------------------------------------------
920s     APBS -- Adaptive Poisson-Boltzmann Solver
920s     Version APBS 3.4.1
920s     
920s     Nathan A. Baker (nathan.baker@pnnl.gov)
920s     Pacific Northwest National Laboratory
920s     
920s     Additional contributing authors listed in the code documentation.
920s     
920s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
920s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
920s     Northwest Division for the U.S. Department of Energy.
920s     
920s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
920s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
920s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
920s     Portions Copyright (c) 1995, Michael Holst.
920s     All rights reserved.
920s     
920s     Redistribution and use in source and binary forms, with or without
920s     modification, are permitted provided that the following conditions are met:
920s     
920s     * Redistributions of source code must retain the above copyright notice, this
920s       list of conditions and the following disclaimer.
920s     
920s     * Redistributions in binary form must reproduce the above copyright notice,
920s       this list of conditions and the following disclaimer in the documentation
920s       and/or other materials provided with the distribution.
920s     
920s     * Neither the name of the developer nor the names of its contributors may be
920s       used to endorse or promote products derived from this software without
920s       specific prior written permission.
920s     
920s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
920s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
920s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
920s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
920s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
920s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
920s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
920s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
920s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
920s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
920s ----------------------------------------------------------------------
920s     APBS uses FETK (the Finite Element ToolKit) to solve the
920s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
920s     of finite element modeling class libraries developed by the Michael Holst
920s     research group and written in an object-oriented form of C.  FEtk is
920s     designed to solve general coupled systems of nonlinear partial differential
920s     equations using adaptive finite element methods, inexact Newton methods,
920s     and algebraic multilevel methods.  More information about FEtk may be found
920s     at <http://www.FEtk.ORG>.
920s ----------------------------------------------------------------------
920s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
920s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
920s     which has been modified by Patrice Koehl
920s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
920s     memory usage when solving the Poisson-Boltzmann equation.
920s ----------------------------------------------------------------------
920s     Please cite your use of APBS as:
920s 
920s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
920s     nanosystems: application to microtubules and the ribosome. Proc.
920s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
920s     
920s 
920s This executable compiled on Mar  2 2024 at 20:11:10
920s 
920s Parsing input file apbs-mol-parallel-PE2.in...
920s rank 0 size 1..Processor 2 results:
920s   2.401768459091e+02
920s   8.142935605696e+02
920s   1.485255306569e+03
920s .
920s Parsed input file.
920s Got paths for 1 molecules
920s Reading PQR-format atom data from ion.pqr.
920s   1 atoms
920s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
920s   Net charge 1.00e+00 e
920s Preparing to run 6 PBE calculations.
920s ----------------------------------------
920s CALCULATION #1 (solvated): MULTIGRID
920s   Setting up problem...
920s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
920s   Debye length:  0 A
920s   Current memory usage:  61.262 MB total, 61.262 MB high water
920s   Using cubic spline charge discretization.
920s   Partition overlap fraction = 0.1
920s   Processor array = 2 x 2 x 1
920s   Grid dimensions: 65 x 65 x 65
920s   Grid spacings: 0.781 x 0.781 x 0.781
920s   Grid lengths: 50.000 x 50.000 x 50.000
920s   Grid center: (0.000, 0.000, 0.000)
920s   Multigrid levels: 5
920s   Molecule ID: 1
920s   Linearized traditional PBE
920s   Multiple Debye-Huckel sphere boundary conditions
920s   0 ion species (0.000 M ionic strength):
920s   Solute dielectric: 1.000
920s   Solvent dielectric: 78.540
920s   Using "molecular" surface definition; no smoothing
920s   Solvent probe radius: 1.400 A
920s   Temperature:  298.150 K
920s   Electrostatic energies will be calculated
920s   Total electrostatic energy = 2.401768459091E+02 kJ/mol
920s   Calculating forces...
920s ----------------------------------------
920s CALCULATION #2 (solvated): MULTIGRID
920s   Setting up problem...
920s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
920s   Debye length:  0 A
920s   Current memory usage:  61.262 MB total, 122.067 MB high water
920s   Using cubic spline charge discretization.
920s   Partition overlap fraction = 0.1
920s   Processor array = 2 x 2 x 1
920s   Grid dimensions: 65 x 65 x 65
920s   Grid spacings: 0.296 x 0.296 x 0.383
920s   Grid lengths: 18.944 x 18.944 x 24.495
920s   Grid center: (-2.411, 2.411, 0.000)
920s   Multigrid levels: 5
920s   Molecule ID: 1
920s   Linearized traditional PBE
920s   Boundary conditions from focusing
920s   0 ion species (0.000 M ionic strength):
920s   Solute dielectric: 1.000
920s   Solvent dielectric: 78.540
920s   Using "molecular" surface definition; no smoothing
920s   Solvent probe radius: 1.400 A
920s   Temperature:  298.150 K
920s   Electrostatic energies will be calculated
920s   Total electrostatic energy = 8.142935605696E+02 kJ/mol
920s   Calculating forces...
920s [focusFillBound()]: WARNING:
920s     Unusually large potential values
920s     detected on the focusing boundary!
920s     Convergence not guaranteed for NPBE/NRPBE calculations!
920s 
920s ----------------------------------------
920s CALCULATION #3 (solvated): MULTIGRID
920s   Setting up problem...
920s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
920s   Debye length:  0 A
920s   Current memory usage:  61.262 MB total, 122.067 MB high water
920s   Using cubic spline charge discretization.
920s   Partition overlap fraction = 0.1
920s   Processor array = 2 x 2 x 1
920s   Grid dimensions: 65 x 65 x 65
920s   Grid spacings: 0.112 x 0.112 x 0.188
920s   Grid lengths: 7.178 x 7.178 x 12.000
920s   Grid center: (-2.411, 2.411, 0.000)
920s   Multigrid levels: 5
920s   Molecule ID: 1
920s   Linearized traditional PBE
920s   Boundary conditions from focusing
920s   0 ion species (0.000 M ionic strength):
920s   Solute dielectric: 1.000
920s   Solvent dielectric: 78.540
920s   Using "molecular" surface definition; no smoothing
920s   Solvent probe radius: 1.400 A
920s   Temperature:  298.150 K
920s   Electrostatic energies will be calculated
920s   Total electrostatic energy = 1.485255306569E+03 kJ/mol
920s   Calculating forces...
920s ----------------------------------------
920s CALCULATION #4 (reference): MULTIGRID
920s   Setting up problem...
920s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
920s   Debye length:  0 A
920s   Current memory usage:  61.189 MB total, 122.067 MB high water
920s   Using cubic spline charge discretization.
920s   Partition overlap fraction = 0.1
920s   Processor array = 2 x 2 x 1
920s   Grid dimensions: 65 x 65 x 65
920s   Grid spacings: 0.781 x 0.781 x 0.781
920s   Grid lengths: 50.000 x 50.000 x 50.000
920s   Grid center: (0.000, 0.000, 0.000)
920s   Multigrid levels: 5
920s   Molecule ID: 1
920s   Linearized traditional PBE
920s   Multiple Debye-Huckel sphere boundary conditions
920s   0 ion species (0.000 M ionic strength):
920s   Solute dielectric: 1.000
920s   Solvent dielectric: 1.000
920s   Using "molecular" surface definition; no smoothing
920s   Solvent probe radius: 1.400 A
920s   Temperature:  298.150 K
920s   Electrostatic energies will be calculated
920s   Total electrostatic energy = 2.977178707146E+02 kJ/mol
920s   Calculating forces...
920s ----------------------------------------
920s CALCULATION #5 (reference): MULTIGRID
920s   Setting up problem...
920s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
920s   Debye length:  0 A
920s   Current memory usage:  61.189 MB total, 122.067 MB high water
920s   Using cubic spline charge discretization.
920s   Partition overlap fraction = 0.1
920s   Processor array = 2 x 2 x 1
920s   Grid dimensions: 65 x 65 x 65
920s   Grid spacings: 0.296 x 0.296 x 0.383
920s   Grid lengths: 18.944 x 18.944 x 24.495
920s   Grid center: (-2.411, 2.411, 0.000)
920s   Multigrid levels: 5
920s   Molecule ID: 1
920s   Linearized traditional PBE
920s   Boundary conditions from focusing
920s   0 ion species (0.000 M ionic strength):
920s   Solute dielectric: 1.000
920s   Solvent dielectric: 1.000
920s   Using "molecular" surface definition; no smoothing
920s   Solvent probe radius: 1.400 A
920s   Temperature:  298.150 K
920s   Electrostatic energies will be calculated
920s   Total electrostatic energy = 8.799304557596E+02 kJ/mol
920s   Calculating forces...
920s [focusFillBound()]: WARNING:
920s     Unusually large potential values
920s     detected on the focusing boundary!
920s     Convergence not guaranteed for NPBE/NRPBE calculations!
920s 
920s ----------------------------------------
920s CALCULATION #6 (reference): MULTIGRID
920s   Setting up problem...
920s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
920s   Debye length:  0 A
920s   Current memory usage:  61.189 MB total, 122.067 MB high water
920s   Using cubic spline charge discretization.
920s   Partition overlap fraction = 0.1
920s   Processor array = 2 x 2 x 1
920s   Grid dimensions: 65 x 65 x 65
920s   Grid spacings: 0.112 x 0.112 x 0.188
920s   Grid lengths: 7.178 x 7.178 x 12.000
920s   Grid center: (-2.411, 2.411, 0.000)
920s   Multigrid levels: 5
920s   Molecule ID: 1
920s   Linearized traditional PBE
920s   Boundary conditions from focusing
920s   0 ion species (0.000 M ionic strength):
920s   Solute dielectric: 1.000
920s   Solvent dielectric: 1.000
920s   Using "molecular" surface definition; no smoothing
920s   Solvent probe radius: 1.400 A
920s   Temperature:  298.150 K
920s   Electrostatic energies will be calculated
920s   Total electrostatic energy = 1.542873949141E+03 kJ/mol
920s   Calculating forces...
920s ----------------------------------------
920s PRINT STATEMENTS
920s 
920s print energy 1 (solvated) - 2 (reference) end
920s   Local net energy (PE 0) = -5.761864257239E+01 kJ/mol
920s   Global net ELEC energy = -5.761864257239E+01 kJ/mol
920s ----------------------------------------
920s CLEANING UP AND SHUTTING DOWN...
920s Destroying force arrays.
920s No energy arrays to destroy.
920s Destroying multigrid structures.
920s Destroying finite element structures.
920s Destroying 1 molecules
920s Final memory usage:  0.001 MB total, 122.067 MB high water
920s 
920s 
920s Thanks for using APBS!
920s 
920s   2.977178707146e+02
920s   8.799304557596e+02
920s   1.542873949141e+03
920s   -5.761864257239e+01
920s 
948s Processor 3 results:
948s   2.401768459091e+02
948s   8.142778325440e+02
948s   1.485246665692e+03
948s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out
948s BINARY:  /usr/bin/apbs
948s INPUT:   apbs-mol-parallel-PE3.in
948s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in']
948s asc_getToken: Error occurred (bailing out).
948s Vio_scanf: Format problem with input.
948s 
948s 
948s ----------------------------------------------------------------------
948s     APBS -- Adaptive Poisson-Boltzmann Solver
948s     Version APBS 3.4.1
948s     
948s     Nathan A. Baker (nathan.baker@pnnl.gov)
948s     Pacific Northwest National Laboratory
948s     
948s     Additional contributing authors listed in the code documentation.
948s     
948s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
948s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
948s     Northwest Division for the U.S. Department of Energy.
948s     
948s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
948s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
948s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
948s     Portions Copyright (c) 1995, Michael Holst.
948s     All rights reserved.
948s     
948s     Redistribution and use in source and binary forms, with or without
948s     modification, are permitted provided that the following conditions are met:
948s     
948s     * Redistributions of source code must retain the above copyright notice, this
948s       list of conditions and the following disclaimer.
948s     
948s     * Redistributions in binary form must reproduce the above copyright notice,
948s       this list of conditions and the following disclaimer in the documentation
948s       and/or other materials provided with the distribution.
948s     
948s     * Neither the name of the developer nor the names of its contributors may be
948s       used to endorse or promote products derived from this software without
948s       specific prior written permission.
948s     
948s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
948s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
948s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
948s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
948s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
948s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
948s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
948s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
948s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
948s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
948s ----------------------------------------------------------------------
948s     APBS uses FETK (the Finite Element ToolKit) to solve the
948s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
948s     of finite element modeling class libraries developed by the Michael Holst
948s     research group and written in an object-oriented form of C.  FEtk is
948s     designed to solve general coupled systems of nonlinear partial differential
948s     equations using adaptive finite element methods, inexact Newton methods,
948s     and algebraic multilevel methods.  More information about FEtk may be found
948s     at <http://www.FEtk.ORG>.
948s ----------------------------------------------------------------------
948s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
948s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
948s     which has been modified by Patrice Koehl
948s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
948s     memory usage when solving the Poisson-Boltzmann equation.
948s ----------------------------------------------------------------------
948s     Please cite your use of APBS as:
948s 
948s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
948s     nanosystems: application to microtubules and the ribosome. Proc.
948s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
948s     
948s 
948s This executable compiled on Mar  2 2024 at 20:11:10
948s 
948s Parsing input file apbs-mol-parallel-PE3.in...
948s rank 0 size 1...
948s Parsed input file.
948s Got paths for 1 molecules
948s Reading PQR-format atom data from ion.pqr.
948s   1 atoms
948s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
948s   Net charge 1.00e+00 e
948s Preparing to run 6 PBE calculations.
948s ----------------------------------------
948s CALCULATION #1 (solvated): MULTIGRID
948s   Setting up problem...
948s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
948s   Debye length:  0 A
948s   Current memory usage:  61.262 MB total, 61.262 MB high water
948s   Using cubic spline charge discretization.
948s   Partition overlap fraction = 0.1
948s   Processor array = 2 x 2 x 1
948s   Grid dimensions: 65 x 65 x 65
948s   Grid spacings: 0.781 x 0.781 x 0.781
948s   Grid lengths: 50.000 x 50.000 x 50.000
948s   Grid center: (0.000, 0.000, 0.000)
948s   Multigrid levels: 5
948s   Molecule ID: 1
948s   Linearized traditional PBE
948s   Multiple Debye-Huckel sphere boundary conditions
948s   0 ion species (0.000 M ionic strength):
948s   Solute dielectric: 1.000
948s   Solvent dielectric: 78.540
948s   Using "molecular" surface definition; no smoothing
948s   Solvent probe radius: 1.400 A
948s   Temperature:  298.150 K
948s   Electrostatic energies will be calculated
948s   Total electrostatic energy = 2.401768459091E+02 kJ/mol
948s   Calculating forces...
948s ----------------------------------------
948s CALCULATION #2 (solvated): MULTIGRID
948s   Setting up problem...
948s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
948s   Debye length:  0 A
948s   Current memory usage:  61.262 MB total, 122.067 MB high water
948s   Using cubic spline charge discretization.
948s   Partition overlap fraction = 0.1
948s   Processor array = 2 x 2 x 1
948s   Grid dimensions: 65 x 65 x 65
948s   Grid spacings: 0.296 x 0.296 x 0.383
948s   Grid lengths: 18.944 x 18.944 x 24.495
948s   Grid center: (2.411, 2.411, 0.000)
948s   Multigrid levels: 5
948s   Molecule ID: 1
948s   Linearized traditional PBE
948s   Boundary conditions from focusing
948s   0 ion species (0.000 M ionic strength):
948s   Solute dielectric: 1.000
948s   Solvent dielectric: 78.540
948s   Using "molecular" surface definition; no smoothing
948s   Solvent probe radius: 1.400 A
948s   Temperature:  298.150 K
948s   Electrostatic energies will be calculated
948s   Total electrostatic energy = 8.142778325440E+02 kJ/mol
948s   Calculating forces...
948s [focusFillBound()]: WARNING:
948s     Unusually large potential values
948s     detected on the focusing boundary!
948s     Convergence not guaranteed for NPBE/NRPBE calculations!
948s 
948s ----------------------------------------
948s CALCULATION #3 (solvated): MULTIGRID
948s   Setting up problem...
948s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
948s   Debye length:  0 A
948s   Current memory usage:  61.262 MB total, 122.067 MB high water
948s   Using cubic spline charge discretization.
948s   Partition overlap fraction = 0.1
948s   Processor array = 2 x 2 x 1
948s   Grid dimensions: 65 x 65 x 65
948s   Grid spacings: 0.112 x 0.112 x 0.188
948s   Grid lengths: 7.178 x 7.178 x 12.000
948s   Grid center: (2.411, 2.411, 0.000)
948s   Multigrid levels: 5
948s   Molecule ID: 1
948s   Linearized traditional PBE
948s   Boundary conditions from focusing
948s   0 ion species (0.000 M ionic strength):
948s   Solute dielectric: 1.000
948s   Solvent dielectric: 78.540
948s   Using "molecular" surface definition; no smoothing
948s   Solvent probe radius: 1.400 A
948s   Temperature:  298.150 K
948s   Electrostatic energies will be calculated
948s   Total electrostatic energy = 1.485246665692E+03 kJ/mol
948s   Calculating forces...
948s ----------------------------------------
948s CALCULATION #4 (reference): MULTIGRID
948s   Setting up problem...
948s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
948s   Debye length:  0 A
948s   Current memory usage:  61.189 MB total, 122.067 MB high water
948s   Using cubic spline charge discretization.
948s   Partition overlap fraction = 0.1
948s   Processor array = 2 x 2 x 1
948s   Grid dimensions: 65 x 65 x 65
948s   Grid spacings: 0.781 x 0.781 x 0.781
948s   Grid lengths: 50.000 x 50.000 x 50.000
948s   Grid center: (0.000, 0.000, 0.000)
948s   Multigrid levels: 5
948s   Molecule ID: 1
948s   Linearized traditional PBE
948s   Multiple Debye-Huckel sphere boundary conditions
948s   0 ion species (0.000 M ionic strength):
948s   Solute dielectric: 1.000
948s   Solvent dielectric: 1.000
948s   Using "molecular" surface definition; no smoothing
948s   Solvent probe radius: 1.400 A
948s   Temperature:  298.150 K
948s   Electrostatic energies will be calculated
948s   Total electrostatic energy = 2.977178707146E+02 kJ/mol
948s   Calculating forces...
948s ----------------------------------------
948s CALCULATION #5 (reference): MULTIGRID
948s   Setting up problem...
948s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
948s   Debye length:  0 A
948s   Current memory usage:  61.189 MB total, 122.067 MB high water
948s   Using cubic spline charge discretization.
948s   Partition overlap fraction = 0.1
948s   Processor array = 2 x 2 x 1
948s   Grid dimensions: 65 x 65 x 65
948s   Grid spacings: 0.296 x 0.296 x 0.383
948s   Grid lengths: 18.944 x 18.944 x 24.495
948s   Grid center: (2.411, 2.411, 0.000)
948s   Multigrid levels: 5
948s   Molecule ID: 1
948s   Linearized traditional PBE
948s   Boundary conditions from focusing
948s   0 ion species (0.000 M ionic strength):
948s   Solute dielectric: 1.000
948s   Solvent dielectric: 1.000
948s   Using "molecular" surface definition; no smoothing
948s   Solvent probe radius: 1.400 A
948s   Temperature:  298.150 K
948s   Electrostatic energies will be calculated
948s   Total electrostatic energy = 8.799304557596E+02 kJ/mol
948s   Calculating forces...
948s [focusFillBound()]: WARNING:
948s     Unusually large potential values
948s     detected on the focusing boundary!
948s     Convergence not guaranteed for NPBE/NRPBE calculations!
948s 
948s ----------------------------------------
948s CALCULATION #6 (reference): MULTIGRID
948s   Setting up problem...
948s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
948s   Debye length:  0 A
948s   Current memory usage:  61.189 MB total, 122.067 MB high water
948s   Using cubic spline charge discretization.
948s   Partition overlap fraction = 0.1
948s   Processor array = 2 x 2 x 1
948s   Grid dimensions: 65 x 65 x 65
948s   Grid spacings: 0.112 x 0.112 x 0.188
948s   Grid lengths: 7.178 x 7.178 x 12.000
948s   Grid center: (2.411, 2.411, 0.000)
948s   Multigrid levels: 5
948s   Molecule ID: 1
948s   Linearized traditional PBE
948s   Boundary conditions from focusing
948s   0 ion species (0.000 M ionic strength):
948s   Solute dielectric: 1.000
948s   Solvent dielectric: 1.000
948s   Using "molecular" surface definition; no smoothing
948s   Solvent probe radius: 1.400 A
948s   Temperature:  298.150 K
948s   Electrostatic energies will be calculated
948s   Total electrostatic energy = 1.542873949141E+03 kJ/mol
948s   Calculating forces...
948s ----------------------------------------
948s PRINT STATEMENTS
948s 
948s print energy 1 (solvated) - 2 (reference) end
948s   Local net energy (PE 0) = -5.762728344954E+01 kJ/mol
948s   Global net ELEC energy = -5.762728344954E+01 kJ/mol
948s ----------------------------------------
948s CLEANING UP AND SHUTTING DOWN...
948s Destroying force arrays.
948s No energy arrays to destroy.
948s Destroying multigrid structures.
948s Destroying finite element structures.
948s Destroying 1 molecules
948s Final memory usage:  0.001 MB total, 122.067 MB high water
948s 
948s 
948s Thanks for using APBS!
948s 
948s   2.977178707146e+02
948s   8.799304557596e+02
948s   1.542873949141e+03
948s   -5.762728344954e+01
948s 
948s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02)
948s *** PASSED ***
948s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03)
948s *** PASSED ***
948s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03)
948s *** PASSED ***
948s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
948s *** PASSED ***
948s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03)
948s *** PASSED ***
948s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03)
948s *** PASSED ***
948s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02)
948s *** PASSED ***
948s Elapsed time: 116.264036 seconds
948s --------------------------------------------------------------------------------
948s --------------------------------------------------------------------------------
948s Testing input file apbs-smol-parallel.in
948s 
948s Splitting the input file into 4 separate files using the inputgen utility
948s 
976s Processor 0 results:
976s   2.383232191816e+02
976s   8.145369591602e+02
976s   1.485524998001e+03
976s   2.977178707009e+02
976s   8.799304557588e+02
976s   1.542873949131e+03
976s   -5.734895113069e+01
976s 
976s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out
976s EXPECTED COMPUTED: 7
976s EXPECTED EXPECTED: 7
976s COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003]
976s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02']
976s COMPUTED RESULT 960.7073836226
976s COMPUTED RESULT 3257.1427835731997
976s COMPUTED RESULT 5941.0039478710005
976s COMPUTED RESULT 1190.8714828309999
976s COMPUTED RESULT 3519.7218230368003
976s COMPUTED RESULT 6171.495796544
976s COMPUTED RESULT -230.49184867463003
976s BINARY:  /usr/bin/apbs
976s INPUT:   apbs-smol-parallel-PE0.in
976s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in']
976s asc_getToken: Error occurred (bailing out).
976s Vio_scanf: Format problem with input.
976s 
976s 
976s ----------------------------------------------------------------------
976s     APBS -- Adaptive Poisson-Boltzmann Solver
976s     Version APBS 3.4.1
976s     
976s     Nathan A. Baker (nathan.baker@pnnl.gov)
976s     Pacific Northwest National Laboratory
976s     
976s     Additional contributing authors listed in the code documentation.
976s     
976s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
976s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
976s     Northwest Division for the U.S. Department of Energy.
976s     
976s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
976s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
976s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
976s     Portions Copyright (c) 1995, Michael Holst.
976s     All rights reserved.
976s     
976s     Redistribution and use in source and binary forms, with or without
976s     modification, are permitted provided that the following conditions are met:
976s     
976s     * Redistributions of source code must retain the above copyright notice, this
976s       list of conditions and the following disclaimer.
976s     
976s     * Redistributions in binary form must reproduce the above copyright notice,
976s       this list of conditions and the following disclaimer in the documentation
976s       and/or other materials provided with the distribution.
976s     
976s     * Neither the name of the developer nor the names of its contributors may be
976s       used to endorse or promote products derived from this software without
976s       specific prior written permission.
976s     
976s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
976s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
976s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
976s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
976s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
976s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
976s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
976s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
976s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
976s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
976s ----------------------------------------------------------------------
976s     APBS uses FETK (the Finite Element ToolKit) to solve the
976s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
976s     of finite element modeling class libraries developed by the Michael Holst
976s     research group and written in an object-oriented form of C.  FEtk is
976s     designed to solve general coupled systems of nonlinear partial differential
976s     equations using adaptive finite element methods, inexact Newton methods,
976s     and algebraic multilevel methods.  More information about FEtk may be found
976s     at <http://www.FEtk.ORG>.
976s ----------------------------------------------------------------------
976s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
976s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
976s     which has been modified by Patrice Koehl
976s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
976s     memory usage when solving the Poisson-Boltzmann equation.
976s ----------------------------------------------------------------------
976s     Please cite your use of APBS as:
976s 
976s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
976s     nanosystems: application to microtubules and the ribosome. Proc.
976s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
976s     
976s 
976s This executable compiled on Mar  2 2024 at 20:11:10
976s 
976s Parsing input file apbs-smol-parallel-PE0.in...
976s rank 0 size 1...
976s Parsed input file.
976s Got paths for 1 molecules
976s Reading PQR-format atom data from ion.pqr.
976s   1 atoms
976s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
976s   Net charge 1.00e+00 e
976s Preparing to run 6 PBE calculations.
976s ----------------------------------------
976s CALCULATION #1 (solvated): MULTIGRID
976s   Setting up problem...
976s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
976s   Debye length:  0 A
976s   Current memory usage:  61.262 MB total, 61.262 MB high water
976s   Using cubic spline charge discretization.
976s   Partition overlap fraction = 0.1
976s   Processor array = 2 x 2 x 1
976s   Grid dimensions: 65 x 65 x 65
976s   Grid spacings: 0.781 x 0.781 x 0.781
976s   Grid lengths: 50.000 x 50.000 x 50.000
976s   Grid center: (0.000, 0.000, 0.000)
976s   Multigrid levels: 5
976s   Molecule ID: 1
976s   Linearized traditional PBE
976s   Multiple Debye-Huckel sphere boundary conditions
976s   0 ion species (0.000 M ionic strength):
976s   Solute dielectric: 1.000
976s   Solvent dielectric: 78.540
976s   Using "molecular" surface definition;harmonic average smoothing
976s   Solvent probe radius: 1.400 A
976s   Temperature:  298.150 K
976s   Electrostatic energies will be calculated
976s   Total electrostatic energy = 2.383232191816E+02 kJ/mol
976s   Calculating forces...
976s ----------------------------------------
976s CALCULATION #2 (solvated): MULTIGRID
976s   Setting up problem...
976s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
976s   Debye length:  0 A
976s   Current memory usage:  61.262 MB total, 122.067 MB high water
976s   Using cubic spline charge discretization.
976s   Partition overlap fraction = 0.1
976s   Processor array = 2 x 2 x 1
976s   Grid dimensions: 65 x 65 x 65
976s   Grid spacings: 0.296 x 0.296 x 0.383
976s   Grid lengths: 18.944 x 18.944 x 24.495
976s   Grid center: (-2.411, -2.411, 0.000)
976s   Multigrid levels: 5
976s   Molecule ID: 1
976s   Linearized traditional PBE
976s   Boundary conditions from focusing
976s   0 ion species (0.000 M ionic strength):
976s   Solute dielectric: 1.000
976s   Solvent dielectric: 78.540
976s   Using "molecular" surface definition;harmonic average smoothing
976s   Solvent probe radius: 1.400 A
976s   Temperature:  298.150 K
976s   Electrostatic energies will be calculated
976s   Total electrostatic energy = 8.145369591602E+02 kJ/mol
976s   Calculating forces...
976s [focusFillBound()]: WARNING:
976s     Unusually large potential values
976s     detected on the focusing boundary!
976s     Convergence not guaranteed for NPBE/NRPBE calculations!
976s 
976s ----------------------------------------
976s CALCULATION #3 (solvated): MULTIGRID
976s   Setting up problem...
976s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
976s   Debye length:  0 A
976s   Current memory usage:  61.262 MB total, 122.067 MB high water
976s   Using cubic spline charge discretization.
976s   Partition overlap fraction = 0.1
976s   Processor array = 2 x 2 x 1
976s   Grid dimensions: 65 x 65 x 65
976s   Grid spacings: 0.112 x 0.112 x 0.188
976s   Grid lengths: 7.178 x 7.178 x 12.000
976s   Grid center: (-2.411, -2.411, 0.000)
976s   Multigrid levels: 5
976s   Molecule ID: 1
976s   Linearized traditional PBE
976s   Boundary conditions from focusing
976s   0 ion species (0.000 M ionic strength):
976s   Solute dielectric: 1.000
976s   Solvent dielectric: 78.540
976s   Using "molecular" surface definition;harmonic average smoothing
976s   Solvent probe radius: 1.400 A
976s   Temperature:  298.150 K
976s   Electrostatic energies will be calculated
976s   Total electrostatic energy = 1.485524998001E+03 kJ/mol
976s   Calculating forces...
976s ----------------------------------------
976s CALCULATION #4 (reference): MULTIGRID
976s   Setting up problem...
976s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
976s   Debye length:  0 A
976s   Current memory usage:  61.189 MB total, 122.067 MB high water
976s   Using cubic spline charge discretization.
976s   Partition overlap fraction = 0.1
976s   Processor array = 2 x 2 x 1
976s   Grid dimensions: 65 x 65 x 65
976s   Grid spacings: 0.781 x 0.781 x 0.781
976s   Grid lengths: 50.000 x 50.000 x 50.000
976s   Grid center: (0.000, 0.000, 0.000)
976s   Multigrid levels: 5
976s   Molecule ID: 1
976s   Linearized traditional PBE
976s   Multiple Debye-Huckel sphere boundary conditions
976s   0 ion species (0.000 M ionic strength):
976s   Solute dielectric: 1.000
976s   Solvent dielectric: 1.000
976s   Using "molecular" surface definition;harmonic average smoothing
976s   Solvent probe radius: 1.400 A
976s   Temperature:  298.150 K
976s   Electrostatic energies will be calculated
976s   Total electrostatic energy = 2.977178707009E+02 kJ/mol
976s   Calculating forces...
976s ----------------------------------------
976s CALCULATION #5 (reference): MULTIGRID
976s   Setting up problem...
976s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
976s   Debye length:  0 A
976s   Current memory usage:  61.189 MB total, 122.067 MB high water
976s   Using cubic spline charge discretization.
976s   Partition overlap fraction = 0.1
976s   Processor array = 2 x 2 x 1
976s   Grid dimensions: 65 x 65 x 65
976s   Grid spacings: 0.296 x 0.296 x 0.383
976s   Grid lengths: 18.944 x 18.944 x 24.495
976s   Grid center: (-2.411, -2.411, 0.000)
976s   Multigrid levels: 5
976s   Molecule ID: 1
976s   Linearized traditional PBE
976s   Boundary conditions from focusing
976s   0 ion species (0.000 M ionic strength):
976s   Solute dielectric: 1.000
976s   Solvent dielectric: 1.000
976s   Using "molecular" surface definition;harmonic average smoothing
976s   Solvent probe radius: 1.400 A
976s   Temperature:  298.150 K
976s   Electrostatic energies will be calculated
976s   Total electrostatic energy = 8.799304557588E+02 kJ/mol
976s   Calculating forces...
976s [focusFillBound()]: WARNING:
976s     Unusually large potential values
976s     detected on the focusing boundary!
976s     Convergence not guaranteed for NPBE/NRPBE calculations!
976s 
976s ----------------------------------------
976s CALCULATION #6 (reference): MULTIGRID
976s   Setting up problem...
976s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
976s   Debye length:  0 A
976s   Current memory usage:  61.189 MB total, 122.067 MB high water
976s   Using cubic spline charge discretization.
976s   Partition overlap fraction = 0.1
976s   Processor array = 2 x 2 x 1
976s   Grid dimensions: 65 x 65 x 65
976s   Grid spacings: 0.112 x 0.112 x 0.188
976s   Grid lengths: 7.178 x 7.178 x 12.000
976s   Grid center: (-2.411, -2.411, 0.000)
976s   Multigrid levels: 5
976s   Molecule ID: 1
976s   Linearized traditional PBE
976s   Boundary conditions from focusing
976s   0 ion species (0.000 M ionic strength):
976s   Solute dielectric: 1.000
976s   Solvent dielectric: 1.000
976s   Using "molecular" surface definition;harmonic average smoothing
976s   Solvent probe radius: 1.400 A
976s   Temperature:  298.150 K
976s   Electrostatic energies will be calculated
976s   Total electrostatic energy = 1.542873949131E+03 kJ/mol
976s   Calculating forces...
976s ----------------------------------------
976s PRINT STATEMENTS
976s 
976s print energy 1 (solvated) - 2 (reference) end
976s   Local net energy (PE 0) = -5.734895113069E+01 kJ/mol
976s   Global net ELEC energy = -5.734895113069E+01 kJ/mol
976s ----------------------------------------
976s CLEANING UP AND SHUTTING DOWN...
976s Destroying force arrays.
976s No energy arrays to destroy.
976s Destroying multigrid structures.
976s Destroying finite element structures.
976s Destroying 1 molecules
976s Final memory usage:  0.001 MB total, 122.067 MB high water
976s 
976s 
976s Thanks for using APBS!
976s 
1002s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out
1002s BINARY:  /usr/bin/apbs
1002s INPUT:   apbs-smol-parallel-PE1.in
1002s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in']
1002s asc_getToken: Error occurred (bailing out).
1002s Vio_scanf: Format problem with input.
1002s 
1002s 
1002s ----------------------------------------------------------------------
1002s     APBS -- Adaptive Poisson-Boltzmann Solver
1002s     Version APBS 3.4.1
1002s     
1002s     Nathan A. Baker (nathan.baker@pnnl.gov)
1002s     Pacific Northwest National Laboratory
1002s     
1002s     Additional contributing authors listed in the code documentation.
1002s     
1002s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1002s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1002s     Northwest Division for the U.S. Department of Energy.
1002s     
1002s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1002s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1002s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1002s     Portions Copyright (c) 1995, Michael Holst.
1002s     All rights reserved.
1002s     
1002s     Redistribution and use in source and binary forms, with or without
1002s     modification, are permitted provided that the following conditions are met:
1002s     
1002s     * Redistributions of source code must retain the above copyright notice, this
1002s       list of conditions and the following disclaimer.
1002s     
1002s     * Redistributions in binary form must reproduce the above copyright notice,
1002s       this list of conditions and the following disclaimer in the documentation
1002s       and/or other materials provided with the distribution.
1002s     
1002s     * Neither the name of the developer nor the names of its contributors may be
1002s       used to endorse or promote products derived from this software without
1002s       specific prior written permission.
1002s     
1002s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1002s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1002s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1002s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1002s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1002s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1002s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1002s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1002s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1002s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1002s ----------------------------------------------------------------------
1002s     APBS uses FETK (the Finite Element ToolKit) to solve the
1002s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1002s     of finite element modeling class libraries developed by the Michael Holst
1002s     research group and written in an object-oriented form of C.  FEtk is
1002s     designed to solve general coupled systems of nonlinear partial differential
1002s     equations using adaptive finite element methods, inexact Newton methods,
1002s     and algebraic multilevel methods.  More information about FEtk may be found
1002s     at <http://www.FEtk.ORG>.
1002s ----------------------------------------------------------------------
1002s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1002s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1002s     which has been modified by Patrice Koehl
1002s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1002s     memory usage when solving the Poisson-Boltzmann equation.
1002s ----------------------------------------------------------------------
1002s     Please cite your use of APBS as:
1002s 
1002s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1002s     nanosystems: application to microtubules and the ribosome. Proc.
1002s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1002s     
1002s 
1002s This executable compiled on Mar  2 2024 at 20:11:10
1002s 
1002s Parsing input file apbs-smol-parallel-PE1.in...
1002s rank 0 size 1...
1002s Parsed input file.
1002s Got paths for 1 molecules
1002s Reading PQR-format atom data from ion.pqr.
1002s   1 atoms
1002s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
1002s   Net charge 1.00e+00 e
1002s Preparing to run 6 PBE calculations.
1002s ----------------------------------------
1002s CALCULATION #1 (solvated): MULTIGRID
1002s   Setting up problem...
1002s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1002s   Debye length:  0 A
1002s   Current memory usage:  61.262 MB total, 61.262 MB high water
1002s   Using cubic spline charge discretization.
1002s   Partition overlap fraction = 0.1
1002s   Processor array = 2 x 2 x 1
1002s   Grid dimensions: 65 x 65 x 65
1002s   Grid spacings: 0.781 x 0.781 x 0.781
1002s   Grid lengths: 50.000 x 50.000 x 50.000
1002s   Grid center: (0.000, 0.000, 0.000)
1002s   Multigrid levels: 5
1002s   Molecule ID: 1
1002s   Linearized traditional PBE
1002s   Multiple Debye-Huckel sphere boundary conditions
1002s   0 ion species (0.000 M ionic strength):
1002s   Solute dielectric: 1.000
1002s   Solvent dielectric: 78.540
1002s   Using "molecular" surface definition;harmonic average smoothing
1002s   Solvent probe radius: 1.400 A
1002s   Temperature:  298.150 K
1002s   Electrostatic energies will be calculated
1002s   Total electrostatic energy = 2.383232191816E+02 kJ/mol
1002s   Calculating forces...
1002s ----------------------------------------
1002s CALCULATION #2 (solvated): MULTIGRID
1002s   Setting up problem...
1002s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1002s   Debye length:  0 A
1002s   Current memory usage:  61.262 MB total, 122.067 MB high water
1002s   Using cubic spline charge discretization.
1002s   Partition overlap fraction = 0.1
1002s   Processor array = 2 x 2 x 1
1002s   Grid dimensions: 65 x 65 x 65
1002s   Grid spacings: 0.296 x 0.296 x 0.383
1002s   Grid lengths: 18.944 x 18.944 x 24.495
1002s   Grid center: (2.411, -2.411, 0.000)
1002s   Multigrid levels: 5
1002s   Molecule ID: 1
1002s   Linearized traditional PBE
1002s   Boundary conditions from focusing
1002s   0 ion species (0.000 M ionic strength):
1002s   Solute dielectric: 1.000
1002s   Solvent dielectric: 78.540
1002s   Using "molecular" surface definition;harmonic average smoothing
1002s   Solvent probe radius: 1.400 A
1002s   Temperature:  298.150 K
1002s   Electrostatic energies will be calculated
1002s   Total electrostatic energy = 8.145419898332E+02 kJ/mol
1002s   Calculating forces...
1002s [focusFillBound()]: WARNING:
1002s     Unusually large potential values
1002s     detected on the focusing boundary!
1002s     Convergence not guaranteed for NPBE/NRPBE calculations!
1002s 
1002s ----------------------------------------
1002s CALCULATION #3 (solvated): MULTIGRID
1002s   Setting up problem...
1002s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1002s   Debye length:  0 A
1002s   Current memory usage:  61.262 MB total, 122.067 MB high water
1002s   Using cubic spline charge discretization.
1002s   Partition overlap fraction = 0.1
1002s   Processor array = 2 x 2 x 1
1002s   Grid dimensions: 65 x 65 x 65
1002s   Grid spacings: 0.112 x 0.112 x 0.188
1002s   Grid lengths: 7.178 x 7.178 x 12.000
1002s   Grid center: (2.411, -2.411, 0.000)
1002s   Multigrid levels: 5
1002s   Molecule ID: 1
1002s   Linearized traditional PBE
1002s   Boundary conditions from focusing
1002s   0 ion species (0.000 M ionic strength):
1002s   Solute dielectric: 1.000
1002s   Solvent dielectric: 78.540
1002s   Using "molecular" surface definition;harmonic average smoothing
1002s   Solvent probe radius: 1.400 A
1002s   Temperature:  298.150 K
1002s   Electrostatic energies will be calculated
1002s   Total electrostatic energy = 1.485529328612E+03 kJ/mol
1002s   Calculating forces...
1002s ----------------------------------------
1002s CALCULATION #4 (reference): MULTIGRID
1002s   Setting up problem...
1002s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1002s   Debye length:  0 A
1002s   Current memory usage:  61.189 MB total, 122.067 MB high water
1002s   Using cubic spline charge discretization.
1002s   Partition overlap fraction = 0.1
1002s   Processor array = 2 x 2 x 1
1002s   Grid dimensions: 65 x 65 x 65
1002s   Grid spacings: 0.781 x 0.781 x 0.781
1002s   Grid lengths: 50.000 x 50.000 x 50.000
1002s   Grid center: (0.000, 0.000, 0.000)
1002s   Multigrid levels: 5
1002s   Molecule ID: 1
1002s   Linearized traditional PBE
1002s   Multiple Debye-Huckel sphere boundary conditions
1002s   0 ion species (0.000 M ionic strength):
1002s   Solute dielectric: 1.000
1002s   Solvent dielectric: 1.000
1002s   Using "molecular" surface definition;harmonic average smoothing
1002s   Solvent probe radius: 1.400 A
1002s   Temperature:  298.150 K
1002s   Electrostatic energies will be calculated
1002s   Total electrostatic energy = 2.977178707009E+02 kJ/mol
1002s   Calculating forces...
1002s ----------------------------------------
1002s CALCULATION #5 (reference): MULTIGRID
1002s   Setting up problem...
1002s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1002s   Debye length:  0 A
1002s   Current memory usage:  61.189 MB total, 122.067 MB high water
1002s   Using cubic spline charge discretization.
1002s   Partition overlap fraction = 0.1
1002s   Processor array = 2 x 2 x 1
1002s   Grid dimensions: 65 x 65 x 65
1002s   Grid spacings: 0.296 x 0.296 x 0.383
1002s   Grid lengths: 18.944 x 18.944 x 24.495
1002s   Grid center: (2.411, -2.411, 0.000)
1002s   Multigrid levels: 5
1002s   Molecule ID: 1
1002s   Linearized traditional PBE
1002s   Boundary conditions from focusing
1002s   0 ion species (0.000 M ionic strength):
1002s   Solute dielectric: 1.000
1002s   Solvent dielectric: 1.000
1002s   Using "molecular" surface definition;harmonic average smoothing
1002s   Solvent probe radius: 1.400 A
1002s   Temperature:  298.150 K
1002s   Electrostatic energies will be calculated
1002s   Total electrostatic energy = 8.799304557588E+02 kJ/mol
1002s   Calculating forces...
1002s [focusFillBound()]: WARNING:
1002s     Unusually large potential values
1002s     detected on the focusing boundary!
1002s     Convergence not guaranteed for NPBE/NRPBE calculations!
1002s 
1002s ----------------------------------------
1002s CALCULATION #6 (reference): MULTIGRID
1002s   Setting up problem...
1002s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1002s   Debye length:  0 A
1002s   Current memory usage:  61.189 MB total, 122.067 MB high water
1002s   Using cubic spline charge discretization.
1002s   Partition overlap fraction = 0.1
1002s   Processor array = 2 x 2 x 1
1002s   Grid dimensions: 65 x 65 x 65
1002s   Grid spacings: 0.112 x 0.112 x 0.188
1002s   Grid lengths: 7.178 x 7.178 x 12.000
1002s   Grid center: (2.411, -2.411, 0.000)
1002s   Multigrid levels: 5
1002s   Molecule ID: 1
1002s   Linearized traditional PBE
1002s   Boundary conditions from focusing
1002s   0 ion species (0.000 M ionic strength):
1002s   Solute dielectric: 1.000
1002s   Solvent dielectric: 1.000
1002s   Using "molecular" surface definition;harmonic average smoothing
1002s   Solvent probe radius: 1.400 A
1002s   Temperature:  298.150 K
1002s   Electrostatic energies will be calculated
1002s   Total electrostatic energy = 1.542873949131E+03 kJ/mol
1002s   Calculating forces...
1002s ----------------------------------------
1002s PRINT STATEMENTS
1002s 
1002s print energy 1 (solvated) - 2 (reference) end
1002s   Local net energy (PE 0) = -5.734462051928E+01 kJ/mol
1002s   Global net ELEC energy = -5.734462051928E+01 kJ/mol
1002s ----------------------------------------
1002s CLEANING UP AND SHUTTING DOWN...
1002s Destroying force arrays.
1002s No energy arrays to destroy.
1002s Destroying multigrid structures.
1002s Destroying finite element structures.
1002s Destroying 1 molecules
1002s Final memory usage:  0.001 MB total, 122.067 MB high water
1002s 
1002s 
1002s Thanks for using APBS!
1002s 
1002s Processor 1 results:
1002s   2.383232191816e+02
1002s   8.145419898332e+02
1002s   1.485529328612e+03
1002s   2.977178707009e+02
1002s   8.799304557588e+02
1002s   1.542873949131e+03
1002s   -5.734462051928e+01
1002s 
1025s Processor 2 results:
1025s   2.383232191909e+02
1025s   8.145369593489e+02
1025s   1.485524997676e+03
1025s   2.977178707146e+02
1025s   8.799304557596e+02
1025s   1.542873949141e+03
1025s   -5.734895146550e+01
1025s 
1025s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out
1025s BINARY:  /usr/bin/apbs
1025s INPUT:   apbs-smol-parallel-PE2.in
1025s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in']
1025s asc_getToken: Error occurred (bailing out).
1025s Vio_scanf: Format problem with input.
1025s 
1025s 
1025s ----------------------------------------------------------------------
1025s     APBS -- Adaptive Poisson-Boltzmann Solver
1025s     Version APBS 3.4.1
1025s     
1025s     Nathan A. Baker (nathan.baker@pnnl.gov)
1025s     Pacific Northwest National Laboratory
1025s     
1025s     Additional contributing authors listed in the code documentation.
1025s     
1025s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1025s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1025s     Northwest Division for the U.S. Department of Energy.
1025s     
1025s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1025s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1025s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1025s     Portions Copyright (c) 1995, Michael Holst.
1025s     All rights reserved.
1025s     
1025s     Redistribution and use in source and binary forms, with or without
1025s     modification, are permitted provided that the following conditions are met:
1025s     
1025s     * Redistributions of source code must retain the above copyright notice, this
1025s       list of conditions and the following disclaimer.
1025s     
1025s     * Redistributions in binary form must reproduce the above copyright notice,
1025s       this list of conditions and the following disclaimer in the documentation
1025s       and/or other materials provided with the distribution.
1025s     
1025s     * Neither the name of the developer nor the names of its contributors may be
1025s       used to endorse or promote products derived from this software without
1025s       specific prior written permission.
1025s     
1025s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1025s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1025s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1025s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1025s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1025s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1025s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1025s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1025s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1025s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1025s ----------------------------------------------------------------------
1025s     APBS uses FETK (the Finite Element ToolKit) to solve the
1025s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1025s     of finite element modeling class libraries developed by the Michael Holst
1025s     research group and written in an object-oriented form of C.  FEtk is
1025s     designed to solve general coupled systems of nonlinear partial differential
1025s     equations using adaptive finite element methods, inexact Newton methods,
1025s     and algebraic multilevel methods.  More information about FEtk may be found
1025s     at <http://www.FEtk.ORG>.
1025s ----------------------------------------------------------------------
1025s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1025s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1025s     which has been modified by Patrice Koehl
1025s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1025s     memory usage when solving the Poisson-Boltzmann equation.
1025s ----------------------------------------------------------------------
1025s     Please cite your use of APBS as:
1025s 
1025s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1025s     nanosystems: application to microtubules and the ribosome. Proc.
1025s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1025s     
1025s 
1025s This executable compiled on Mar  2 2024 at 20:11:10
1025s 
1025s Parsing input file apbs-smol-parallel-PE2.in...
1025s rank 0 size 1...
1025s Parsed input file.
1025s Got paths for 1 molecules
1025s Reading PQR-format atom data from ion.pqr.
1025s   1 atoms
1025s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
1025s   Net charge 1.00e+00 e
1025s Preparing to run 6 PBE calculations.
1025s ----------------------------------------
1025s CALCULATION #1 (solvated): MULTIGRID
1025s   Setting up problem...
1025s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1025s   Debye length:  0 A
1025s   Current memory usage:  61.262 MB total, 61.262 MB high water
1025s   Using cubic spline charge discretization.
1025s   Partition overlap fraction = 0.1
1025s   Processor array = 2 x 2 x 1
1025s   Grid dimensions: 65 x 65 x 65
1025s   Grid spacings: 0.781 x 0.781 x 0.781
1025s   Grid lengths: 50.000 x 50.000 x 50.000
1025s   Grid center: (0.000, 0.000, 0.000)
1025s   Multigrid levels: 5
1025s   Molecule ID: 1
1025s   Linearized traditional PBE
1025s   Multiple Debye-Huckel sphere boundary conditions
1025s   0 ion species (0.000 M ionic strength):
1025s   Solute dielectric: 1.000
1025s   Solvent dielectric: 78.540
1025s   Using "molecular" surface definition;harmonic average smoothing
1025s   Solvent probe radius: 1.400 A
1025s   Temperature:  298.150 K
1025s   Electrostatic energies will be calculated
1025s   Total electrostatic energy = 2.383232191909E+02 kJ/mol
1025s   Calculating forces...
1025s ----------------------------------------
1025s CALCULATION #2 (solvated): MULTIGRID
1025s   Setting up problem...
1025s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1025s   Debye length:  0 A
1025s   Current memory usage:  61.262 MB total, 122.067 MB high water
1025s   Using cubic spline charge discretization.
1025s   Partition overlap fraction = 0.1
1025s   Processor array = 2 x 2 x 1
1025s   Grid dimensions: 65 x 65 x 65
1025s   Grid spacings: 0.296 x 0.296 x 0.383
1025s   Grid lengths: 18.944 x 18.944 x 24.495
1025s   Grid center: (-2.411, 2.411, 0.000)
1025s   Multigrid levels: 5
1025s   Molecule ID: 1
1025s   Linearized traditional PBE
1025s   Boundary conditions from focusing
1025s   0 ion species (0.000 M ionic strength):
1025s   Solute dielectric: 1.000
1025s   Solvent dielectric: 78.540
1025s   Using "molecular" surface definition;harmonic average smoothing
1025s   Solvent probe radius: 1.400 A
1025s   Temperature:  298.150 K
1025s   Electrostatic energies will be calculated
1025s   Total electrostatic energy = 8.145369593489E+02 kJ/mol
1025s   Calculating forces...
1025s [focusFillBound()]: WARNING:
1025s     Unusually large potential values
1025s     detected on the focusing boundary!
1025s     Convergence not guaranteed for NPBE/NRPBE calculations!
1025s 
1025s ----------------------------------------
1025s CALCULATION #3 (solvated): MULTIGRID
1025s   Setting up problem...
1025s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1025s   Debye length:  0 A
1025s   Current memory usage:  61.262 MB total, 122.067 MB high water
1025s   Using cubic spline charge discretization.
1025s   Partition overlap fraction = 0.1
1025s   Processor array = 2 x 2 x 1
1025s   Grid dimensions: 65 x 65 x 65
1025s   Grid spacings: 0.112 x 0.112 x 0.188
1025s   Grid lengths: 7.178 x 7.178 x 12.000
1025s   Grid center: (-2.411, 2.411, 0.000)
1025s   Multigrid levels: 5
1025s   Molecule ID: 1
1025s   Linearized traditional PBE
1025s   Boundary conditions from focusing
1025s   0 ion species (0.000 M ionic strength):
1025s   Solute dielectric: 1.000
1025s   Solvent dielectric: 78.540
1025s   Using "molecular" surface definition;harmonic average smoothing
1025s   Solvent probe radius: 1.400 A
1025s   Temperature:  298.150 K
1025s   Electrostatic energies will be calculated
1025s   Total electrostatic energy = 1.485524997676E+03 kJ/mol
1025s   Calculating forces...
1025s ----------------------------------------
1025s CALCULATION #4 (reference): MULTIGRID
1025s   Setting up problem...
1025s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1025s   Debye length:  0 A
1025s   Current memory usage:  61.189 MB total, 122.067 MB high water
1025s   Using cubic spline charge discretization.
1025s   Partition overlap fraction = 0.1
1025s   Processor array = 2 x 2 x 1
1025s   Grid dimensions: 65 x 65 x 65
1025s   Grid spacings: 0.781 x 0.781 x 0.781
1025s   Grid lengths: 50.000 x 50.000 x 50.000
1025s   Grid center: (0.000, 0.000, 0.000)
1025s   Multigrid levels: 5
1025s   Molecule ID: 1
1025s   Linearized traditional PBE
1025s   Multiple Debye-Huckel sphere boundary conditions
1025s   0 ion species (0.000 M ionic strength):
1025s   Solute dielectric: 1.000
1025s   Solvent dielectric: 1.000
1025s   Using "molecular" surface definition;harmonic average smoothing
1025s   Solvent probe radius: 1.400 A
1025s   Temperature:  298.150 K
1025s   Electrostatic energies will be calculated
1025s   Total electrostatic energy = 2.977178707146E+02 kJ/mol
1025s   Calculating forces...
1025s ----------------------------------------
1025s CALCULATION #5 (reference): MULTIGRID
1025s   Setting up problem...
1025s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1025s   Debye length:  0 A
1025s   Current memory usage:  61.189 MB total, 122.067 MB high water
1025s   Using cubic spline charge discretization.
1025s   Partition overlap fraction = 0.1
1025s   Processor array = 2 x 2 x 1
1025s   Grid dimensions: 65 x 65 x 65
1025s   Grid spacings: 0.296 x 0.296 x 0.383
1025s   Grid lengths: 18.944 x 18.944 x 24.495
1025s   Grid center: (-2.411, 2.411, 0.000)
1025s   Multigrid levels: 5
1025s   Molecule ID: 1
1025s   Linearized traditional PBE
1025s   Boundary conditions from focusing
1025s   0 ion species (0.000 M ionic strength):
1025s   Solute dielectric: 1.000
1025s   Solvent dielectric: 1.000
1025s   Using "molecular" surface definition;harmonic average smoothing
1025s   Solvent probe radius: 1.400 A
1025s   Temperature:  298.150 K
1025s   Electrostatic energies will be calculated
1025s   Total electrostatic energy = 8.799304557596E+02 kJ/mol
1025s   Calculating forces...
1025s [focusFillBound()]: WARNING:
1025s     Unusually large potential values
1025s     detected on the focusing boundary!
1025s     Convergence not guaranteed for NPBE/NRPBE calculations!
1025s 
1025s ----------------------------------------
1025s CALCULATION #6 (reference): MULTIGRID
1025s   Setting up problem...
1025s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1025s   Debye length:  0 A
1025s   Current memory usage:  61.189 MB total, 122.067 MB high water
1025s   Using cubic spline charge discretization.
1025s   Partition overlap fraction = 0.1
1025s   Processor array = 2 x 2 x 1
1025s   Grid dimensions: 65 x 65 x 65
1025s   Grid spacings: 0.112 x 0.112 x 0.188
1025s   Grid lengths: 7.178 x 7.178 x 12.000
1025s   Grid center: (-2.411, 2.411, 0.000)
1025s   Multigrid levels: 5
1025s   Molecule ID: 1
1025s   Linearized traditional PBE
1025s   Boundary conditions from focusing
1025s   0 ion species (0.000 M ionic strength):
1025s   Solute dielectric: 1.000
1025s   Solvent dielectric: 1.000
1025s   Using "molecular" surface definition;harmonic average smoothing
1025s   Solvent probe radius: 1.400 A
1025s   Temperature:  298.150 K
1025s   Electrostatic energies will be calculated
1025s   Total electrostatic energy = 1.542873949141E+03 kJ/mol
1025s   Calculating forces...
1025s ----------------------------------------
1025s PRINT STATEMENTS
1025s 
1025s print energy 1 (solvated) - 2 (reference) end
1025s   Local net energy (PE 0) = -5.734895146550E+01 kJ/mol
1025s   Global net ELEC energy = -5.734895146550E+01 kJ/mol
1025s ----------------------------------------
1025s CLEANING UP AND SHUTTING DOWN...
1025s Destroying force arrays.
1025s No energy arrays to destroy.
1025s Destroying multigrid structures.
1025s Destroying finite element structures.
1025s Destroying 1 molecules
1025s Final memory usage:  0.001 MB total, 122.067 MB high water
1025s 
1025s 
1025s Thanks for using APBS!
1025s 
1044s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out
1044s BINARY:  /usr/bin/apbs
1044s INPUT:   apbs-smol-parallel-PE3.in
1044s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in']
1044s asc_getToken: Error occurred (bailing out).
1044s Vio_scanf: Format problem with input.
1044s 
1044s 
1044s ----------------------------------------------------------------------
1044s     APBS -- Adaptive Poisson-Boltzmann Solver
1044s     Version APBS 3.4.1
1044s     
1044s     Nathan A. Baker (nathan.baker@pnnl.gov)
1044s     Pacific Northwest National Laboratory
1044s     
1044s     Additional contributing authors listed in the code documentation.
1044s     
1044s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1044s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1044s     Northwest Division for the U.S. Department of Energy.
1044s     
1044s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1044s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1044s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1044s     Portions Copyright (c) 1995, Michael Holst.
1044s     All rights reserved.
1044s     
1044s     Redistribution and use in source and binary forms, with or without
1044s     modification, are permitted provided that the following conditions are met:
1044s     
1044s     * Redistributions of source code must retain the above copyright notice, this
1044s       list of conditions and the following disclaimer.
1044s     
1044s     * Redistributions in binary form must reproduce the above copyright notice,
1044s       this list of conditions and the following disclaimer in the documentation
1044s       and/or other materials provided with the distribution.
1044s     
1044s     * Neither the name of the developer nor the names of its contributors may be
1044s       used to endorse or promote products derived from this software without
1044s       specific prior written permission.
1044s     
1044s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1044s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1044s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1044s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1044s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1044s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1044s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1044s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1044s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1044s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1044s ----------------------------------------------------------------------
1044s     APBS uses FETK (the Finite Element ToolKit) to solve the
1044s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1044s     of finite element modeling class libraries developed by the Michael Holst
1044s     research group and written in an object-oriented form of C.  FEtk is
1044s     designed to solve general coupled systems of nonlinear partial differential
1044s     equations using adaptive finite element methods, inexact Newton methods,
1044s     and algebraic multilevel methods.  More information about FEtk may be found
1044s     at <http://www.FEtk.ORG>.
1044s ----------------------------------------------------------------------
1044s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1044s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1044s     which has been modified by Patrice Koehl
1044s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1044s     memory usage when solving the Poisson-Boltzmann equation.
1044s ----------------------------------------------------------------------
1044s     Please cite your use of APBS as:
1044s 
1044s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1044s     nanosystems: application to microtubules and the ribosome. Proc.
1044s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1044s     
1044s 
1044s This executable compiled on Mar  2 2024 at 20:11:10
1044s 
1044s Parsing input file apbs-smol-parallel-PE3.in...
1044s rank 0 size 1...
1044s Parsed input file.
1044s Got paths for 1 molecules
1044s Reading PQR-format atom data from ion.pqr.
1044s   1 atoms
1044s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
1044s   Net charge 1.00e+00 e
1044s Preparing to run 6 PBE calculations.
1044s ----------------------------------------
1044s CALCULATION #1 (solvated): MULTIGRID
1044s   Setting up problem...
1044s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1044s   Debye length:  0 A
1044s   Current memory usage:  61.262 MB total, 61.262 MB high water
1044s   Using cubic spline charge discretization.
1044s   Partition overlap fraction = 0.1
1044s   Processor array = 2 x 2 x 1
1044s   Grid dimensions: 65 x 65 x 65
1044s   Grid spacings: 0.781 x 0.781 x 0.781
1044s   Grid lengths: 50.000 x 50.000 x 50.000
1044s   Grid center: (0.000, 0.000, 0.000)
1044s   Multigrid levels: 5
1044s   Molecule ID: 1
1044s   Linearized traditional PBE
1044s   Multiple Debye-Huckel sphere boundary conditions
1044s   0 ion species (0.000 M ionic strength):
1044s   Solute dielectric: 1.000
1044s   Solvent dielectric: 78.540
1044s   Using "molecular" surface definition;harmonic average smoothing
1044s   Solvent probe radius: 1.400 A
1044s   Temperature:  298.150 K
1044s   Electrostatic energies will be calculated
1044s   Total electrostatic energy = 2.383232191909E+02 kJ/mol
1044s   Calculating forces...
1044s ----------------------------------------
1044s CALCULATION #2 (solvated): MULTIGRID
1044s   Setting up problem...
1044s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1044s   Debye length:  0 A
1044s   Current memory usage:  61.262 MB total, 122.067 MB high water
1044s   Using cubic spline charge discretization.
1044s   Partition overlap fraction = 0.1
1044s   Processor array = 2 x 2 x 1
1044s   Grid dimensions: 65 x 65 x 65
1044s   Grid spacings: 0.296 x 0.296 x 0.383
1044s   Grid lengths: 18.944 x 18.944 x 24.495
1044s   Grid center: (2.411, 2.411, 0.000)
1044s   Multigrid levels: 5
1044s   Molecule ID: 1
1044s   Linearized traditional PBE
1044s   Boundary conditions from focusing
1044s   0 ion species (0.000 M ionic strength):
1044s   Solute dielectric: 1.000
1044s   Solvent dielectric: 78.540
1044s   Using "molecular" surface definition;harmonic average smoothing
1044s   Solvent probe radius: 1.400 A
1044s   Temperature:  298.150 K
1044s   Electrostatic energies will be calculated
1044s   Total electrostatic energy = 8.145419900310E+02 kJ/mol
1044s   Calculating forces...
1044s [focusFillBound()]: WARNING:
1044s     Unusually large potential values
1044s     detected on the focusing boundary!
1044s     Convergence not guaranteed for NPBE/NRPBE calculations!
1044s 
1044s ----------------------------------------
1044s CALCULATION #3 (solvated): MULTIGRID
1044s   Setting up problem...
1044s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1044s   Debye length:  0 A
1044s   Current memory usage:  61.262 MB total, 122.067 MB high water
1044s   Using cubic spline charge discretization.
1044s   Partition overlap fraction = 0.1
1044s   Processor array = 2 x 2 x 1
1044s   Grid dimensions: 65 x 65 x 65
1044s   Grid spacings: 0.112 x 0.112 x 0.188
1044s   Grid lengths: 7.178 x 7.178 x 12.000
1044s   Grid center: (2.411, 2.411, 0.000)
1044s   Multigrid levels: 5
1044s   Molecule ID: 1
1044s   Linearized traditional PBE
1044s   Boundary conditions from focusing
1044s   0 ion species (0.000 M ionic strength):
1044s   Solute dielectric: 1.000
1044s   Solvent dielectric: 78.540
1044s   Using "molecular" surface definition;harmonic average smoothing
1044s   Solvent probe radius: 1.400 A
1044s   Temperature:  298.150 K
1044s   Electrostatic energies will be calculated
1044s   Total electrostatic energy = 1.485529328301E+03 kJ/mol
1044s   Calculating forces...
1044s ----------------------------------------
1044s CALCULATION #4 (reference): MULTIGRID
1044s   Setting up problem...
1044s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1044s   Debye length:  0 A
1044s   Current memory usage:  61.189 MB total, 122.067 MB high water
1044s   Using cubic spline charge discretization.
1044s   Partition overlap fraction = 0.1
1044s   Processor array = 2 x 2 x 1
1044s   Grid dimensions: 65 x 65 x 65
1044s   Grid spacings: 0.781 x 0.781 x 0.781
1044s   Grid lengths: 50.000 x 50.000 x 50.000
1044s   Grid center: (0.000, 0.000, 0.000)
1044s   Multigrid levels: 5
1044s   Molecule ID: 1
1044s   Linearized traditional PBE
1044s   Multiple Debye-Huckel sphere boundary conditions
1044s   0 ion species (0.000 M ionic strength):
1044s   Solute dielectric: 1.000
1044s   Solvent dielectric: 1.000
1044s   Using "molecular" surface definition;harmonic average smoothing
1044s   Solvent probe radius: 1.400 A
1044s   Temperature:  298.150 K
1044s   Electrostatic energies will be calculated
1044s   Total electrostatic energy = 2.977178707146E+02 kJ/mol
1044s   Calculating forces...
1044s ----------------------------------------
1044s CALCULATION #5 (reference): MULTIGRID
1044s   Setting up problem...
1044s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1044s   Debye length:  0 A
1044s   Current memory usage:  61.189 MB total, 122.067 MB high water
1044s   Using cubic spline charge discretization.
1044s   Partition overlap fraction = 0.1
1044s   Processor array = 2 x 2 x 1
1044s   Grid dimensions: 65 x 65 x 65
1044s   Grid spacings: 0.296 x 0.296 x 0.383
1044s   Grid lengths: 18.944 x 18.944 x 24.495
1044s   Grid center: (2.411, 2.411, 0.000)
1044s   Multigrid levels: 5
1044s   Molecule ID: 1
1044s   Linearized traditional PBE
1044s   Boundary conditions from focusing
1044s   0 ion species (0.000 M ionic strength):
1044s   Solute dielectric: 1.000
1044s   Solvent dielectric: 1.000
1044s   Using "molecular" surface definition;harmonic average smoothing
1044s   Solvent probe radius: 1.400 A
1044s   Temperature:  298.150 K
1044s   Electrostatic energies will be calculated
1044s   Total electrostatic energy = 8.799304557596E+02 kJ/mol
1044s   Calculating forces...
1044s [focusFillBound()]: WARNING:
1044s     Unusually large potential values
1044s     detected on the focusing boundary!
1044s     Convergence not guaranteed for NPBE/NRPBE calculations!
1044s 
1044s ----------------------------------------
1044s CALCULATION #6 (reference): MULTIGRID
1044s   Setting up problem...
1044s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
1044s   Debye length:  0 A
1044s   Current memory usage:  61.189 MB total, 122.067 MB high water
1044s   Using cubic spline charge discretization.
1044s   Partition overlap fraction = 0.1
1044s   Processor array = 2 x 2 x 1
1044s   Grid dimensions: 65 x 65 x 65
1044s   Grid spacings: 0.112 x 0.112 x 0.188
1044s   Grid lengths: 7.178 x 7.178 x 12.000
1044s   Grid center: (2.411, 2.411, 0.000)
1044s   Multigrid levels: 5
1044s   Molecule ID: 1
1044s   Linearized traditional PBE
1044s   Boundary conditions from focusing
1044s   0 ion species (0.000 M ionic strength):
1044s   Solute dielectric: 1.000
1044s   Solvent dielectric: 1.000
1044s   Using "molecular" surface definition;harmonic average smoothing
1044s   Solvent probe radius: 1.400 A
1044s   Temperature:  298.150 K
1044s   Electrostatic energies will be calculated
1044s   Total electrostatic energy = 1.542873949141E+03 kJ/mol
1044s   Calculating forces...
1044s ----------------------------------------
1044s PRINT STATEMENTS
1044s 
1044s print energy 1 (solvated) - 2 (reference) end
1044s   Local net energy (PE 0) = -5.734462084052E+01 kJ/mol
1044s   Global net ELEC energy = -5.734462084052E+01 kJ/mol
1044s ----------------------------------------
1044s CLEANING UP AND SHUTTING DOWN...
1044s Destroying force arrays.
1044s No energy arrays to destroy.
1044s Destroying multigrid structures.
1044s Destroying finite element structures.
1044s Destroying 1 molecules
1044s Final memory usage:  0.001 MB total, 122.067 MB high water
1044s 
1044s 
1044s Thanks for using APBS!
1044s 
1044s Processor 3 results:
1044s   2.383232191909e+02
1044s   8.145419900310e+02
1044s   1.485529328301e+03
1044s   2.977178707146e+02
1044s   8.799304557596e+02
1044s   1.542873949141e+03
1044s   -5.734462084052e+01
1044s 
1044s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02)
1044s *** PASSED ***
1044s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03)
1044s *** PASSED ***
1044s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03)
1044s *** PASSED ***
1044s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
1044s *** PASSED ***
1044s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03)
1044s *** PASSED ***
1044s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03)
1044s *** PASSED ***
1044s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02)
1044s *** PASSED ***
1044s Elapsed time: 95.659075 seconds
1044s --------------------------------------------------------------------------------
1044s Total elapsed time: 256.968152 seconds
1044s Test results have been logged
1044s --------------------------------------------------------------------------------
1044s --------------------------------------------------------------------------------
1044s Testing input file apbs-mol-auto.in
1044s 
1417s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out
1417s EXPECTED COMPUTED: 7
1417s EXPECTED EXPECTED: 7
1417s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599]
1417s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02']
1417s COMPUTED RESULT 953.292876745
1417s COMPUTED RESULT 3258.1578983732998
1417s COMPUTED RESULT 5942.108652589999
1417s COMPUTED RESULT 1190.8714828309999
1417s COMPUTED RESULT 3519.7218230368003
1417s COMPUTED RESULT 6171.495796544
1417s COMPUTED RESULT -229.38714395599
1417s Running tests for actin-dimer-auto section
1417s BINARY:  /usr/bin/apbs
1417s INPUT:   apbs-mol-auto.in
1417s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in']
1417s asc_getToken: Error occurred (bailing out).
1417s Vio_scanf: Format problem with input.
1417s 
1417s 
1417s ----------------------------------------------------------------------
1417s     APBS -- Adaptive Poisson-Boltzmann Solver
1417s     Version APBS 3.4.1
1417s     
1417s     Nathan A. Baker (nathan.baker@pnnl.gov)
1417s     Pacific Northwest National Laboratory
1417s     
1417s     Additional contributing authors listed in the code documentation.
1417s     
1417s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1417s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1417s     Northwest Division for the U.S. Department of Energy.
1417s     
1417s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1417s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1417s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1417s     Portions Copyright (c) 1995, Michael Holst.
1417s     All rights reserved.
1417s     
1417s     Redistribution and use in source and binary forms, with or without
1417s     modification, are permitted provided that the following conditions are met:
1417s     
1417s     * Redistributions of source code must retain the above copyright notice, this
1417s       list of conditions and the following disclaimer.
1417s     
1417s     * Redistributions in binary form must reproduce the above copyright notice,
1417s       this list of conditions and the following disclaimer in the documentation
1417s       and/or other materials provided with the distribution.
1417s     
1417s     * Neither the name of the developer nor the names of its contributors may be
1417s       used to endorse or promote products derived from this software without
1417s       specific prior written permission.
1417s     
1417s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1417s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1417s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1417s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1417s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1417s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1417s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1417s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1417s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1417s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1417s ----------------------------------------------------------------------
1417s     APBS uses FETK (the Finite Element ToolKit) to solve the
1417s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1417s     of finite element modeling class libraries developed by the Michael Holst
1417s     research group and written in an object-oriented form of C.  FEtk is
1417s     designed to solve general coupled systems of nonlinear partial differential
1417s     equations using adaptive finite element methods, inexact Newton methods,
1417s     and algebraic multilevel methods.  More information about FEtk may be found
1417s     at <http://www.FEtk.ORG>.
1417s ----------------------------------------------------------------------
1417s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1417s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1417s     which has been modified by Patrice Koehl
1417s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1417s     memory usage when solving the Poisson-Boltzmann equation.
1417s ----------------------------------------------------------------------
1417s     Please cite your use of APBS as:
1417s 
1417s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1417s     nanosystems: application to microtubules and the ribosome. Proc.
1417s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1417s     
1417s 
1417s This executable compiled on Mar  2 2024 at 20:11:10
1417s 
1417s Parsing input file apbs-mol-auto.in...
1417s rank 0 size 1...
1417s Parsed input file.
1417s Got paths for 3 molecules
1417s Reading PQR-format atom data from mol1.pqr.
1417s asc_getToken: Error occurred (bailing out).
1417s Vio_scanf: Format problem with input.
1417s   5877 atoms
1417s   Centered at (1.535e+01, -3.100e-02, 2.993e+00)
1417s   Net charge -1.20e+01 e
1417s Reading PQR-format atom data from mol2.pqr.
1417s asc_getToken: Error occurred (bailing out).
1417s Vio_scanf: Format problem with input.
1417s   5877 atoms
1417s   Centered at (-1.404e+01, -3.356e+00, 3.049e+01)
1417s   Net charge -1.20e+01 e
1417s Reading PQR-format atom data from complex.pqr.
1417s   11754 atoms
1417s   Centered at (2.518e+00, -2.465e+00, 1.674e+01)
1417s   Net charge -2.40e+01 e
1417s Preparing to run 6 PBE calculations.
1417s ----------------------------------------
1417s CALCULATION #1 (mol1): MULTIGRID
1417s   Setting up problem...
1417s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1417s   Debye length:  13.5959 A
1417s   Current memory usage:  1004.896 MB total, 1004.896 MB high water
1417s   Using linear spline charge discretization.
1417s   Grid dimensions: 161 x 161 x 161
1417s   Grid spacings: 0.975 x 0.756 x 1.012
1417s   Grid lengths: 156.000 x 121.000 x 162.000
1417s   Grid center: (2.518, -2.465, 16.742)
1417s   Multigrid levels: 4
1417s   Molecule ID: 1
1417s   Nonlinear traditional PBE
1417s   Single Debye-Huckel sphere boundary conditions
1417s   2 ion species (0.050 M ionic strength):
1417s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1417s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1417s   Solute dielectric: 2.000
1417s   Solvent dielectric: 78.400
1417s   Using "molecular" surface definition; no smoothing
1417s   Solvent probe radius: 1.400 A
1417s   Temperature:  298.150 K
1417s   Electrostatic energies will be calculated
1417s   Total electrostatic energy = 1.527617850342E+05 kJ/mol
1417s   Calculating forces...
1417s ----------------------------------------
1417s CALCULATION #2 (mol1): MULTIGRID
1417s   Setting up problem...
1417s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1417s   Debye length:  13.5959 A
1417s   Current memory usage:  1004.896 MB total, 1995.284 MB high water
1417s   Using linear spline charge discretization.
1417s   Grid dimensions: 161 x 161 x 161
1417s   Grid spacings: 0.700 x 0.569 x 0.725
1417s   Grid lengths: 112.000 x 91.000 x 116.000
1417s   Grid center: (2.518, -2.465, 16.742)
1417s   Multigrid levels: 4
1417s   Molecule ID: 1
1417s   Nonlinear traditional PBE
1417s   Boundary conditions from focusing
1417s   2 ion species (0.050 M ionic strength):
1417s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1417s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1417s   Solute dielectric: 2.000
1417s   Solvent dielectric: 78.400
1417s   Using "molecular" surface definition; no smoothing
1417s   Solvent probe radius: 1.400 A
1417s   Temperature:  298.150 K
1417s   Electrostatic energies will be calculated
1417s   Total electrostatic energy = 2.919510754196E+05 kJ/mol
1417s   Calculating forces...
1417s ----------------------------------------
1417s CALCULATION #3 (mol2): MULTIGRID
1417s   Setting up problem...
1417s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1417s   Debye length:  13.5959 A
1417s   Current memory usage:  1005.881 MB total, 1995.284 MB high water
1417s   Using linear spline charge discretization.
1417s   Grid dimensions: 161 x 161 x 161
1417s   Grid spacings: 0.975 x 0.756 x 1.012
1417s   Grid lengths: 156.000 x 121.000 x 162.000
1417s   Grid center: (2.518, -2.465, 16.742)
1417s   Multigrid levels: 4
1417s   Molecule ID: 2
1417s   Nonlinear traditional PBE
1417s   Single Debye-Huckel sphere boundary conditions
1417s   2 ion species (0.050 M ionic strength):
1417s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1417s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1417s   Solute dielectric: 2.000
1417s   Solvent dielectric: 78.400
1417s   Using "molecular" surface definition; no smoothing
1417s   Solvent probe radius: 1.400 A
1417s   Temperature:  298.150 K
1417s   Electrostatic energies will be calculated
1417s   Total electrostatic energy = 1.527671844880E+05 kJ/mol
1417s   Calculating forces...
1417s ----------------------------------------
1417s CALCULATION #4 (mol2): MULTIGRID
1417s   Setting up problem...
1417s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1417s   Debye length:  13.5959 A
1417s   Current memory usage:  1005.881 MB total, 1997.252 MB high water
1417s   Using linear spline charge discretization.
1417s   Grid dimensions: 161 x 161 x 161
1417s   Grid spacings: 0.700 x 0.569 x 0.725
1417s   Grid lengths: 112.000 x 91.000 x 116.000
1417s   Grid center: (2.518, -2.465, 16.742)
1417s   Multigrid levels: 4
1417s   Molecule ID: 2
1417s   Nonlinear traditional PBE
1417s   Boundary conditions from focusing
1417s   2 ion species (0.050 M ionic strength):
1417s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1417s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1417s   Solute dielectric: 2.000
1417s   Solvent dielectric: 78.400
1417s   Using "molecular" surface definition; no smoothing
1417s   Solvent probe radius: 1.400 A
1417s   Temperature:  298.150 K
1417s   Electrostatic energies will be calculated
1417s   Total electrostatic energy = 2.915468859278E+05 kJ/mol
1417s   Calculating forces...
1417s ----------------------------------------
1417s CALCULATION #5 (complex): MULTIGRID
1417s   Setting up problem...
1417s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1417s   Debye length:  13.5959 A
1417s   Current memory usage:  1018.381 MB total, 1997.252 MB high water
1417s   Using linear spline charge discretization.
1417s   Grid dimensions: 161 x 161 x 161
1417s   Grid spacings: 0.975 x 0.756 x 1.012
1417s   Grid lengths: 156.000 x 121.000 x 162.000
1417s   Grid center: (2.518, -2.465, 16.742)
1417s   Multigrid levels: 4
1417s   Molecule ID: 3
1417s   Nonlinear traditional PBE
1417s   Single Debye-Huckel sphere boundary conditions
1417s   2 ion species (0.050 M ionic strength):
1417s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1417s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1417s   Solute dielectric: 2.000
1417s   Solvent dielectric: 78.400
1417s   Using "molecular" surface definition; no smoothing
1417s   Solvent probe radius: 1.400 A
1417s   Temperature:  298.150 K
1417s   Electrostatic energies will be calculated
1417s   Total electrostatic energy = 3.056317807611E+05 kJ/mol
1417s   Calculating forces...
1417s ----------------------------------------
1417s CALCULATION #6 (complex): MULTIGRID
1417s   Setting up problem...
1417s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1417s   Debye length:  13.5959 A
1417s   Current memory usage:  1018.381 MB total, 2013.407 MB high water
1417s   Using linear spline charge discretization.
1417s   Grid dimensions: 161 x 161 x 161
1417s   Grid spacings: 0.700 x 0.569 x 0.725
1417s   Grid lengths: 112.000 x 91.000 x 116.000
1417s   Grid center: (2.518, -2.465, 16.742)
1417s   Multigrid levels: 4
1417s   Molecule ID: 3
1417s   Nonlinear traditional PBE
1417s   Boundary conditions from focusing
1417s   2 ion species (0.050 M ionic strength):
1417s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1417s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1417s   Solute dielectric: 2.000
1417s   Solvent dielectric: 78.400
1417s   Using "molecular" surface definition; no smoothing
1417s   Solvent probe radius: 1.400 A
1417s   Temperature:  298.150 K
1417s   Electrostatic energies will be calculated
1417s   Total electrostatic energy = 5.836028296532E+05 kJ/mol
1417s   Calculating forces...
1417s ----------------------------------------
1417s PRINT STATEMENTS
1417s 
1417s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end
1417s   Local net energy (PE 0) = 1.048683058628E+02 kJ/mol
1417s   Global net ELEC energy = 1.048683058628E+02 kJ/mol
1417s ----------------------------------------
1417s CLEANING UP AND SHUTTING DOWN...
1417s Destroying force arrays.
1417s No energy arrays to destroy.
1417s Destroying multigrid structures.
1417s Destroying finite element structures.
1417s Destroying 3 molecules
1417s Final memory usage:  0.001 MB total, 2013.407 MB high water
1417s 
1417s 
1417s Thanks for using APBS!
1417s 
1417s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05)
1417s *** PASSED ***
1417s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05)
1417s *** PASSED ***
1417s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05)
1417s *** PASSED ***
1417s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05)
1417s *** PASSED ***
1417s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05)
1417s *** PASSED ***
1417s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05)
1417s *** PASSED ***
1417s Testing computed result against expected result (1.048683058628e+02, 1.048683060915e+02)
1417s *** PASSED ***
1417s Elapsed time: 372.640297 seconds
1417s --------------------------------------------------------------------------------
1417s --------------------------------------------------------------------------------
1417s Testing input file apbs-smol-auto.in
1417s 
1669s Checking for intermediate energies in input file apbs-mol-auto.out
1669s EXPECTED COMPUTED: 7
1669s EXPECTED EXPECTED: 7
1669s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058628]
1669s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02']
1669s COMPUTED RESULT 152761.7850342
1669s COMPUTED RESULT 291951.0754196
1669s COMPUTED RESULT 152767.184488
1669s COMPUTED RESULT 291546.8859278
1669s COMPUTED RESULT 305631.7807611
1669s COMPUTED RESULT 583602.8296532
1669s COMPUTED RESULT 104.8683058628
1669s BINARY:  /usr/bin/apbs
1669s INPUT:   apbs-smol-auto.in
1669s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in']
1669s asc_getToken: Error occurred (bailing out).
1669s Vio_scanf: Format problem with input.
1669s 
1669s 
1669s ----------------------------------------------------------------------
1669s     APBS -- Adaptive Poisson-Boltzmann Solver
1669s     Version APBS 3.4.1
1669s     
1669s     Nathan A. Baker (nathan.baker@pnnl.gov)
1669s     Pacific Northwest National Laboratory
1669s     
1669s     Additional contributing authors listed in the code documentation.
1669s     
1669s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1669s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1669s     Northwest Division for the U.S. Department of Energy.
1669s     
1669s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1669s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1669s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1669s     Portions Copyright (c) 1995, Michael Holst.
1669s     All rights reserved.
1669s     
1669s     Redistribution and use in source and binary forms, with or without
1669s     modification, are permitted provided that the following conditions are met:
1669s     
1669s     * Redistributions of source code must retain the above copyright notice, this
1669s       list of conditions and the following disclaimer.
1669s     
1669s     * Redistributions in binary form must reproduce the above copyright notice,
1669s       this list of conditions and the following disclaimer in the documentation
1669s       and/or other materials provided with the distribution.
1669s     
1669s     * Neither the name of the developer nor the names of its contributors may be
1669s       used to endorse or promote products derived from this software without
1669s       specific prior written permission.
1669s     
1669s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1669s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1669s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1669s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1669s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1669s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1669s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1669s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1669s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1669s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1669s ----------------------------------------------------------------------
1669s     APBS uses FETK (the Finite Element ToolKit) to solve the
1669s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1669s     of finite element modeling class libraries developed by the Michael Holst
1669s     research group and written in an object-oriented form of C.  FEtk is
1669s     designed to solve general coupled systems of nonlinear partial differential
1669s     equations using adaptive finite element methods, inexact Newton methods,
1669s     and algebraic multilevel methods.  More information about FEtk may be found
1669s     at <http://www.FEtk.ORG>.
1669s ----------------------------------------------------------------------
1669s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1669s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1669s     which has been modified by Patrice Koehl
1669s     <http://koehllab.genTesting computed result against expected result (1.528632421825e+05, 1.528632421825e+05)
1669s *** PASSED ***
1669s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05)
1669s *** PASSED ***
1669s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05)
1669s *** PASSED ***
1669s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05)
1669s *** PASSED ***
1669s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05)
1669s *** PASSED ***
1669s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05)
1669s *** PASSED ***
1669s Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02)
1669s *** PASSED ***
1669s Elapsed time: 251.975402 seconds
1669s --------------------------------------------------------------------------------
1669s Total elapsed time: 624.615699 seconds
1669s Test results have been logged
1669s --------------------------------------------------------------------------------
1669s --------------------------------------------------------------------------------
1669s Testing input file alkanes.in
1669s 
1669s omecenter.ucdavis.edu/> for improved efficiency and
1669s     memory usage when solving the Poisson-Boltzmann equation.
1669s ----------------------------------------------------------------------
1669s     Please cite your use of APBS as:
1669s 
1669s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1669s     nanosystems: application to microtubules and the ribosome. Proc.
1669s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1669s     
1669s 
1669s This executable compiled on Mar  2 2024 at 20:11:10
1669s 
1669s Parsing input file apbs-smol-auto.in...
1669s rank 0 size 1...
1669s Parsed input file.
1669s Got paths for 3 molecules
1669s Reading PQR-format atom data from mol1.pqr.
1669s asc_getToken: Error occurred (bailing out).
1669s Vio_scanf: Format problem with input.
1669s   5877 atoms
1669s   Centered at (1.535e+01, -3.100e-02, 2.993e+00)
1669s   Net charge -1.20e+01 e
1669s Reading PQR-format atom data from mol2.pqr.
1669s asc_getToken: Error occurred (bailing out).
1669s Vio_scanf: Format problem with input.
1669s   5877 atoms
1669s   Centered at (-1.404e+01, -3.356e+00, 3.049e+01)
1669s   Net charge -1.20e+01 e
1669s Reading PQR-format atom data from complex.pqr.
1669s   11754 atoms
1669s   Centered at (2.518e+00, -2.465e+00, 1.674e+01)
1669s   Net charge -2.40e+01 e
1669s Preparing to run 6 PBE calculations.
1669s ----------------------------------------
1669s CALCULATION #1 (mol1): MULTIGRID
1669s   Setting up problem...
1669s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1669s   Debye length:  13.5959 A
1669s   Current memory usage:  1004.896 MB total, 1004.896 MB high water
1669s   Using linear spline charge discretization.
1669s   Grid dimensions: 161 x 161 x 161
1669s   Grid spacings: 0.975 x 0.756 x 1.012
1669s   Grid lengths: 156.000 x 121.000 x 162.000
1669s   Grid center: (2.518, -2.465, 16.742)
1669s   Multigrid levels: 4
1669s   Molecule ID: 1
1669s   Nonlinear traditional PBE
1669s   Single Debye-Huckel sphere boundary conditions
1669s   2 ion species (0.050 M ionic strength):
1669s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1669s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1669s   Solute dielectric: 2.000
1669s   Solvent dielectric: 78.400
1669s   Using "molecular" surface definition;harmonic average smoothing
1669s   Solvent probe radius: 1.400 A
1669s   Temperature:  298.150 K
1669s   Electrostatic energies will be calculated
1669s   Total electrostatic energy = 1.528632421825E+05 kJ/mol
1669s   Calculating forces...
1669s ----------------------------------------
1669s CALCULATION #2 (mol1): MULTIGRID
1669s   Setting up problem...
1669s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1669s   Debye length:  13.5959 A
1669s   Current memory usage:  1004.896 MB total, 1995.284 MB high water
1669s   Using linear spline charge discretization.
1669s   Grid dimensions: 161 x 161 x 161
1669s   Grid spacings: 0.700 x 0.569 x 0.725
1669s   Grid lengths: 112.000 x 91.000 x 116.000
1669s   Grid center: (2.518, -2.465, 16.742)
1669s   Multigrid levels: 4
1669s   Molecule ID: 1
1669s   Nonlinear traditional PBE
1669s   Boundary conditions from focusing
1669s   2 ion species (0.050 M ionic strength):
1669s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1669s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1669s   Solute dielectric: 2.000
1669s   Solvent dielectric: 78.400
1669s   Using "molecular" surface definition;harmonic average smoothing
1669s   Solvent probe radius: 1.400 A
1669s   Temperature:  298.150 K
1669s   Electrostatic energies will be calculated
1669s   Total electrostatic energy = 2.920618662320E+05 kJ/mol
1669s   Calculating forces...
1669s ----------------------------------------
1669s CALCULATION #3 (mol2): MULTIGRID
1669s   Setting up problem...
1669s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1669s   Debye length:  13.5959 A
1669s   Current memory usage:  1005.881 MB total, 1995.284 MB high water
1669s   Using linear spline charge discretization.
1669s   Grid dimensions: 161 x 161 x 161
1669s   Grid spacings: 0.975 x 0.756 x 1.012
1669s   Grid lengths: 156.000 x 121.000 x 162.000
1669s   Grid center: (2.518, -2.465, 16.742)
1669s   Multigrid levels: 4
1669s   Molecule ID: 2
1669s   Nonlinear traditional PBE
1669s   Single Debye-Huckel sphere boundary conditions
1669s   2 ion species (0.050 M ionic strength):
1669s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1669s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1669s   Solute dielectric: 2.000
1669s   Solvent dielectric: 78.400
1669s   Using "molecular" surface definition;harmonic average smoothing
1669s   Solvent probe radius: 1.400 A
1669s   Temperature:  298.150 K
1669s   Electrostatic energies will be calculated
1669s   Total electrostatic energy = 1.529297900572E+05 kJ/mol
1669s   Calculating forces...
1669s ----------------------------------------
1669s CALCULATION #4 (mol2): MULTIGRID
1669s   Setting up problem...
1669s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1669s   Debye length:  13.5959 A
1669s   Current memory usage:  1005.881 MB total, 1997.252 MB high water
1669s   Using linear spline charge discretization.
1669s   Grid dimensions: 161 x 161 x 161
1669s   Grid spacings: 0.700 x 0.569 x 0.725
1669s   Grid lengths: 112.000 x 91.000 x 116.000
1669s   Grid center: (2.518, -2.465, 16.742)
1669s   Multigrid levels: 4
1669s   Molecule ID: 2
1669s   Nonlinear traditional PBE
1669s   Boundary conditions from focusing
1669s   2 ion species (0.050 M ionic strength):
1669s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1669s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1669s   Solute dielectric: 2.000
1669s   Solvent dielectric: 78.400
1669s   Using "molecular" surface definition;harmonic average smoothing
1669s   Solvent probe radius: 1.400 A
1669s   Temperature:  298.150 K
1669s   Electrostatic energies will be calculated
1669s   Total electrostatic energy = 2.916592202835E+05 kJ/mol
1669s   Calculating forces...
1669s ----------------------------------------
1669s CALCULATION #5 (complex): MULTIGRID
1669s   Setting up problem...
1669s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1669s   Debye length:  13.5959 A
1669s   Current memory usage:  1018.381 MB total, 1997.252 MB high water
1669s   Using linear spline charge discretization.
1669s   Grid dimensions: 161 x 161 x 161
1669s   Grid spacings: 0.975 x 0.756 x 1.012
1669s   Grid lengths: 156.000 x 121.000 x 162.000
1669s   Grid center: (2.518, -2.465, 16.742)
1669s   Multigrid levels: 4
1669s   Molecule ID: 3
1669s   Nonlinear traditional PBE
1669s   Single Debye-Huckel sphere boundary conditions
1669s   2 ion species (0.050 M ionic strength):
1669s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1669s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1669s   Solute dielectric: 2.000
1669s   Solvent dielectric: 78.400
1669s   Using "molecular" surface definition;harmonic average smoothing
1669s   Solvent probe radius: 1.400 A
1669s   Temperature:  298.150 K
1669s   Electrostatic energies will be calculated
1669s   Total electrostatic energy = 3.059244262535E+05 kJ/mol
1669s   Calculating forces...
1669s ----------------------------------------
1669s CALCULATION #6 (complex): MULTIGRID
1669s   Setting up problem...
1669s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1669s   Debye length:  13.5959 A
1669s   Current memory usage:  1018.381 MB total, 2013.407 MB high water
1669s   Using linear spline charge discretization.
1669s   Grid dimensions: 161 x 161 x 161
1669s   Grid spacings: 0.700 x 0.569 x 0.725
1669s   Grid lengths: 112.000 x 91.000 x 116.000
1669s   Grid center: (2.518, -2.465, 16.742)
1669s   Multigrid levels: 4
1669s   Molecule ID: 3
1669s   Nonlinear traditional PBE
1669s   Boundary conditions from focusing
1669s   2 ion species (0.050 M ionic strength):
1669s     2.000 A-radius, 1.000 e-charge, 0.050 M concentration
1669s     2.000 A-radius, -1.000 e-charge, 0.050 M concentration
1669s   Solute dielectric: 2.000
1669s   Solvent dielectric: 78.400
1669s   Using "molecular" surface definition;harmonic average smoothing
1669s   Solvent probe radius: 1.400 A
1669s   Temperature:  298.150 K
1669s   Electrostatic energies will be calculated
1669s   Total electrostatic energy = 5.838306706232E+05 kJ/mol
1669s   Calculating forces...
1669s ----------------------------------------
1669s PRINT STATEMENTS
1669s 
1669s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end
1669s   Local net energy (PE 0) = 1.095841077691E+02 kJ/mol
1669s   Global net ELEC energy = 1.095841077691E+02 kJ/mol
1669s ----------------------------------------
1669s CLEANING UP AND SHUTTING DOWN...
1669s Destroying force arrays.
1669s No energy arrays to destroy.
1669s Destroying multigrid structures.
1669s Destroying finite element structures.
1669s Destroying 3 molecules
1669s Final memory usage:  0.001 MB total, 2013.407 MB high water
1669s 
1669s 
1669s Thanks for using APBS!
1669s 
1716s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01)
1716s *** PASSED ***
1716s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01)
1716s *** PASSED ***
1716s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01)
1716s *** PASSED ***
1716s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00)
1716s *** PASSED ***
1716s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00)
1716s *** PASSED ***
1716s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01)
1716s *** PASSED ***
1716s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01)
1716s *** PASSED ***
1716s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00)
1716s *** PASSED ***
1716s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01)
1716s *** PASSED ***
1716s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01)
1716s *** PASSED ***
1716s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01)
1716s *** PASSED ***
1716s Elapsed time: 47.251846 seconds
1716s --------------------------------------------------------------------------------
1716s Total elapsed time: 47.251846 seconds
1716s Test results have been logged
1716s --------------------------------------------------------------------------------
1716s --------------------------------------------------------------------------------
1716s Testing input file 1d7h-dmso-mol.in
1716s 
1716s Checking for intermediate energies in input file apbs-smol-auto.out
1716s EXPECTED COMPUTED: 7
1716s EXPECTED EXPECTED: 7
1716s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691]
1716s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02']
1716s COMPUTED RESULT 152863.2421825
1716s COMPUTED RESULT 292061.866232
1716s COMPUTED RESULT 152929.7900572
1716s COMPUTED RESULT 291659.2202835
1716s COMPUTED RESULT 305924.4262535
1716s COMPUTED RESULT 583830.6706232
1716s COMPUTED RESULT 109.5841077691
1716s Running tests for alkanes section
1716s BINARY:  /usr/bin/apbs
1716s INPUT:   alkanes.in
1716s COMMAND: ['/usr/bin/apbs', 'alkanes.in']
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s 
1716s 
1716s ----------------------------------------------------------------------
1716s     APBS -- Adaptive Poisson-Boltzmann Solver
1716s     Version APBS 3.4.1
1716s     
1716s     Nathan A. Baker (nathan.baker@pnnl.gov)
1716s     Pacific Northwest National Laboratory
1716s     
1716s     Additional contributing authors listed in the code documentation.
1716s     
1716s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1716s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1716s     Northwest Division for the U.S. Department of Energy.
1716s     
1716s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1716s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1716s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1716s     Portions Copyright (c) 1995, Michael Holst.
1716s     All rights reserved.
1716s     
1716s     Redistribution and use in source and binary forms, with or without
1716s     modification, are permitted provided that the following conditions are met:
1716s     
1716s     * Redistributions of source code must retain the above copyright notice, this
1716s       list of conditions and the following disclaimer.
1716s     
1716s     * Redistributions in binary form must reproduce the above copyright notice,
1716s       this list of conditions and the following disclaimer in the documentation
1716s       and/or other materials provided with the distribution.
1716s     
1716s     * Neither the name of the developer nor the names of its contributors may be
1716s       used to endorse or promote products derived from this software without
1716s       specific prior written permission.
1716s     
1716s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1716s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1716s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1716s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1716s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1716s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1716s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1716s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1716s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1716s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1716s ----------------------------------------------------------------------
1716s     APBS uses FETK (the Finite Element ToolKit) to solve the
1716s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1716s     of finite element modeling class libraries developed by the Michael Holst
1716s     research group and written in an object-oriented form of C.  FEtk is
1716s     designed to solve general coupled systems of nonlinear partial differential
1716s     equations using adaptive finite element methods, inexact Newton methods,
1716s     and algebraic multilevel methods.  More information about FEtk may be found
1716s     at <http://www.FEtk.ORG>.
1716s ----------------------------------------------------------------------
1716s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1716s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1716s     which has been modified by Patrice Koehl
1716s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1716s     memory usage when solving the Poisson-Boltzmann equation.
1716s ----------------------------------------------------------------------
1716s     Please cite your use of APBS as:
1716s 
1716s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1716s     nanosystems: application to microtubules and the ribosome. Proc.
1716s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1716s     
1716s 
1716s This executable compiled on Mar  2 2024 at 20:11:10
1716s 
1716s Parsing input file alkanes.in...
1716s rank 0 size 1...
1716s Parsed input file.
1716s Reading parameter data from parm.dat.
1716s Got paths for 11 molecules
1716s Reading PDB-format atom data from 2-methylbutane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   17 atoms
1716s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
1716s   Net charge 4.33e+00 e
1716s Reading PDB-format atom data from butane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   14 atoms
1716s   Centered at (3.917e+00, 7.025e-01, -8.575e+00)
1716s   Net charge 3.51e+00 e
1716s Reading PDB-format atom data from cyclohexane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   18 atoms
1716s   Centered at (1.123e+00, 5.880e-01, 7.680e-01)
1716s   Net charge 4.93e+00 e
1716s Reading PDB-format atom data from cyclopentane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   13 atoms
1716s   Centered at (1.320e+00, 5.255e-01, 1.289e+00)
1716s   Net charge 3.88e+00 e
1716s Reading PDB-format atom data from ethane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   8 atoms
1716s   Centered at (2.210e-01, -2.100e-02, 7.650e-01)
1716s   Net charge 1.87e+00 e
1716s Reading PDB-format atom data from hexane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   20 atoms
1716s   Centered at (4.951e+00, -9.500e-03, -8.406e+00)
1716s   Net charge 5.16e+00 e
1716s Reading PDB-format atom data from isobutane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   14 atoms
1716s   Centered at (1.859e+01, 1.864e+01, 1.921e+01)
1716s   Net charge 3.51e+00 e
1716s Reading PDB-format atom data from methane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   5 atoms
1716s   Centered at (1.803e+01, 1.779e+01, 1.782e+01)
1716s   Net charge 1.05e+00 e
1716s Reading PDB-format atom data from neopentane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   17 atoms
1716s   Centered at (1.867e+01, 1.894e+01, 1.920e+01)
1716s   Net charge 4.33e+00 e
1716s Reading PDB-format atom data from pentane.pdb.
1716s asc_getToken: Error occurred (bailing out).
1716s Vio_scanf: Format problem with input.
1716s   17 atoms
1716s   Centered at (4.460e+00, 1.615e-01, -8.566e+00)
1716s   Net charge 4.33e+00 e
1716s Reading PDB-format atom data from propane.pdb.
1716s   11 atoms
1716s   Centered at (1.836e+01, 1.896e+01, 1.861e+01)
1716s   Net charge 2.69e+00 e
1716s Preparing to run 11 PBE calculations.
1716s ----------------------------------------
1716s CALCULATION #1 (solvated-2-methylbutane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 3.815624614267E+00
1716s   SASA for atom 1: 0.000000000000E+00
1716s   SASA for atom 2: 6.122920124655E-01
1716s   SASA for atom 3: 3.957497153740E+00
1716s   SASA for atom 4: 4.308445014544E+00
1716s   SASA for atom 5: 1.843264951960E+01
1716s   SASA for atom 6: 1.837011296483E+01
1716s   SASA for atom 7: 1.666599184724E+01
1716s   SASA for atom 8: 1.480031796315E+01
1716s   SASA for atom 9: 1.603020354037E+01
1716s   SASA for atom 10: 1.473778140838E+01
1716s   SASA for atom 11: 1.611879699297E+01
1716s   SASA for atom 12: 1.810954398660E+01
1716s   SASA for atom 13: 1.420100931324E+01
1716s   SASA for atom 14: 1.437298483886E+01
1716s   SASA for atom 15: 1.814081226399E+01
1716s   SASA for atom 16: 2.152820898091E+01
1716s 
1716s Total solvent accessible surface area: 214.202 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 3.243280922127E-02
1716s   Surface tension*area energy for atom 1: 0.000000000000E+00
1716s   Surface tension*area energy for atom 2: 5.204482105957E-03
1716s   Surface tension*area energy for atom 3: 3.363872580679E-02
1716s   Surface tension*area energy for atom 4: 3.662178262362E-02
1716s   Surface tension*area energy for atom 5: 1.566775209166E-01
1716s   Surface tension*area energy for atom 6: 1.561459602010E-01
1716s   Surface tension*area energy for atom 7: 1.416609307015E-01
1716s   Surface tension*area energy for atom 8: 1.258027026868E-01
1716s   Surface tension*area energy for atom 9: 1.362567300932E-01
1716s   Surface tension*area energy for atom 10: 1.252711419712E-01
1716s   Surface tension*area energy for atom 11: 1.370097744402E-01
1716s   Surface tension*area energy for atom 12: 1.539311238861E-01
1716s   Surface tension*area energy for atom 13: 1.207085791625E-01
1716s   Surface tension*area energy for atom 14: 1.221703711303E-01
1716s   Surface tension*area energy for atom 15: 1.541969042439E-01
1716s   Surface tension*area energy for atom 16: 1.829897763377E-01
1716s 
1716s Total surface tension energy: 1.82072 kJ/mol
1716s 
1716s Total solvent accessible volume: 253.665 A^3
1716s 
1716s Total pressure*volume energy: 60.7274 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.271287875274E+00
1716s   WCA energy for atom 1: -5.600872869478E+00
1716s   WCA energy for atom 2: -5.773775123943E+00
1716s   WCA energy for atom 3: -6.072801488986E+00
1716s   WCA energy for atom 4: -6.378470721845E+00
1716s   WCA energy for atom 5: -1.573474558351E+00
1716s   WCA energy for atom 6: -1.582338715648E+00
1716s   WCA energy for atom 7: -1.504044838266E+00
1716s   WCA energy for atom 8: -1.351002262819E+00
1716s   WCA energy for atom 9: -1.437367175239E+00
1716s   WCA energy for atom 10: -1.384626257493E+00
1716s   WCA energy for atom 11: -1.468867560891E+00
1716s   WCA energy for atom 12: -1.557005662832E+00
1716s   WCA energy for atom 13: -1.473759654043E+00
1716s   WCA energy for atom 14: -1.502261431335E+00
1716s   WCA energy for atom 15: -1.550940901474E+00
1716s   WCA energy for atom 16: -1.667828659696E+00
1716s 
1716s Total WCA energy: -48.1507 kJ/mol
1716s 
1716s Total non-polar energy = 1.439739455792E+01 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #2 (solvated-butane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 4.405515699447E+00
1716s   SASA for atom 1: 8.213673337951E-01
1716s   SASA for atom 2: 8.064333822716E-01
1716s   SASA for atom 3: 4.375647796400E+00
1716s   SASA for atom 4: 1.855251124959E+01
1716s   SASA for atom 5: 2.147609518526E+01
1716s   SASA for atom 6: 1.852645435176E+01
1716s   SASA for atom 7: 1.660345529247E+01
1716s   SASA for atom 8: 1.658782115377E+01
1716s   SASA for atom 9: 1.658260977421E+01
1716s   SASA for atom 10: 1.658260977421E+01
1716s   SASA for atom 11: 2.145003828744E+01
1716s   SASA for atom 12: 1.852124297220E+01
1716s   SASA for atom 13: 1.856293400871E+01
1716s 
1716s Total solvent accessible surface area: 193.855 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 3.744688344530E-02
1716s   Surface tension*area energy for atom 1: 6.981622337259E-03
1716s   Surface tension*area energy for atom 2: 6.854683749309E-03
1716s   Surface tension*area energy for atom 3: 3.719300626940E-02
1716s   Surface tension*area energy for atom 4: 1.576963456215E-01
1716s   Surface tension*area energy for atom 5: 1.825468090747E-01
1716s   Surface tension*area energy for atom 6: 1.574748619900E-01
1716s   Surface tension*area energy for atom 7: 1.411293699860E-01
1716s   Surface tension*area energy for atom 8: 1.409964798071E-01
1716s   Surface tension*area energy for atom 9: 1.409521830808E-01
1716s   Surface tension*area energy for atom 10: 1.409521830808E-01
1716s   Surface tension*area energy for atom 11: 1.823253254433E-01
1716s   Surface tension*area energy for atom 12: 1.574305652637E-01
1716s   Surface tension*area energy for atom 13: 1.577849390741E-01
1716s 
1716s Total surface tension energy: 1.64777 kJ/mol
1716s 
1716s Total solvent accessible volume: 217.863 A^3
1716s 
1716s Total pressure*volume energy: 52.1564 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.728858147814E+00
1716s   WCA energy for atom 1: -6.204037472587E+00
1716s   WCA energy for atom 2: -6.202937735018E+00
1716s   WCA energy for atom 3: -6.728762249931E+00
1716s   WCA energy for atom 4: -1.623549989062E+00
1716s   WCA energy for atom 5: -1.709092300778E+00
1716s   WCA energy for atom 6: -1.625196457114E+00
1716s   WCA energy for atom 7: -1.484289341167E+00
1716s   WCA energy for atom 8: -1.485410538626E+00
1716s   WCA energy for atom 9: -1.485593139015E+00
1716s   WCA energy for atom 10: -1.484878734279E+00
1716s   WCA energy for atom 11: -1.708585062695E+00
1716s   WCA energy for atom 12: -1.625094916482E+00
1716s   WCA energy for atom 13: -1.624416805392E+00
1716s 
1716s Total WCA energy: -41.7207 kJ/mol
1716s 
1716s Total non-polar energy = 1.208346456826E+01 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #3 (solvated-cyclohexane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 7.840324549863E-01
1716s   SASA for atom 1: 8.064333822716E-01
1716s   SASA for atom 2: 8.288343095569E-01
1716s   SASA for atom 3: 7.840324549863E-01
1716s   SASA for atom 4: 7.989664065098E-01
1716s   SASA for atom 5: 8.363012853187E-01
1716s   SASA for atom 6: 2.001169752764E+01
1716s   SASA for atom 7: 1.616048802948E+01
1716s   SASA for atom 8: 2.001169752764E+01
1716s   SASA for atom 9: 1.619175630687E+01
1716s   SASA for atom 10: 1.616048802948E+01
1716s   SASA for atom 11: 1.993352683418E+01
1716s   SASA for atom 12: 2.001169752764E+01
1716s   SASA for atom 13: 1.618133354774E+01
1716s   SASA for atom 14: 1.617091078861E+01
1716s   SASA for atom 15: 2.001690890721E+01
1716s   SASA for atom 16: 1.993873821374E+01
1716s   SASA for atom 17: 1.617091078861E+01
1716s 
1716s Total solvent accessible surface area: 221.799 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 6.664275867383E-03
1716s   Surface tension*area energy for atom 1: 6.854683749309E-03
1716s   Surface tension*area energy for atom 2: 7.045091631234E-03
1716s   Surface tension*area energy for atom 3: 6.664275867383E-03
1716s   Surface tension*area energy for atom 4: 6.791214455333E-03
1716s   Surface tension*area energy for atom 5: 7.108560925209E-03
1716s   Surface tension*area energy for atom 6: 1.700994289850E-01
1716s   Surface tension*area energy for atom 7: 1.373641482506E-01
1716s   Surface tension*area energy for atom 8: 1.700994289850E-01
1716s   Surface tension*area energy for atom 9: 1.376299286084E-01
1716s   Surface tension*area energy for atom 10: 1.373641482506E-01
1716s   Surface tension*area energy for atom 11: 1.694349780905E-01
1716s   Surface tension*area energy for atom 12: 1.700994289850E-01
1716s   Surface tension*area energy for atom 13: 1.375413351558E-01
1716s   Surface tension*area energy for atom 14: 1.374527417032E-01
1716s   Surface tension*area energy for atom 15: 1.701437257113E-01
1716s   Surface tension*area energy for atom 16: 1.694792748168E-01
1716s   Surface tension*area energy for atom 17: 1.374527417032E-01
1716s 
1716s Total surface tension energy: 1.88529 kJ/mol
1716s 
1716s Total solvent accessible volume: 267.435 A^3
1716s 
1716s Total pressure*volume energy: 64.0239 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -5.793234697241E+00
1716s   WCA energy for atom 1: -5.784370526583E+00
1716s   WCA energy for atom 2: -5.791799130412E+00
1716s   WCA energy for atom 3: -5.788504399087E+00
1716s   WCA energy for atom 4: -5.797319672490E+00
1716s   WCA energy for atom 5: -5.787358035342E+00
1716s   WCA energy for atom 6: -1.523887929614E+00
1716s   WCA energy for atom 7: -1.413678912317E+00
1716s   WCA energy for atom 8: -1.521751604392E+00
1716s   WCA energy for atom 9: -1.414741802525E+00
1716s   WCA energy for atom 10: -1.413367854344E+00
1716s   WCA energy for atom 11: -1.523407238081E+00
1716s   WCA energy for atom 12: -1.523000623583E+00
1716s   WCA energy for atom 13: -1.413922068538E+00
1716s   WCA energy for atom 14: -1.416316744211E+00
1716s   WCA energy for atom 15: -1.524577474659E+00
1716s   WCA energy for atom 16: -1.523300410052E+00
1716s   WCA energy for atom 17: -1.414522566061E+00
1716s 
1716s Total WCA energy: -52.3691 kJ/mol
1716s 
1716s Total non-polar energy = 1.354016672221E+01 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #4 (solvated-cyclopentane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 9.490526193215E+00
1716s   SASA for atom 1: 9.512927120500E+00
1716s   SASA for atom 2: 2.299828534626E+00
1716s   SASA for atom 3: 1.919012770776E+00
1716s   SASA for atom 4: 2.307295510388E+00
1716s   SASA for atom 5: 2.325838699632E+01
1716s   SASA for atom 6: 2.325838699632E+01
1716s   SASA for atom 7: 2.045987617019E+01
1716s   SASA for atom 8: 2.067875411190E+01
1716s   SASA for atom 9: 2.028790064456E+01
1716s   SASA for atom 10: 1.897463299431E+01
1716s   SASA for atom 11: 2.048593306801E+01
1716s   SASA for atom 12: 2.070481100972E+01
1716s 
1716s Total solvent accessible surface area: 193.638 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 8.066947264233E-02
1716s   Surface tension*area energy for atom 1: 8.085988052425E-02
1716s   Surface tension*area energy for atom 2: 1.954854254432E-02
1716s   Surface tension*area energy for atom 3: 1.631160855160E-02
1716s   Surface tension*area energy for atom 4: 1.961201183830E-02
1716s   Surface tension*area energy for atom 5: 1.976962894687E-01
1716s   Surface tension*area energy for atom 6: 1.976962894687E-01
1716s   Surface tension*area energy for atom 7: 1.739089474466E-01
1716s   Surface tension*area energy for atom 8: 1.757694099511E-01
1716s   Surface tension*area energy for atom 9: 1.724471554788E-01
1716s   Surface tension*area energy for atom 10: 1.612843804516E-01
1716s   Surface tension*area energy for atom 11: 1.741304310781E-01
1716s   Surface tension*area energy for atom 12: 1.759908935826E-01
1716s 
1716s Total surface tension energy: 1.64593 kJ/mol
1716s 
1716s Total solvent accessible volume: 217.998 A^3
1716s 
1716s Total pressure*volume energy: 52.1887 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.343496616804E+00
1716s   WCA energy for atom 1: -6.327869601807E+00
1716s   WCA energy for atom 2: -6.334858040579E+00
1716s   WCA energy for atom 3: -6.296075406417E+00
1716s   WCA energy for atom 4: -6.345600816761E+00
1716s   WCA energy for atom 5: -1.663697465126E+00
1716s   WCA energy for atom 6: -1.662444032853E+00
1716s   WCA energy for atom 7: -1.572325104493E+00
1716s   WCA energy for atom 8: -1.604626551065E+00
1716s   WCA energy for atom 9: -1.586431484963E+00
1716s   WCA energy for atom 10: -1.554291291374E+00
1716s   WCA energy for atom 11: -1.574315220751E+00
1716s   WCA energy for atom 12: -1.604941679892E+00
1716s 
1716s Total WCA energy: -44.471 kJ/mol
1716s 
1716s Total non-polar energy = 9.363673200142E+00 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #5 (solvated-ethane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 5.995981536705E+00
1716s   SASA for atom 1: 5.966113633657E+00
1716s   SASA for atom 2: 2.121552620704E+01
1716s   SASA for atom 3: 2.124158310486E+01
1716s   SASA for atom 4: 2.125200586399E+01
1716s   SASA for atom 5: 2.123116034573E+01
1716s   SASA for atom 6: 2.125200586399E+01
1716s   SASA for atom 7: 2.127285138225E+01
1716s 
1716s Total solvent accessible surface area: 139.427 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 5.096584306199E-02
1716s   Surface tension*area energy for atom 1: 5.071196588609E-02
1716s   Surface tension*area energy for atom 2: 1.803319727598E-01
1716s   Surface tension*area energy for atom 3: 1.805534563913E-01
1716s   Surface tension*area energy for atom 4: 1.806420498439E-01
1716s   Surface tension*area energy for atom 5: 1.804648629387E-01
1716s   Surface tension*area energy for atom 6: 1.806420498439E-01
1716s   Surface tension*area energy for atom 7: 1.808192367491E-01
1716s 
1716s Total surface tension energy: 1.18513 kJ/mol
1716s 
1716s Total solvent accessible volume: 140.346 A^3
1716s 
1716s Total pressure*volume energy: 33.5988 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -7.360066353115E+00
1716s   WCA energy for atom 1: -7.355483516201E+00
1716s   WCA energy for atom 2: -1.776106201066E+00
1716s   WCA energy for atom 3: -1.773973940651E+00
1716s   WCA energy for atom 4: -1.775401936843E+00
1716s   WCA energy for atom 5: -1.773464835521E+00
1716s   WCA energy for atom 6: -1.774382856097E+00
1716s   WCA energy for atom 7: -1.772366599434E+00
1716s 
1716s Total WCA energy: -25.3612 kJ/mol
1716s 
1716s Total non-polar energy = 9.422717598546E+00 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #6 (solvated-hexane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 4.405515699447E+00
1716s   SASA for atom 1: 8.213673337951E-01
1716s   SASA for atom 2: 3.285469335181E-01
1716s   SASA for atom 3: 2.986790304710E-01
1716s   SASA for atom 4: 1.855251124959E+01
1716s   SASA for atom 5: 2.147609518526E+01
1716s   SASA for atom 6: 1.852645435176E+01
1716s   SASA for atom 7: 1.655655287639E+01
1716s   SASA for atom 8: 1.655134149682E+01
1716s   SASA for atom 9: 1.360170066332E+01
1716s   SASA for atom 10: 1.357043238593E+01
1716s   SASA for atom 11: 1.381536722546E+01
1716s   SASA for atom 12: 1.384142412329E+01
1716s   SASA for atom 13: 7.765654792245E-01
1716s   SASA for atom 14: 1.684839013200E+01
1716s   SASA for atom 15: 1.682233323417E+01
1716s   SASA for atom 16: 4.166572475070E+00
1716s   SASA for atom 17: 2.179398933870E+01
1716s   SASA for atom 18: 1.877660057086E+01
1716s   SASA for atom 19: 1.876096643216E+01
1716s 
1716s Total solvent accessible surface area: 250.291 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 3.744688344530E-02
1716s   Surface tension*area energy for atom 1: 6.981622337259E-03
1716s   Surface tension*area energy for atom 2: 2.792648934903E-03
1716s   Surface tension*area energy for atom 3: 2.538771759003E-03
1716s   Surface tension*area energy for atom 4: 1.576963456215E-01
1716s   Surface tension*area energy for atom 5: 1.825468090747E-01
1716s   Surface tension*area energy for atom 6: 1.574748619900E-01
1716s   Surface tension*area energy for atom 7: 1.407306994493E-01
1716s   Surface tension*area energy for atom 8: 1.406864027230E-01
1716s   Surface tension*area energy for atom 9: 1.156144556382E-01
1716s   Surface tension*area energy for atom 10: 1.153486752804E-01
1716s   Surface tension*area energy for atom 11: 1.174306214164E-01
1716s   Surface tension*area energy for atom 12: 1.176521050479E-01
1716s   Surface tension*area energy for atom 13: 6.600806573408E-03
1716s   Surface tension*area energy for atom 14: 1.432113161220E-01
1716s   Surface tension*area energy for atom 15: 1.429898324905E-01
1716s   Surface tension*area energy for atom 16: 3.541586603809E-02
1716s   Surface tension*area energy for atom 17: 1.852489093789E-01
1716s   Surface tension*area energy for atom 18: 1.596011048523E-01
1716s   Surface tension*area energy for atom 19: 1.594682146734E-01
1716s 
1716s Total surface tension energy: 2.12748 kJ/mol
1716s 
1716s Total solvent accessible volume: 298.053 A^3
1716s 
1716s Total pressure*volume energy: 71.3539 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.635406071935E+00
1716s   WCA energy for atom 1: -5.957247427848E+00
1716s   WCA energy for atom 2: -5.524801144538E+00
1716s   WCA energy for atom 3: -5.522294168859E+00
1716s   WCA energy for atom 4: -1.605314409440E+00
1716s   WCA energy for atom 5: -1.701051761776E+00
1716s   WCA energy for atom 6: -1.606669162773E+00
1716s   WCA energy for atom 7: -1.442505934938E+00
1716s   WCA energy for atom 8: -1.443059002759E+00
1716s   WCA energy for atom 9: -1.328947132810E+00
1716s   WCA energy for atom 10: -1.328906972440E+00
1716s   WCA energy for atom 11: -1.331566344214E+00
1716s   WCA energy for atom 12: -1.328041776815E+00
1716s   WCA energy for atom 13: -5.937562025661E+00
1716s   WCA energy for atom 14: -1.442277774427E+00
1716s   WCA energy for atom 15: -1.442777091510E+00
1716s   WCA energy for atom 16: -6.602262542378E+00
1716s   WCA energy for atom 17: -1.698172146664E+00
1716s   WCA energy for atom 18: -1.600970858835E+00
1716s   WCA energy for atom 19: -1.600841970217E+00
1716s 
1716s Total WCA energy: -57.0807 kJ/mol
1716s 
1716s Total non-polar energy = 1.640068943201E+01 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #7 (solvated-isobutane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 3.464676753463E+00
1716s   SASA for atom 1: 1.984493338158E+01
1716s   SASA for atom 2: 1.778643845361E+01
1716s   SASA for atom 3: 1.671289426332E+01
1716s   SASA for atom 4: 0.000000000000E+00
1716s   SASA for atom 5: 3.531879535319E+00
1716s   SASA for atom 6: 1.673895116114E+01
1716s   SASA for atom 7: 1.793756846098E+01
1716s   SASA for atom 8: 1.973549441072E+01
1716s   SASA for atom 9: 1.710895911022E+01
1716s   SASA for atom 10: 4.599657069253E+00
1716s   SASA for atom 11: 1.937069784121E+01
1716s   SASA for atom 12: 1.654613011726E+01
1716s   SASA for atom 13: 1.936548646165E+01
1716s 
1716s Total solvent accessible surface area: 192.744 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 2.944975240444E-02
1716s   Surface tension*area energy for atom 1: 1.686819337434E-01
1716s   Surface tension*area energy for atom 2: 1.511847268556E-01
1716s   Surface tension*area energy for atom 3: 1.420596012382E-01
1716s   Surface tension*area energy for atom 4: 0.000000000000E+00
1716s   Surface tension*area energy for atom 5: 3.002097605021E-02
1716s   Surface tension*area energy for atom 6: 1.422810848697E-01
1716s   Surface tension*area energy for atom 7: 1.524693319183E-01
1716s   Surface tension*area energy for atom 8: 1.677517024912E-01
1716s   Surface tension*area energy for atom 9: 1.454261524369E-01
1716s   Surface tension*area energy for atom 10: 3.909708508865E-02
1716s   Surface tension*area energy for atom 11: 1.646509316503E-01
1716s   Surface tension*area energy for atom 12: 1.406421059967E-01
1716s   Surface tension*area energy for atom 13: 1.646066349240E-01
1716s 
1716s Total surface tension energy: 1.63832 kJ/mol
1716s 
1716s Total solvent accessible volume: 218.943 A^3
1716s 
1716s Total pressure*volume energy: 52.415 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.381016335247E+00
1716s   WCA energy for atom 1: -1.612317964554E+00
1716s   WCA energy for atom 2: -1.588013719598E+00
1716s   WCA energy for atom 3: -1.532162371190E+00
1716s   WCA energy for atom 4: -5.987950445279E+00
1716s   WCA energy for atom 5: -6.393089030861E+00
1716s   WCA energy for atom 6: -1.533454887042E+00
1716s   WCA energy for atom 7: -1.587650918485E+00
1716s   WCA energy for atom 8: -1.614083521570E+00
1716s   WCA energy for atom 9: -1.442402031577E+00
1716s   WCA energy for atom 10: -6.408813541353E+00
1716s   WCA energy for atom 11: -1.605830214390E+00
1716s   WCA energy for atom 12: -1.529385873788E+00
1716s   WCA energy for atom 13: -1.605662490385E+00
1716s 
1716s Total WCA energy: -40.8218 kJ/mol
1716s 
1716s Total non-polar energy = 1.323144287435E+01 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #8 (solvated-methane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 1.231304303117E+01
1716s   SASA for atom 1: 2.323233009850E+01
1716s   SASA for atom 2: 2.345641941977E+01
1716s   SASA for atom 3: 2.377431357320E+01
1716s   SASA for atom 4: 2.264344420771E+01
1716s 
1716s Total solvent accessible surface area: 105.42 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 1.046608657649E-01
1716s   Surface tension*area energy for atom 1: 1.974748058372E-01
1716s   Surface tension*area energy for atom 2: 1.993795650680E-01
1716s   Surface tension*area energy for atom 3: 2.020816653722E-01
1716s   Surface tension*area energy for atom 4: 1.924692757655E-01
1716s 
1716s Total surface tension energy: 0.896066 kJ/mol
1716s 
1716s Total solvent accessible volume: 95.985 A^3
1716s 
1716s Total pressure*volume energy: 22.9788 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -8.133807570805E+00
1716s   WCA energy for atom 1: -1.962181541765E+00
1716s   WCA energy for atom 2: -1.964078319162E+00
1716s   WCA energy for atom 3: -1.963015006647E+00
1716s   WCA energy for atom 4: -1.957425549100E+00
1716s 
1716s Total WCA energy: -15.9805 kJ/mol
1716s 
1716s Total non-polar energy = 7.894367190329E+00 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #9 (solvated-neopentane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 2.441701074100E+00
1716s   SASA for atom 1: 1.663993494942E+01
1716s   SASA for atom 2: 1.715586152630E+01
1716s   SASA for atom 3: 1.645753666466E+01
1716s   SASA for atom 4: 0.000000000000E+00
1716s   SASA for atom 5: 2.389432243768E+00
1716s   SASA for atom 6: 1.638457735076E+01
1716s   SASA for atom 7: 1.667641460637E+01
1716s   SASA for atom 8: 1.721839808108E+01
1716s   SASA for atom 9: 2.419300146815E+00
1716s   SASA for atom 10: 1.640021148945E+01
1716s   SASA for atom 11: 1.666599184724E+01
1716s   SASA for atom 12: 1.719234118325E+01
1716s   SASA for atom 13: 2.449168049862E+00
1716s   SASA for atom 14: 1.723403221977E+01
1716s   SASA for atom 15: 1.639500010989E+01
1716s   SASA for atom 16: 1.663472356985E+01
1716s 
1716s Total solvent accessible surface area: 210.755 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 2.075445912985E-02
1716s   Surface tension*area energy for atom 1: 1.414394470700E-01
1716s   Surface tension*area energy for atom 2: 1.458248229736E-01
1716s   Surface tension*area energy for atom 3: 1.398890616496E-01
1716s   Surface tension*area energy for atom 4: 0.000000000000E+00
1716s   Surface tension*area energy for atom 5: 2.031017407203E-02
1716s   Surface tension*area energy for atom 6: 1.392689074814E-01
1716s   Surface tension*area energy for atom 7: 1.417495241541E-01
1716s   Surface tension*area energy for atom 8: 1.463563836891E-01
1716s   Surface tension*area energy for atom 9: 2.056405124793E-02
1716s   Surface tension*area energy for atom 10: 1.394017976603E-01
1716s   Surface tension*area energy for atom 11: 1.416609307015E-01
1716s   Surface tension*area energy for atom 12: 1.461349000577E-01
1716s   Surface tension*area energy for atom 13: 2.081792842383E-02
1716s   Surface tension*area energy for atom 14: 1.464892738680E-01
1716s   Surface tension*area energy for atom 15: 1.393575009340E-01
1716s   Surface tension*area energy for atom 16: 1.413951503437E-01
1716s 
1716s Total surface tension energy: 1.79141 kJ/mol
1716s 
1716s Total solvent accessible volume: 251.127 A^3
1716s 
1716s Total pressure*volume energy: 60.1198 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.011082520236E+00
1716s   WCA energy for atom 1: -1.497367782613E+00
1716s   WCA energy for atom 2: -1.498546483218E+00
1716s   WCA energy for atom 3: -1.492562171495E+00
1716s   WCA energy for atom 4: -5.447325863939E+00
1716s   WCA energy for atom 5: -6.004516149175E+00
1716s   WCA energy for atom 6: -1.492776531092E+00
1716s   WCA energy for atom 7: -1.496078170066E+00
1716s   WCA energy for atom 8: -1.501529655270E+00
1716s   WCA energy for atom 9: -5.996267554365E+00
1716s   WCA energy for atom 10: -1.492194267752E+00
1716s   WCA energy for atom 11: -1.496027211216E+00
1716s   WCA energy for atom 12: -1.500561393960E+00
1716s   WCA energy for atom 13: -6.000218612907E+00
1716s   WCA energy for atom 14: -1.500859921426E+00
1716s   WCA energy for atom 15: -1.492908499790E+00
1716s   WCA energy for atom 16: -1.494057174414E+00
1716s 
1716s Total WCA energy: -47.4149 kJ/mol
1716s 
1716s Total non-polar energy = 1.449633815052E+01 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #10 (solvated-pentane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 4.405515699447E+00
1716s   SASA for atom 1: 8.213673337951E-01
1716s   SASA for atom 2: 3.285469335181E-01
1716s   SASA for atom 3: 7.466975761774E-01
1716s   SASA for atom 4: 1.855251124959E+01
1716s   SASA for atom 5: 2.147609518526E+01
1716s   SASA for atom 6: 1.852645435176E+01
1716s   SASA for atom 7: 1.655655287639E+01
1716s   SASA for atom 8: 1.655134149682E+01
1716s   SASA for atom 9: 1.360170066332E+01
1716s   SASA for atom 10: 1.357043238593E+01
1716s   SASA for atom 11: 1.685881289113E+01
1716s   SASA for atom 12: 1.687444702982E+01
1716s   SASA for atom 13: 4.196440378117E+00
1716s   SASA for atom 14: 1.881308022781E+01
1716s   SASA for atom 15: 1.882350298694E+01
1716s   SASA for atom 16: 2.182004623652E+01
1716s 
1716s Total solvent accessible surface area: 222.524 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 3.744688344530E-02
1716s   Surface tension*area energy for atom 1: 6.981622337259E-03
1716s   Surface tension*area energy for atom 2: 2.792648934903E-03
1716s   Surface tension*area energy for atom 3: 6.346929397508E-03
1716s   Surface tension*area energy for atom 4: 1.576963456215E-01
1716s   Surface tension*area energy for atom 5: 1.825468090747E-01
1716s   Surface tension*area energy for atom 6: 1.574748619900E-01
1716s   Surface tension*area energy for atom 7: 1.407306994493E-01
1716s   Surface tension*area energy for atom 8: 1.406864027230E-01
1716s   Surface tension*area energy for atom 9: 1.156144556382E-01
1716s   Surface tension*area energy for atom 10: 1.153486752804E-01
1716s   Surface tension*area energy for atom 11: 1.432999095746E-01
1716s   Surface tension*area energy for atom 12: 1.434327997535E-01
1716s   Surface tension*area energy for atom 13: 3.566974321399E-02
1716s   Surface tension*area energy for atom 14: 1.599111819364E-01
1716s   Surface tension*area energy for atom 15: 1.599997753890E-01
1716s   Surface tension*area energy for atom 16: 1.854703930104E-01
1716s 
1716s Total surface tension energy: 1.89145 kJ/mol
1716s 
1716s Total solvent accessible volume: 258.93 A^3
1716s 
1716s Total pressure*volume energy: 61.9878 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.655804319869E+00
1716s   WCA energy for atom 1: -6.027315962813E+00
1716s   WCA energy for atom 2: -5.696430965386E+00
1716s   WCA energy for atom 3: -6.016749084714E+00
1716s   WCA energy for atom 4: -1.608595384643E+00
1716s   WCA energy for atom 5: -1.703300955380E+00
1716s   WCA energy for atom 6: -1.609931495887E+00
1716s   WCA energy for atom 7: -1.457107525189E+00
1716s   WCA energy for atom 8: -1.457741620594E+00
1716s   WCA energy for atom 9: -1.354235498709E+00
1716s   WCA energy for atom 10: -1.354106470090E+00
1716s   WCA energy for atom 11: -1.456736412636E+00
1716s   WCA energy for atom 12: -1.455995435596E+00
1716s   WCA energy for atom 13: -6.633650611186E+00
1716s   WCA energy for atom 14: -1.605996088477E+00
1716s   WCA energy for atom 15: -1.606549890103E+00
1716s   WCA energy for atom 16: -1.700042300035E+00
1716s 
1716s Total WCA energy: -49.4003 kJ/mol
1716s 
1716s Total non-polar energy = 1.447900211546E+01 kJ/mol
1716s ----------------------------------------
1716s CALCULATION #11 (solvated-propane): APOLAR
1716s 
1716s Solvent Accessible Surface Area (SASA) for each atom:
1716s   SASA for atom 0: 3.173464698754E+00
1716s   SASA for atom 1: 1.931858404557E+01
1716s   SASA for atom 2: 2.014198201675E+01
1716s   SASA for atom 3: 2.149694070352E+01
1716s   SASA for atom 4: 1.904078819252E+00
1716s   SASA for atom 5: 2.067354273233E+01
1716s   SASA for atom 6: 1.937590922077E+01
1716s   SASA for atom 7: 3.098794941136E+00
1716s   SASA for atom 8: 1.942802301642E+01
1716s   SASA for atom 9: 1.973028303116E+01
1716s   SASA for atom 10: 2.204934693736E+01
1716s 
1716s Total solvent accessible surface area: 170.391 A^2
1716s 
1716s Surface tension*area energies (gamma * SASA) for each atom:
1716s   Surface tension*area energy for atom 0: 2.697444993941E-02
1716s   Surface tension*area energy for atom 1: 1.642079643873E-01
1716s   Surface tension*area energy for atom 2: 1.712068471424E-01
1716s   Surface tension*area energy for atom 3: 1.827239959799E-01
1716s   Surface tension*area energy for atom 4: 1.618466996365E-02
1716s   Surface tension*area energy for atom 5: 1.757251132248E-01
1716s   Surface tension*area energy for atom 6: 1.646952283766E-01
1716s   Surface tension*area energy for atom 7: 2.633975699966E-02
1716s   Surface tension*area energy for atom 8: 1.651381956396E-01
1716s   Surface tension*area energy for atom 9: 1.677074057649E-01
1716s   Surface tension*area energy for atom 10: 1.874194489675E-01
1716s 
1716s Total surface tension energy: 1.44832 kJ/mol
1716s 
1716s Total solvent accessible volume: 183.573 A^3
1716s 
1716s Total pressure*volume energy: 43.9474 kJ/mol
1716s 
1716s WCA dispersion Energies for each atom:
1716s   WCA energy for atom 0: -6.818670105515E+00
1716s   WCA energy for atom 1: -1.641297645338E+00
1716s   WCA energy for atom 2: -1.649584120441E+00
1716s   WCA energy for atom 3: -1.711408141255E+00
1716s   WCA energy for atom 4: -6.624720142882E+00
1716s   WCA energy for atom 5: -1.610117050515E+00
1716s   WCA energy for atom 6: -1.596858009746E+00
1716s   WCA energy for atom 7: -6.816460624835E+00
1716s   WCA energy for atom 8: -1.642782751806E+00
1716s   WCA energy for atom 9: -1.645779566650E+00
1716s   WCA energy for atom 10: -1.714436154542E+00
1716s 
1716s Total WCA energy: -33.4721 kJ/mol
1716s 
1716s Total non-polar energy = 1.192358496286E+01 kJ/mol
1716s ----------------------------------------
1716s PRINT STATEMENTS
1716s 
1716s print APOL energy 1 (solvated-2-methylbutane) end
1716s   Global net APOL energy = 1.439739455792E+01 kJ/mol
1716s 
1716s print APOL energy 2 (solvated-butane) end
1716s   Global net APOL energy = 1.208346456826E+01 kJ/mol
1716s 
1716s print APOL energy 3 (solvated-cyclohexane) end
1716s   Global net APOL energy = 1.354016672221E+01 kJ/mol
1716s 
1716s print APOL energy 4 (solvated-cyclopentane) end
1716s   Global net APOL energy = 9.363673200142E+00 kJ/mol
1716s 
1716s print APOL energy 5 (solvated-ethane) end
1716s   Global net APOL energy = 9.422717598546E+00 kJ/mol
1716s 
1716s print APOL energy 6 (solvated-hexane) end
1716s   Global net APOL energy = 1.640068943201E+01 kJ/mol
1716s 
1716s print APOL energy 7 (solvated-isobutane) end
1716s   Global net APOL energy = 1.323144287435E+01 kJ/mol
1716s 
1716s print APOL energy 8 (solvated-methane) end
1716s   Global net APOL energy = 7.894367190329E+00 kJ/mol
1716s 
1716s print APOL energy 9 (solvated-neopentane) end
1716s   Global net APOL energy = 1.449633815052E+01 kJ/mol
1716s 
1716s print APOL energy 10 (solvated-pentane) end
1716s   Global net APOL energy = 1.447900211546E+01 kJ/mol
1716s 
1716s print APOL energy 11 (solvated-propane) end
1716s   Global net APOL energy = 1.192358496286E+01 kJ/mol
1716s ----------------------------------------
1716s CLEANING UP AND SHUTTING DOWN...
1716s Destroying force arrays.
1716s No energy arrays to destroy.
1716s Destroying multigrid structures.
1716s Destroying finite element structures.
1716s Destroying 11 molecules
1716s Final memory usage:  0.001 MB total, 2.204 MB high water
1716s 
1716s 
1716s Thanks for using APBS!
1716s 
1754s Checking for intermediate energies in input file alkanes.out
1754s EXPECTED COMPUTED: 11
1754s EXPECTED EXPECTED: 11
1754s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286]
1754s EXPECTED: ['1.439739455792E+01', '1.208346456826E+01', '1.354016672221E+01', '9.363673200142E+00', '9.422717598546E+00', '1.640068943201E+01', '1.323144287435E+01', '7.894367190329E+00', '1.449633815052E+01', '1.447900211546E+01', '1.192358496286E+01']
1754s COMPUTED RESULT 14.39739455792
1754s COMPUTED RESULT 12.08346456826
1754s COMPUTED RESULT 13.54016672221
1754s COMPUTED RESULT 9.363673200142
1754s COMPUTED RESULT 9.422717598546
1754s COMPUTED RESULT 16.40068943201
1754s COMPUTED RESULT 13.23144287435
1754s COMPUTED RESULT 7.894367190329
1754s COMPUTED RESULT 14.49633815052
1754s COMPUTED RESULT 14.47900211546
1754s COMPUTED RESULT 11.92358496286
1754s Running tests for FKBP section
1754s BINARY:  /usr/bin/apbs
1754s INPUT:   1d7h-dmso-mol.in
1754s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in']
1754s asc_getToken: Error occurred (bailing out).
1754s Vio_scanf: Format problem with input.
1754s 
1754s 
1754s ----------------------------------------------------------------------
1754s     APBS -- Adaptive Poisson-Boltzmann Solver
1754s     Version APBS 3.4.1
1754s     
1754s     Nathan A. Baker (nathan.baker@pnnl.gov)
1754s     Pacific Northwest National Laboratory
1754s     
1754s     Additional contributing authors listed in the code documentation.
1754s     
1754s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1754s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1754s     Northwest Division for the U.S. Department of Energy.
1754s     
1754s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1754s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1754s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1754s     Portions Copyright (c) 1995, Michael Holst.
1754s     All rights reserved.
1754s     
1754s     Redistribution and use in source and binary forms, with or without
1754s     modification, are permitted provided that the following conditions are met:
1754s     
1754s     * Redistributions of source code must retain the above copyright notice, this
1754s       list of conditions and the following disclaimer.
1754s     
1754s     * Redistributions in binary form must reproduce the above copyright notice,
1754s       this list of conditions and the following disclaimer in the documentation
1754s       and/or other materials provided with the distribution.
1754s     
1754s     * Neither the name of the developer nor the names of its contributors may be
1754s       used to endorse or promote products derived from this software without
1754s       specific prior written permission.
1754s     
1754s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1754s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1754s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1754s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1754s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1754s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1754s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1754s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1754s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1754s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1754s ----------------------------------------------------------------------
1754s     APBS uses FETK (the Finite Element ToolKit) to solve the
1754s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1754s     of finite element modeling class libraries developed by the Michael Holst
1754s     research group and written in an object-oriented form of C.  FEtk is
1754s     designed to solve general coupled systems of nonlinear partial differential
1754s     equations using adaptive finite element methods, inexact Newton methods,
1754s     and algebraic multilevel methods.  More information about FEtk may be found
1754s     at <http://www.FEtk.ORG>.
1754s -------Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01)
1754s *** PASSED ***
1754s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02)
1754s *** PASSED ***
1754s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01)
1754s *** PASSED ***
1754s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02)
1754s *** PASSED ***
1754s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04)
1754s *** PASSED ***
1754s Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01)
1754s *** PASSED ***
1754s Elapsed time: 37.563129 seconds
1754s --------------------------------------------------------------------------------
1754s --------------------------------------------------------------------------------
1754s Testing input file 1d7h-dmso-smol.in
1754s 
1754s ---------------------------------------------------------------
1754s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1754s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1754s     which has been modified by Patrice Koehl
1754s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1754s     memory usage when solving the Poisson-Boltzmann equation.
1754s ----------------------------------------------------------------------
1754s     Please cite your use of APBS as:
1754s 
1754s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1754s     nanosystems: application to microtubules and the ribosome. Proc.
1754s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1754s     
1754s 
1754s This executable compiled on Mar  2 2024 at 20:11:10
1754s 
1754s Parsing input file 1d7h-dmso-mol.in...
1754s rank 0 size 1...
1754s Parsed input file.
1754s Got paths for 3 molecules
1754s Reading PQR-format atom data from 1d7h-dmso-complex.pqr.
1754s asc_getToken: Error occurred (bailing out).
1754s Vio_scanf: Format problem with input.
1754s   1673 atoms
1754s   Centered at (2.587e+01, 1.835e+01, 1.911e+01)
1754s   Net charge 9.91e-01 e
1754s Reading PQR-format atom data from dmso-min.pqr.
1754s asc_getToken: Error occurred (bailing out).
1754s Vio_scanf: Format problem with input.
1754s   10 atoms
1754s   Centered at (1.775e+01, 1.777e+01, 2.049e+01)
1754s   Net charge 2.78e-17 e
1754s Reading PQR-format atom data from 1d7h-min.pqr.
1754s   1663 atoms
1754s   Centered at (2.587e+01, 1.835e+01, 1.911e+01)
1754s   Net charge 9.91e-01 e
1754s Preparing to run 12 PBE calculations.
1754s ----------------------------------------
1754s CALCULATION #1 (complex-solv-coarse): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  30.4176 A
1754s   Current memory usage:  102.625 MB total, 102.625 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 1.500 x 1.500 x 1.500
1754s   Grid lengths: 96.000 x 96.000 x 96.000
1754s   Grid center: (25.875, 18.349, 19.112)
1754s   Multigrid levels: 5
1754s   Molecule ID: 1
1754s   Linearized traditional PBE
1754s   Multiple Debye-Huckel sphere boundary conditions
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 78.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 1.060899690259E+04 kJ/mol
1754s   Calculating forces...
1754s [focusFillBound()]: WARNING:
1754s     Unusually large potential values
1754s     detected on the focusing boundary!
1754s     Convergence not guaranteed for NPBE/NRPBE calculations!
1754s 
1754s ----------------------------------------
1754s CALCULATION #2 (complex-solv-fine): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  30.4176 A
1754s   Current memory usage:  102.625 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 0.225 x 0.225 x 0.225
1754s   Grid lengths: 14.400 x 14.400 x 14.400
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 1
1754s   Linearized traditional PBE
1754s   Boundary conditions from focusing
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 78.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 4.276523673491E+04 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s CALCULATION #3 (complex-ref-coarse): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  4.87072 A
1754s   Current memory usage:  102.625 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 1.500 x 1.500 x 1.500
1754s   Grid lengths: 96.000 x 96.000 x 96.000
1754s   Grid center: (25.875, 18.349, 19.112)
1754s   Multigrid levels: 5
1754s   Molecule ID: 1
1754s   Linearized traditional PBE
1754s   Multiple Debye-Huckel sphere boundary conditions
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 2.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 1.399234956777E+04 kJ/mol
1754s   Calculating forces...
1754s [focusFillBound()]: WARNING:
1754s     Unusually large potential values
1754s     detected on the focusing boundary!
1754s     Convergence not guaranteed for NPBE/NRPBE calculations!
1754s 
1754s ----------------------------------------
1754s CALCULATION #4 (complex-ref-fine): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  4.87072 A
1754s   Current memory usage:  102.625 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 0.225 x 0.225 x 0.225
1754s   Grid lengths: 14.400 x 14.400 x 14.400
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 1
1754s   Linearized traditional PBE
1754s   Boundary conditions from focusing
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 2.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 4.610066575192E+04 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s CALCULATION #5 (dmso-solv-coarse): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  30.4176 A
1754s   Current memory usage:  62.396 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 1.500 x 1.500 x 1.500
1754s   Grid lengths: 96.000 x 96.000 x 96.000
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 2
1754s   Linearized traditional PBE
1754s   Multiple Debye-Huckel sphere boundary conditions
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 78.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 3.961107503213E+01 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s CALCULATION #6 (dmso-solv-fine): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  30.4176 A
1754s   Current memory usage:  62.396 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 0.225 x 0.225 x 0.225
1754s   Grid lengths: 14.400 x 14.400 x 14.400
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 2
1754s   Linearized traditional PBE
1754s   Boundary conditions from focusing
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 78.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 7.121048606059E+02 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s CALCULATION #7 (dmso-ref-coarse): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  4.87072 A
1754s   Current memory usage:  62.396 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 1.500 x 1.500 x 1.500
1754s   Grid lengths: 96.000 x 96.000 x 96.000
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 2
1754s   Linearized traditional PBE
1754s   Multiple Debye-Huckel sphere boundary conditions
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 2.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 6.751571424823E+01 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s CALCULATION #8 (dmso-ref-fine): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  4.87072 A
1754s   Current memory usage:  62.396 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 0.225 x 0.225 x 0.225
1754s   Grid lengths: 14.400 x 14.400 x 14.400
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 2
1754s   Linearized traditional PBE
1754s   Boundary conditions from focusing
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 2.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 7.339101343121E+02 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  30.4176 A
1754s   Current memory usage:  102.404 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 1.500 x 1.500 x 1.500
1754s   Grid lengths: 96.000 x 96.000 x 96.000
1754s   Grid center: (25.875, 18.349, 19.112)
1754s   Multigrid levels: 5
1754s   Molecule ID: 3
1754s   Linearized traditional PBE
1754s   Multiple Debye-Huckel sphere boundary conditions
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 78.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 1.058410584089E+04 kJ/mol
1754s   Calculating forces...
1754s [focusFillBound()]: WARNING:
1754s     Unusually large potential values
1754s     detected on the focusing boundary!
1754s     Convergence not guaranteed for NPBE/NRPBE calculations!
1754s 
1754s ----------------------------------------
1754s CALCULATION #10 (1d7h-solv-fine): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  30.4176 A
1754s   Current memory usage:  102.404 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 0.225 x 0.225 x 0.225
1754s   Grid lengths: 14.400 x 14.400 x 14.400
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 3
1754s   Linearized traditional PBE
1754s   Boundary conditions from focusing
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 78.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 4.205385249581E+04 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  4.87072 A
1754s   Current memory usage:  102.404 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 1.500 x 1.500 x 1.500
1754s   Grid lengths: 96.000 x 96.000 x 96.000
1754s   Grid center: (25.875, 18.349, 19.112)
1754s   Multigrid levels: 5
1754s   Molecule ID: 3
1754s   Linearized traditional PBE
1754s   Multiple Debye-Huckel sphere boundary conditions
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 2.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 1.395961902233E+04 kJ/mol
1754s   Calculating forces...
1754s [focusFillBound()]: WARNING:
1754s     Unusually large potential values
1754s     detected on the focusing boundary!
1754s     Convergence not guaranteed for NPBE/NRPBE calculations!
1754s 
1754s ----------------------------------------
1754s CALCULATION #12 (1d7h-ref-fine): MULTIGRID
1754s   Setting up problem...
1754s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1754s   Debye length:  4.87072 A
1754s   Current memory usage:  102.404 MB total, 182.834 MB high water
1754s   Using linear spline charge discretization.
1754s   Grid dimensions: 65 x 65 x 65
1754s   Grid spacings: 0.225 x 0.225 x 0.225
1754s   Grid lengths: 14.400 x 14.400 x 14.400
1754s   Grid center: (17.751, 17.770, 20.492)
1754s   Multigrid levels: 5
1754s   Molecule ID: 3
1754s   Linearized traditional PBE
1754s   Boundary conditions from focusing
1754s   2 ion species (0.010 M ionic strength):
1754s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1754s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1754s   Solute dielectric: 2.000
1754s   Solvent dielectric: 2.000
1754s   Using "molecular" surface definition; no smoothing
1754s   Solvent probe radius: 0.000 A
1754s   Temperature:  300.000 K
1754s   Electrostatic energies will be calculated
1754s   Total electrostatic energy = 4.538248433997E+04 kJ/mol
1754s   Calculating forces...
1754s ----------------------------------------
1754s PRINT STATEMENTS
1754s 
1754s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
1754s   Local net energy (PE 0) = -3.335429017008E+03 kJ/mol
1754s   Global net ELEC energy = -3.335429017008E+03 kJ/mol
1754s 
1754s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end
1754s   Local net energy (PE 0) = -2.180527370616E+01 kJ/mol
1754s   Global net ELEC energy = -2.180527370616E+01 kJ/mol
1754s 
1754s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end
1754s   Local net energy (PE 0) = -3.328631844166E+03 kJ/mol
1754s   Global net ELEC energy = -3.328631844166E+03 kJ/mol
1754s 
1754s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end
1754s   Local net energy (PE 0) = 1.500810086371E+01 kJ/mol
1754s   Global net ELEC energy = 1.500810086371E+01 kJ/mol
1754s ----------------------------------------
1754s CLEANING UP AND SHUTTING DOWN...
1754s Destroying force arrays.
1754s No energy arrays to destroy.
1754s Destroying multigrid structures.
1754s Destroying finite element structures.
1754s Destroying 3 molecules
1754s Final memory usage:  0.001 MB total, 182.834 MB high water
1754s 
1754s 
1754s Thanks for using APBS!
1754s 
1786s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01)
1786s *** PASSED ***
1786s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02)
1786s *** PASSED ***
1786s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01)
1786s *** PASSED ***
1786s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02)
1786s *** PASSED ***
1786s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04)
1786s *** PASSED ***
1786s Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01)
1786s *** PASSED ***
1786s Checking for intermediate energies in input file 1d7h-dmso-mol.out
1786s EXPECTED COMPUTED: 16
1786s EXPECTED EXPECTED: 16
1786s COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086371]
1786s EXPECTED: ['1.060899690259E+04', '4.276523673491E+04', '1.399234956777E+04', '4.610066575192E+04', '3.961107503213E+01', '7.121048606059E+02', '6.751571424823E+01', '7.339101343121E+02', '1.058410584089E+04', '4.205385249581E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.500810086371E+01']
1786s COMPUTED RESULT 10608.99690259
1786s COMPUTED RESULT 42765.23673491
1786s COMPUTED RESULT 13992.34956777
1786s COMPUTED RESULT 46100.66575192
1786s COMPUTED RESULT 39.61107503213
1786s COMPUTED RESULT 712.1048606059
1786s COMPUTED RESULT 67.51571424823
1786s COMPUTED RESULT 733.9101343121
1786s COMPUTED RESULT 10584.10584089
1786s COMPUTED RESULT 42053.85249581
1786s COMPUTED RESULT 13959.61902233
1786s COMPUTED RESULT 45382.48433997
1786s COMPUTED RESULT -3335.429017008
1786s COMPUTED RESULT -21.80527370616
1786s COMPUTED RESULT -3328.631844166
1786s COMPUTED RESULT 15.00810086371
1786s BINARY:  /usr/bin/apbs
1786s INPUT:   1d7h-dmso-smol.in
1786s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in']
1786s asc_getToken: Error occurred (bailing out).
1786s Vio_scanf: Format problem with input.
1786s 
1786s 
1786s ----------------------------------------------------------------------
1786s     APBS -- Adaptive Poisson-Boltzmann Solver
1786s     Version APBS 3.4.1
1786s     
1786s     Nathan A. Baker (nathan.baker@pnnl.gov)
1786s     Pacific Northwest National Laboratory
1786s     
1786s     Additional contributing authors listed in the code documentation.
1786s     
1786s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1786s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1786s     Northwest Division for the U.S. Department of Energy.
1786s     
1786s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1786s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1786s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1786s     Portions Copyright (c) 1995, Michael Holst.
1786s     All rights reserved.
1786s     
1786s     Redistribution and use in source and binary forms, with or without
1786s     modification, are permitted provided that the following conditions are met:
1786s     
1786s     * Redistributions of source code must retain the above copyright notice, this
1786s       list of conditions and the following disclaimer.
1786s     
1786s     * Redistributions in binary form must reproduce the above copyright notice,
1786s       this list of conditions and the following disclaimer in the documentation
1786s       and/or other materials provided with the distribution.
1786s     
1786s     * Neither the name of the developer nor the names of its contributors may be
1786s       used to endorse or promote products derived from this software without
1786s       specific prior written permission.
1786s     
1786s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1786s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1786s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1786s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1786s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1786s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1786s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1786s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1786s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1786s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1786s ----------------------------------------------------------------------
1786s     APBS uses FETK (the Finite Element ToolKit) to solve the
1786s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1786s     of finite element modeling class libraries developed by the Michael Holst
1786s     research group and written in an object-oriented form of C.  FEtk is
1786s     designed to solve general coupled systems of nonlinear partial differential
1786s     equations using adaptive finite element methods, inexact Newton methods,
1786s     and algebraic multilevel methods.  More information about FEtk may be found
1786s     at <http://www.FEtk.ORG>.
1786s ----------------------------------------------------------------------
1786s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1786s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1786s     which has been modified by Patrice Koehl
1786s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1786s     memory usage when solving the Poisson-Boltzmann equation.
1786s ----------------------------------------------------------------------
1786s     Please cite your use of APBS as:
1786s 
1786s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1786s     nanosystems: application to microtubules and the ribosome. Proc.
1786s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1786s     
1786s 
1786s This executable compiled on Mar  2 2024 at 20:11:10
1786s 
1786s Parsing input file 1d7h-dmso-smol.in...
1786s rank 0 size 1...
1786s Parsed input file.
1786s Got paths for 3 molecules
1786s Reading PQR-format atom data from 1d7h-dmso-complex.pqr.
1786s asc_getToken: Error occurred (bailing out).
1786s Vio_scanf: Format problem with input.
1786s   1673 atoms
1786s   Centered at (2.587e+01, 1.835e+01, 1.911e+01)
1786s   Net charge 9.91e-01 e
1786s Reading PQR-format atom data from dmso-min.pqr.
1786s asc_getToken: Error occurred (bailing out).
1786s Vio_scanf: Format problem with input.
1786s   10 atoms
1786s   Centered at (1.775e+01, 1.777e+01, 2.049e+01)
1786s   Net charge 2.78e-17 e
1786s Reading PQR-format atom data from 1d7h-min.pqr.
1786s   1663 atoms
1786s   Centered at (2.587e+01, 1.835e+01, 1.911e+01)
1786s   Net charge 9.91e-01 e
1786s Preparing to run 12 PBE calculations.
1786s ----------------------------------------
1786s CALCULATION #1 (complex-solv-coarse): MULTIGRID
1786s   Setting up problem...
1786s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1786s   Debye length:  30.4176 A
1786s   Current memory usage:  102.625 MB total, 102.625 MB high water
1786s   Using linear spline charge discretization.
1786s   Grid dimensions: 65 x 65 x 65
1786s   Grid spacings: 1.500 x 1.500 x 1.500
1786s   Grid lengths: 96.000 x 96.000 x 96.000
1786s   Grid center: (25.875, 18.349, 19.112)
1786s   Multigrid levels: 5
1786s   Molecule ID: 1
1786s   Linearized traditional PBE
1786s   Multiple Debye-Huckel sphere boundary conditions
1786s   2 ion species (0.010 M ionic strength):
1786s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1786s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1786s   Solute dielectric: 2.000
1786s   Solvent dielectric: 78.000
1786s   Using "molecular" surface definition;harmonic average smoothing
1786s   Solvent probe radius: 0.000 A
1786s   Temperature:  300.000 K
1786s   Electrostatic energies will be calculated
1786s   Total electrostatic energy = 1.074948704824E+04 kJ/mol
1786s   Calculating forces...
1786s [focusFillBound()]: WARNING:
1786s     Unusually large potential values
1786s     detected on the focusing boundary!
1786s     Convergence not guaranteed for NPBE/NRPBE calculations!
1786s 
1786s ----------------------------------------
1786s CALCULATION #2 (complex-solv-fine): MULTIGRID
1786s   Setting up problem...
1786s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1786s   Debye length:  30.4176 A
1786s   Current memory usage:  102.625 MB total, 182.834 MB high water
1786s   Using linear spline charge discretization.
1786s   Grid dimensions: 65 x 65 x 65
1786s   Grid spacings: 0.225 x 0.225 x 0.225
1786s   Grid lengths: 14.400 x 14.400 x 14.400
1786s   Grid center: (17.751, 17.770, 20.492)
1786s   Multigrid levels: 5
1786s   Molecule ID: 1
1786s   Linearized traditional PBE
1786s   Boundary conditions from focusing
1786s   2 ion species (0.010 M ionic strength):
1786s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1786s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1786s   Solute dielectric: 2.000
1786s   Solvent dielectric: 78.000
1786s   Using "molecular" surface definition;harmonic average smoothing
1786s   Solvent probe radius: 0.000 A
1786s   Temperature:  300.000 K
1786s   Electrostatic energies will be calculated
1786s   Total electrostatic energy = 4.289487256481E+04 kJ/mol
1786s   Calculating forces...
1786s ----------------------------------------
1786s CALCULATION #3 (complex-ref-coarse): MULTIGRID
1786s   Setting up problem...
1786s Elapsed time: 32.834744 seconds
1786s --------------------------------------------------------------------------------
1786s --------------------------------------------------------------------------------
1786s Testing input file 1d7i-dss-mol.in
1786s 
1786s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1786s   Debye length:  4.87072 A
1786s   Current memory usage:  102.625 MB total, 182.834 MB high water
1786s   Using linear spline charge discretization.
1786s   Grid dimensions: 65 x 65 x 65
1786s   Grid spacings: 1.500 x 1.500 x 1.500
1786s   Grid lengths: 96.000 x 96.000 x 96.000
1786s   Grid center: (25.875, 18.349, 19.112)
1786s   Multigrid levels: 5
1786s   Molecule ID: 1
1786s   Linearized traditional PBE
1786s   Multiple Debye-Huckel sphere boundary conditions
1786s   2 ion species (0.010 M ionic strength):
1786s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1786s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1786s   Solute dielectric: 2.000
1786s   Solvent dielectric: 2.000
1786s   Using "molecular" surface definition;harmonic average smoothing
1786s   Solvent probe radius: 0.000 A
1786s   Temperature:  300.000 K
1786s   Electrostatic energies will be calculated
1786s   Total electrostatic energy = 1.399234956777E+04 kJ/mol
1786s   Calculating forces...
1786s [focusFillBound()]: WARNING:
1786s     Unusually large potential values
1786s     detected on the focusing boundary!
1786s     Convergence not guaranteed for NPBE/NRPBE calculations!
1786s 
1786s ----------------------------------------
1786s CALCULATION #4 (complex-ref-fine): MULTIGRID
1786s   Setting up problem...
1786s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1786s   Debye length:  4.87072 A
1786s   Current memory usage:  102.625 MB total, 182.834 MB high water
1786s   Using linear spline charge discretization.
1786s   Grid dimensions: 65 x 65 x 65
1786s   Grid spacings: 0.225 x 0.225 x 0.225
1786s   Grid lengths: 14.400 x 14.400 x 14.400
1786s   Grid center: (17.751, 17.770, 20.492)
1786s   Multigrid levels: 5
1786s   Molecule ID: 1
1786s   Linearized traditional PBE
1786s   Boundary conditions from focusing
1786s   2 ion species (0.010 M ionic strength):
1786s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1786s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1786s   Solute dielectric: 2.000
1786s   Solvent dielectric: 2.000
1786s   Using "molecular" surface definition;harmonic average smoothing
1786s   Solvent probe radius: 0.000 A
1786s   Temperature:  300.000 K
1786s   Electrostatic energies will be calculated
1786s   Total electrostatic energy = 4.610066575192E+04 kJ/mol
1786s   Calculating forces...
1786s ----------------------------------------
1786s CALCULATION #5 (dmso-solv-coarse): MULTIGRID
1786s   Setting up problem...
1786s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1786s   Debye length:  30.4176 A
1786s   Current memory usage:  62.396 MB total, 182.834 MB high water
1786s   Using linear spline charge discretization.
1786s   Grid dimensions: 65 x 65 x 65
1786s   Grid spacings: 1.500 x 1.500 x 1.500
1786s   Grid lengths: 96.000 x 96.000 x 96.000
1786s   Grid center: (17.751, 17.770, 20.492)
1786s   Multigrid levels: 5
1786s   Molecule ID: 2
1786s   Linearized traditional PBE
1786s   Multiple Debye-Huckel sphere boundary conditions
1786s   2 ion species (0.010 M ionic strength):
1786s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1786s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1786s   Solute dielectric: 2.000
1786s   Solvent dielectric: 78.000
1786s   Using "molecular" surface definition;harmonic average smoothing
1786s   Solvent probe radius: 0.000 A
1786s   Temperature:  300.000 K
1786s   Electrostatic energies will be calculated
1786s   Total electrostatic energy = 3.719709905887E+01 kJ/mol
1786s   Calculating forces...
1786s ----------------------------------------
1786s CALCULATION #6 (dmso-solv-fine): MULTIGRID
1786s   Setting up problem...
1786s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1786s   Debye length:  30.4176 A
1786s   Current memory usage:  62.396 MB total, 182.834 MB high water
1786s   Using linear spline charge discretization.
1786s   Grid dimensions: 65 x 65 x 65
1786s   Grid spacings: 0.225 x 0.225 x 0.225
1786s   Grid lengths: 14.400 x 14.400 x 14.400
1786s   Grid center: (17.751, 17.770, 20.492)
1786s   Multigrid levels: 5
1786s   Molecule ID: 2
1786s   Linearized traditional PBE
1786s   Boundary conditions from focusing
1786s   2 ion species (0.010 M ionic strength):
1786s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1786s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1786s   Solute dielectric: 2.000
1786s   Solvent dielectric: 78.000
1786s   Using "molecular" surface definition;harmonic average smoothing
1786s   Solvent probe radius: 0.000 A
1786s   Temperature:  300.000 K
1787s   Electrostatic energies will be calculated
1787s   Total electrostatic energy = 7.125747080979E+02 kJ/mol
1787s   Calculating forces...
1787s ----------------------------------------
1787s CALCULATION #7 (dmso-ref-coarse): MULTIGRID
1787s   Setting up problem...
1787s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1787s   Debye length:  4.87072 A
1787s   Current memory usage:  62.396 MB total, 182.834 MB high water
1787s   Using linear spline charge discretization.
1787s   Grid dimensions: 65 x 65 x 65
1787s   Grid spacings: 1.500 x 1.500 x 1.500
1787s   Grid lengths: 96.000 x 96.000 x 96.000
1787s   Grid center: (17.751, 17.770, 20.492)
1787s   Multigrid levels: 5
1787s   Molecule ID: 2
1787s   Linearized traditional PBE
1787s   Multiple Debye-Huckel sphere boundary conditions
1787s   2 ion species (0.010 M ionic strength):
1787s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1787s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1787s   Solute dielectric: 2.000
1787s   Solvent dielectric: 2.000
1787s   Using "molecular" surface definition;harmonic average smoothing
1787s   Solvent probe radius: 0.000 A
1787s   Temperature:  300.000 K
1787s   Electrostatic energies will be calculated
1787s   Total electrostatic energy = 6.751571424823E+01 kJ/mol
1787s   Calculating forces...
1787s ----------------------------------------
1787s CALCULATION #8 (dmso-ref-fine): MULTIGRID
1787s   Setting up problem...
1787s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1787s   Debye length:  4.87072 A
1787s   Current memory usage:  62.396 MB total, 182.834 MB high water
1787s   Using linear spline charge discretization.
1787s   Grid dimensions: 65 x 65 x 65
1787s   Grid spacings: 0.225 x 0.225 x 0.225
1787s   Grid lengths: 14.400 x 14.400 x 14.400
1787s   Grid center: (17.751, 17.770, 20.492)
1787s   Multigrid levels: 5
1787s   Molecule ID: 2
1787s   Linearized traditional PBE
1787s   Boundary conditions from focusing
1787s   2 ion species (0.010 M ionic strength):
1787s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1787s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1787s   Solute dielectric: 2.000
1787s   Solvent dielectric: 2.000
1787s   Using "molecular" surface definition;harmonic average smoothing
1787s   Solvent probe radius: 0.000 A
1787s   Temperature:  300.000 K
1787s   Electrostatic energies will be calculated
1787s   Total electrostatic energy = 7.339101343121E+02 kJ/mol
1787s   Calculating forces...
1787s ----------------------------------------
1787s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID
1787s   Setting up problem...
1787s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1787s   Debye length:  30.4176 A
1787s   Current memory usage:  102.404 MB total, 182.834 MB high water
1787s   Using linear spline charge discretization.
1787s   Grid dimensions: 65 x 65 x 65
1787s   Grid spacings: 1.500 x 1.500 x 1.500
1787s   Grid lengths: 96.000 x 96.000 x 96.000
1787s   Grid center: (25.875, 18.349, 19.112)
1787s   Multigrid levels: 5
1787s   Molecule ID: 3
1787s   Linearized traditional PBE
1787s   Multiple Debye-Huckel sphere boundary conditions
1787s   2 ion species (0.010 M ionic strength):
1787s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1787s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1787s   Solute dielectric: 2.000
1787s   Solvent dielectric: 78.000
1787s   Using "molecular" surface definition;harmonic average smoothing
1787s   Solvent probe radius: 0.000 A
1787s   Temperature:  300.000 K
1787s   Electrostatic energies will be calculated
1787s   Total electrostatic energy = 1.071654753674E+04 kJ/mol
1787s   Calculating forces...
1787s [focusFillBound()]: WARNING:
1787s     Unusually large potential values
1787s     detected on the focusing boundary!
1787s     Convergence not guaranteed for NPBE/NRPBE calculations!
1787s 
1787s ----------------------------------------
1787s CALCULATION #10 (1d7h-solv-fine): MULTIGRID
1787s   Setting up problem...
1787s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1787s   Debye length:  30.4176 A
1787s   Current memory usage:  102.404 MB total, 182.834 MB high water
1787s   Using linear spline charge discretization.
1787s   Grid dimensions: 65 x 65 x 65
1787s   Grid spacings: 0.225 x 0.225 x 0.225
1787s   Grid lengths: 14.400 x 14.400 x 14.400
1787s   Grid center: (17.751, 17.770, 20.492)
1787s   Multigrid levels: 5
1787s   Molecule ID: 3
1787s   Linearized traditional PBE
1787s   Boundary conditions from focusing
1787s   2 ion species (0.010 M ionic strength):
1787s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1787s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1787s   Solute dielectric: 2.000
1787s   Solvent dielectric: 78.000
1787s   Using "molecular" surface definition;harmonic average smoothing
1787s   Solvent probe radius: 0.000 A
1787s   Temperature:  300.000 K
1787s   Electrostatic energies will be calculated
1787s   Total electrostatic energy = 4.218178203716E+04 kJ/mol
1787s   Calculating forces...
1787s ----------------------------------------
1787s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID
1787s   Setting up problem...
1787s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1787s   Debye length:  4.87072 A
1787s   Current memory usage:  102.404 MB total, 182.834 MB high water
1787s   Using linear spline charge discretization.
1787s   Grid dimensions: 65 x 65 x 65
1787s   Grid spacings: 1.500 x 1.500 x 1.500
1787s   Grid lengths: 96.000 x 96.000 x 96.000
1787s   Grid center: (25.875, 18.349, 19.112)
1787s   Multigrid levels: 5
1787s   Molecule ID: 3
1787s   Linearized traditional PBE
1787s   Multiple Debye-Huckel sphere boundary conditions
1787s   2 ion species (0.010 M ionic strength):
1787s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1787s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1787s   Solute dielectric: 2.000
1787s   Solvent dielectric: 2.000
1787s   Using "molecular" surface definition;harmonic average smoothing
1787s   Solvent probe radius: 0.000 A
1787s   Temperature:  300.000 K
1787s   Electrostatic energies will be calculated
1787s   Total electrostatic energy = 1.395961902233E+04 kJ/mol
1787s   Calculating forces...
1787s [focusFillBound()]: WARNING:
1787s     Unusually large potential values
1787s     detected on the focusing boundary!
1787s     Convergence not guaranteed for NPBE/NRPBE calculations!
1787s 
1787s ----------------------------------------
1787s CALCULATION #12 (1d7h-ref-fine): MULTIGRID
1787s   Setting up problem...
1787s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1787s   Debye length:  4.87072 A
1787s   Current memory usage:  102.404 MB total, 182.834 MB high water
1787s   Using linear spline charge discretization.
1787s   Grid dimensions: 65 x 65 x 65
1787s   Grid spacings: 0.225 x 0.225 x 0.225
1787s   Grid lengths: 14.400 x 14.400 x 14.400
1787s   Grid center: (17.751, 17.770, 20.492)
1787s   Multigrid levels: 5
1787s   Molecule ID: 3
1787s   Linearized traditional PBE
1787s   Boundary conditions from focusing
1787s   2 ion species (0.010 M ionic strength):
1787s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1787s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1787s   Solute dielectric: 2.000
1787s   Solvent dielectric: 2.000
1787s   Using "molecular" surface definition;harmonic average smoothing
1787s   Solvent probe radius: 0.000 A
1787s   Temperature:  300.000 K
1787s   Electrostatic energies will be calculated
1787s   Total electrostatic energy = 4.538248433997E+04 kJ/mol
1787s   Calculating forces...
1787s ----------------------------------------
1787s PRINT STATEMENTS
1787s 
1787s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
1787s   Local net energy (PE 0) = -3.205793187109E+03 kJ/mol
1787s   Global net ELEC energy = -3.205793187109E+03 kJ/mol
1787s 
1787s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end
1787s   Local net energy (PE 0) = -2.133542621421E+01 kJ/mol
1787s   Global net ELEC energy = -2.133542621421E+01 kJ/mol
1787s 
1787s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end
1787s   Local net energy (PE 0) = -3.200702302816E+03 kJ/mol
1787s   Global net ELEC energy = -3.200702302816E+03 kJ/mol
1787s 
1787s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end
1787s   Local net energy (PE 0) = 1.624454192073E+01 kJ/mol
1787s   Global net ELEC energy = 1.624454192073E+01 kJ/mol
1787s ----------------------------------------
1787s CLEANING UP AND SHUTTING DOWN...
1787s Destroying force arrays.
1787s No energy arrays to destroy.
1787s Destroying multigrid structures.
1787s Destroying finite element structures.
1787s Destroying 3 molecules
1787s Final memory usage:  0.001 MB total, 182.834 MB high water
1787s 
1787s 
1787s Thanks for using APBS!
1787s 
1833s Checking for intermediate energies in input file 1d7h-dmso-smol.out
1833s EXPECTED COMPUTED: 16
1833s EXPECTED EXPECTED: 16
1833s COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192073]
1833s EXPECTED: ['1.074948704824E+04', '4.289487256481E+04', '1.399234956777E+04', '4.610066575192E+04', '3.719709905887E+01', '7.125747080979E+02', '6.751571424823E+01', '7.339101343121E+02', '1.071654753674E+04', '4.218178203716E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.624454192072E+01']
1833s COMPUTED RESULT 10749.48704824
1833s COMPUTED RESULT 42894.87256481
1833s COMPUTED RESULT 13992.34956777
1833s COMPUTED RESULT 46100.66575192
1833s COMPUTED RESULT 37.19709905887
1833s COMPUTED RESULT 712.5747080979
1833s COMPUTED RESULT 67.51571424823
1833s COMPUTED RESULT 733.9101343121
1833s COMPUTED RESULT 10716.54753674
1833s COMPUTED RESULT 42181.78203716
1833s COMPUTED RESULT 13959.61902233
1833s COMPUTED RESULT 45382.48433997
1833s COMPUTED RESULT -3205.793187109
1833s COMPUTED RESULT -21.33542621421
1833s COMPUTED RESULT -3200.702302816
1833s COMPUTED RESULT 16.24454192073
1833s BINARY:  /usr/bin/apbs
1833s INPUT:   1d7i-dss-mol.in
1833s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in']
1833s asc_getToken: Error occurred (bailing out).
1833s Vio_scanf: Format problem with input.
1833s 
1833s 
1833s ----------------------------------------------------------------------
1833s     APBS -- Adaptive Poisson-Boltzmann Solver
1833s     Version APBS 3.4.1
1833s     
1833s     Nathan A. Baker (nathan.baker@pnnl.gov)
1833s     Pacific Northwest National Laboratory
1833s     
1833s     Additional contributing authors listed in the code documentation.
1833s     
1833s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1833s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1833s     Northwest Division for the U.S. Department of Energy.
1833s     
1833s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1833s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1833s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1833s     Portions Copyright (c) 1995, Michael Holst.
1833s     All rights reserved.
1833s     
1833s     Redistribution and use in source and binary forms, with or without
1833s     modification, are permitted provided that the following conditions are met:
1833s     
1833s     * Redistributions of source code must retain the above copyright notice, this
1833s       list of conditions and the following disclaimer.
1833s     
1833s     * Redistributions in binary form must reproduce the above copyright notice,
1833s       this list of conditions and the following disclaimer in the documentation
1833s       and/or other materials provided with the distribution.
1833s     
1833s     * Neither the name of the developer nor the names of its contributors may be
1833s       used to endorse or promote products derived from this software without
1833s       specific prior written permission.
1833s     
1833s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1833s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1833s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1833s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1833s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1833s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1833s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1833s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1833s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1833s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1833s ----------------------------------------------------------------------
1833s     APBS uses FETK (the Finite Element ToolKit) to solve the
1833s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1833s     of finite element modeling class libraries developed by the Michael Holst
1833s     research group and written in an object-oriented form of C.  FEtk is
1833s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03)
1833s *** PASSED ***
1833s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04)
1833s *** PASSED ***
1833s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04)
1833s *** PASSED ***
1833s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04)
1833s *** PASSED ***
1833s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01)
1833s *** PASSED ***
1833s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03)
1833s *** PASSED ***
1833s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02)
1833s *** PASSED ***
1833s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03)
1833s *** PASSED ***
1833s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03)
1833s *** PASSED ***
1833s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04)
1833s *** PASSED ***
1833s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04)
1833s *** PASSED ***
1833s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04)
1833s *** PASSED ***
1833s Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01)
1833s *** PASSED ***
1833s Elapsed time: 46.511154 seconds
1833s --------------------------------------------------------------------------------
1833s --------------------------------------------------------------------------------
1833s Testing input file 1d7i-dss-smol.in
1833s 
1833s     designed to solve general coupled systems of nonlinear partial differential
1833s     equations using adaptive finite element methods, inexact Newton methods,
1833s     and algebraic multilevel methods.  More information about FEtk may be found
1833s     at <http://www.FEtk.ORG>.
1833s ----------------------------------------------------------------------
1833s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1833s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1833s     which has been modified by Patrice Koehl
1833s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1833s     memory usage when solving the Poisson-Boltzmann equation.
1833s ----------------------------------------------------------------------
1833s     Please cite your use of APBS as:
1833s 
1833s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1833s     nanosystems: application to microtubules and the ribosome. Proc.
1833s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1833s     
1833s 
1833s This executable compiled on Mar  2 2024 at 20:11:10
1833s 
1833s Parsing input file 1d7i-dss-mol.in...
1833s rank 0 size 1...
1833s Parsed input file.
1833s Got paths for 3 molecules
1833s Reading PQR-format atom data from 1d7i-dss-complex.pqr.
1833s asc_getToken: Error occurred (bailing out).
1833s Vio_scanf: Format problem with input.
1833s   1677 atoms
1833s   Centered at (2.526e+01, 1.899e+01, 1.912e+01)
1833s   Net charge 9.91e-01 e
1833s Reading PQR-format atom data from dss-min.pqr.
1833s asc_getToken: Error occurred (bailing out).
1833s Vio_scanf: Format problem with input.
1833s   14 atoms
1833s   Centered at (1.734e+01, 1.921e+01, 2.050e+01)
1833s   Net charge -8.33e-17 e
1833s Reading PQR-format atom data from 1d7i-min.pqr.
1833s   1663 atoms
1833s   Centered at (2.526e+01, 1.899e+01, 1.912e+01)
1833s   Net charge 9.91e-01 e
1833s Preparing to run 12 PBE calculations.
1833s ----------------------------------------
1833s CALCULATION #1 (complex-solv-coarse): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  30.4176 A
1833s   Current memory usage:  102.869 MB total, 102.869 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 1.500 x 1.500 x 1.500
1833s   Grid lengths: 96.000 x 96.000 x 96.000
1833s   Grid center: (25.264, 18.988, 19.122)
1833s   Multigrid levels: 5
1833s   Molecule ID: 1
1833s   Linearized traditional PBE
1833s   Multiple Debye-Huckel sphere boundary conditions
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 78.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 9.160578033846E+03 kJ/mol
1833s   Calculating forces...
1833s [focusFillBound()]: WARNING:
1833s     Unusually large potential values
1833s     detected on the focusing boundary!
1833s     Convergence not guaranteed for NPBE/NRPBE calculations!
1833s 
1833s ----------------------------------------
1833s CALCULATION #2 (complex-solv-fine): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  30.4176 A
1833s   Current memory usage:  102.869 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 0.225 x 0.225 x 0.225
1833s   Grid lengths: 14.400 x 14.400 x 14.400
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 1
1833s   Linearized traditional PBE
1833s   Boundary conditions from focusing
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 78.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 3.955701871716E+04 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s CALCULATION #3 (complex-ref-coarse): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  4.87072 A
1833s   Current memory usage:  102.869 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 1.500 x 1.500 x 1.500
1833s   Grid lengths: 96.000 x 96.000 x 96.000
1833s   Grid center: (25.264, 18.988, 19.122)
1833s   Multigrid levels: 5
1833s   Molecule ID: 1
1833s   Linearized traditional PBE
1833s   Multiple Debye-Huckel sphere boundary conditions
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 2.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 1.264965939588E+04 kJ/mol
1833s   Calculating forces...
1833s [focusFillBound()]: WARNING:
1833s     Unusually large potential values
1833s     detected on the focusing boundary!
1833s     Convergence not guaranteed for NPBE/NRPBE calculations!
1833s 
1833s ----------------------------------------
1833s CALCULATION #4 (complex-ref-fine): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  4.87072 A
1833s   Current memory usage:  102.869 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 0.225 x 0.225 x 0.225
1833s   Grid lengths: 14.400 x 14.400 x 14.400
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 1
1833s   Linearized traditional PBE
1833s   Boundary conditions from focusing
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 2.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 4.301801664829E+04 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s CALCULATION #5 (dss-solv-coarse): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  30.4176 A
1833s   Current memory usage:  62.482 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 1.500 x 1.500 x 1.500
1833s   Grid lengths: 96.000 x 96.000 x 96.000
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 2
1833s   Linearized traditional PBE
1833s   Multiple Debye-Huckel sphere boundary conditions
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 78.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 9.431133325426E+01 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s CALCULATION #6 (dss-solv-fine): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  30.4176 A
1833s   Current memory usage:  62.482 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 0.225 x 0.225 x 0.225
1833s   Grid lengths: 14.400 x 14.400 x 14.400
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 2
1833s   Linearized traditional PBE
1833s   Boundary conditions from focusing
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 78.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 1.677348113184E+03 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s CALCULATION #7 (dss-ref-coarse): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  4.87072 A
1833s   Current memory usage:  62.482 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 1.500 x 1.500 x 1.500
1833s   Grid lengths: 96.000 x 96.000 x 96.000
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 2
1833s   Linearized traditional PBE
1833s   Multiple Debye-Huckel sphere boundary conditions
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 2.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 1.171079106781E+02 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s CALCULATION #8 (dss-ref-fine): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  4.87072 A
1833s   Current memory usage:  62.482 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 0.225 x 0.225 x 0.225
1833s   Grid lengths: 14.400 x 14.400 x 14.400
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 2
1833s   Linearized traditional PBE
1833s   Boundary conditions from focusing
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 2.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 1.697869784185E+03 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  30.4176 A
1833s   Current memory usage:  102.566 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 1.500 x 1.500 x 1.500
1833s   Grid lengths: 96.000 x 96.000 x 96.000
1833s   Grid center: (25.264, 18.988, 19.122)
1833s   Multigrid levels: 5
1833s   Molecule ID: 3
1833s   Linearized traditional PBE
1833s   Multiple Debye-Huckel sphere boundary conditions
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 78.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 9.040108332204E+03 kJ/mol
1833s   Calculating forces...
1833s [focusFillBound()]: WARNING:
1833s     Unusually large potential values
1833s     detected on the focusing boundary!
1833s     Convergence not guaranteed for NPBE/NRPBE calculations!
1833s 
1833s ----------------------------------------
1833s CALCULATION #10 (1d7i-solv-fine): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  30.4176 A
1833s   Current memory usage:  102.566 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 0.225 x 0.225 x 0.225
1833s   Grid lengths: 14.400 x 14.400 x 14.400
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 3
1833s   Linearized traditional PBE
1833s   Boundary conditions from focusing
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 78.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 3.787747796627E+04 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  4.87072 A
1833s   Current memory usage:  102.566 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 1.500 x 1.500 x 1.500
1833s   Grid lengths: 96.000 x 96.000 x 96.000
1833s   Grid center: (25.264, 18.988, 19.122)
1833s   Multigrid levels: 5
1833s   Molecule ID: 3
1833s   Linearized traditional PBE
1833s   Multiple Debye-Huckel sphere boundary conditions
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 2.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 1.252495566243E+04 kJ/mol
1833s   Calculating forces...
1833s [focusFillBound()]: WARNING:
1833s     Unusually large potential values
1833s     detected on the focusing boundary!
1833s     Convergence not guaranteed for NPBE/NRPBE calculations!
1833s 
1833s ----------------------------------------
1833s CALCULATION #12 (1d7i-ref-fine): MULTIGRID
1833s   Setting up problem...
1833s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1833s   Debye length:  4.87072 A
1833s   Current memory usage:  102.566 MB total, 183.200 MB high water
1833s   Using linear spline charge discretization.
1833s   Grid dimensions: 65 x 65 x 65
1833s   Grid spacings: 0.225 x 0.225 x 0.225
1833s   Grid lengths: 14.400 x 14.400 x 14.400
1833s   Grid center: (17.340, 19.211, 20.503)
1833s   Multigrid levels: 5
1833s   Molecule ID: 3
1833s   Linearized traditional PBE
1833s   Boundary conditions from focusing
1833s   2 ion species (0.010 M ionic strength):
1833s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1833s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1833s   Solute dielectric: 2.000
1833s   Solvent dielectric: 2.000
1833s   Using "molecular" surface definition; no smoothing
1833s   Solvent probe radius: 0.000 A
1833s   Temperature:  300.000 K
1833s   Electrostatic energies will be calculated
1833s   Total electrostatic energy = 4.133237922574E+04 kJ/mol
1833s   Calculating forces...
1833s ----------------------------------------
1833s PRINT STATEMENTS
1833s 
1833s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
1833s   Local net energy (PE 0) = -3.460997931137E+03 kJ/mol
1833s   Global net ELEC energy = -3.460997931137E+03 kJ/mol
1833s 
1833s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end
1833s   Local net energy (PE 0) = -2.052167100108E+01 kJ/mol
1833s   Global net ELEC energy = -2.052167100108E+01 kJ/mol
1833s 
1833s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end
1833s   Local net energy (PE 0) = -3.454901259473E+03 kJ/mol
1833s   Global net ELEC energy = -3.454901259473E+03 kJ/mol
1833s 
1833s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end
1833s   Local net energy (PE 0) = 1.442499933668E+01 kJ/mol
1833s   Global net ELEC energy = 1.442499933668E+01 kJ/mol
1833s ----------------------------------------
1833s CLEANING UP AND SHUTTING DOWN...
1833s Destroying force arrays.
1833s No energy arrays to destroy.
1833s Destroying multigrid structures.
1833s Destroying finite element structures.
1833s Destroying 3 molecules
1833s Final memory usage:  0.001 MB total, 183.200 MB high water
1833s 
1833s 
1833s Thanks for using APBS!
1833s 
1869s Checking for intermediate energies in input file 1d7i-dss-mol.out
1869s EXPECTED COMPUTED: 16
1869s EXPECTED EXPECTED: 16
1869s COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933668]
1869s EXPECTED: ['9.160578033846E+03', '3.955701871716E+04', '1.264965939588E+04', '4.301801664829E+04', '9.431133325426E+01', '1.677348113184E+03', '1.171079106781E+02', '1.697869784185E+03', '9.040108332204E+03', '3.787747796627E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.442500529301E+01']
1869s COMPUTED RESULT 9160.578033846
1869s COMPUTED RESULT 39557.01871716
1869s COMPUTED RESULT 12649.65939588
1869s COMPUTED RESULT 43018.01664829
1869s COMPUTED RESULT 94.31133325426
1869s COMPUTED RESULT 1677.348113184
1869s COMPUTED RESULT 117.1079106781
1869s COMPUTED RESULT 1697.869784185
1869s COMPUTED RESULT 9040.108332204
1869s COMPUTED RESULT 37877.47796627
1869s COMPUTED RESULT 12524.95566243
1869s COMPUTED RESULT 41332.37922574
1869s COMPUTED RESULT -3460.997931137
1869s COMPUTED RESULT -20.52167100108
1869s COMPUTED RESULT -3454.901259473
1869s COMPUTED RESULT 14.42499933668
1869s BINARY:  /usr/bin/apbs
1869s INPUT:   1d7i-dss-smol.in
1869s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in']
1869s asc_getToken: Error occurred (bailing out).
1869s Vio_scanf: Format problem with input.
1869s 
1869s 
1869s ----------------------------------------------------------------------
1869s     APBS -- Adaptive Poisson-Boltzmann Solver
1869s     Version APBS 3.4.1
1869s     
1869s     Nathan A. Baker (nathan.baker@pnnl.gov)
1869s     Pacific Northwest National Laboratory
1869s     
1869s     Additional contributing authors listed in the code documentation.
1869s     
1869s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1869s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1869s     Northwest Division for the U.S. Department of Energy.
1869s     
1869s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1869s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1869s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1869s     Portions Copyright (c) 1995, Michael Holst.
1869s     All rights reserved.
1869s     
1869s     Redistribution and use in source and binary forms, with or without
1869s     modification, are permitted provided that the following conditions are met:
1869s     
1869s     * Redistributions of source code must retain the above copyright notice, this
1869s       list of conditions and the following disclaimer.
1869s     
1869s     * Redistributions in binary form must reproduce the above copyright notice,
1869s       this list of conditions and the following disclaimer in the documentation
1869s       and/or other materials provided with the distribution.
1869s     
1869s     * Neither the name of the developer nor the names of its contributors may be
1869s       used to endorse or promote products derived from this software without
1869s       specific prior written permission.
1869s     
1869s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1869s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1869s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1869s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1869s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1869s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1869s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1869s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1869s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1869s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1869s ----------------------------------------------------------------------
1869s     APBS uses FETK (the Finite Element ToolKit) to solve the
1869s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1869s     of finite element modeling class libraries developed by the Michael Holst
1869s     research group and written in an object-oriented form of C.  FEtk is
1869s     designed to solve general coupled systems of nonlinear partial differential
1869s     equations using adaptive finite element methods, inexact Newton methods,
1869s     and algebraic multilevel methods.  More information about FEtk may be found
1869s     at <http://www.FEtk.ORG>.
1869s ----------------------------------------------------------------------
1869s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1869s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1869s     which has been modified by Patrice Koehl
1869s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1869s     memory usage when solving the Poisson-Boltzmann equation.
1869s ----------------------------------------------------------------------
1869s     Please cite your use of APBS as:
1869s 
1869s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1869s     nanosystems: application to microtubules and the ribosome. Proc.
1869s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1869s     
1869s 
1869s This executable compiled on Mar  2 2024 at 20:11:10
1869s 
1869s Parsing input file 1d7i-dss-smol.in...
1869s rank 0 size 1...
1869s Parsed input file.
1869s Got paths for 3 molecules
1869s Reading PQR-format atom data from 1d7i-dss-complex.pqr.
1869s asc_getToken: Error occurred (bailing out).
1869s Vio_scanf: Format problem with input.
1869s   1677 atoms
1869s   Centered at (2.526e+01, 1.899e+01, 1.912e+01)
1869s   Net charge 9.91e-01 e
1869s Reading PQR-format atom data from dss-min.pqr.
1869s asc_getToken: Error occurred (bailing out).
1869s Vio_scanf: Format problem with input.
1869s   14 atoms
1869s   Centered at (1.734e+01, 1.921e+01, 2.050e+01)
1869s   Net charge -8.33e-17 e
1869s Reading PQR-format atom data from 1d7i-min.pqr.
1869s   1663 atoms
1869s   Centered at (2.526e+01, 1.899e+01, 1.912e+01)
1869s   Net charge 9.91e-01 e
1869s Preparing to run 12 PBE calculations.
1869s ----------------------------------------
1869s CALCULATION #1 (complex-solv-coarse): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  30.4176 A
1869s   Current memory usage:  102.869 MB total, 102.869 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 1.500 x 1.500 x 1.500
1869s   Grid lengths: 96.000 x 96.000 x 96.000
1869s   Grid center: (25.264, 18.988, 19.122)
1869s   Multigrid levels: 5
1869s   Molecule ID: 1
1869s   Linearized traditional PBE
1869s   Multiple Debye-Huckel sphere boundary conditions
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 78.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 9.634884642408E+03 kJ/mol
1869s   Calculating forces...
1869s [focusFillBound()]: WARNING:
1869s     Unusually large potential values
1869s     detected on the focusing boundary!
1869s     Convergence not guaranteed for NPBE/NRPBE calculations!
1869s 
1869s ----------------------------------------
1869s CALCULATION #2 (complex-solv-fine): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  30.4176 A
1869s   Current memory usage:  102.869 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 0.225 x 0.225 x 0.225
1869s   Grid lengths: 14.400 x 14.400 x 14.400
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 1
1869s   Linearized traditional PBE
1869s   Boundary conditions from focusing
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 78.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 4.003177540425E+04 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s CALCULATION #3 (complex-ref-coarse): MULTIGRID
1869s   Setting up problem...
1869s   VpbTesting computed result against expected result (9.634884642408e+03, 9.634884642408e+03)
1869s *** PASSED ***
1869s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04)
1869s *** PASSED ***
1869s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04)
1869s *** PASSED ***
1869s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04)
1869s *** PASSED ***
1869s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01)
1869s *** PASSED ***
1869s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03)
1869s *** PASSED ***
1869s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02)
1869s *** PASSED ***
1869s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03)
1869s *** PASSED ***
1869s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03)
1869s *** PASSED ***
1869s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04)
1869s *** PASSED ***
1869s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04)
1869s *** PASSED ***
1869s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04)
1869s *** PASSED ***
1869s Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01)
1869s *** PASSED ***
1869s Elapsed time: 35.870276 seconds
1869s --------------------------------------------------------------------------------
1869s Total elapsed time: 152.779303 seconds
1869s Test results have been logged
1869s --------------------------------------------------------------------------------
1869s --------------------------------------------------------------------------------
1869s Testing input file apbs-mol.in
1869s 
1869s e_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  4.87072 A
1869s   Current memory usage:  102.869 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 1.500 x 1.500 x 1.500
1869s   Grid lengths: 96.000 x 96.000 x 96.000
1869s   Grid center: (25.264, 18.988, 19.122)
1869s   Multigrid levels: 5
1869s   Molecule ID: 1
1869s   Linearized traditional PBE
1869s   Multiple Debye-Huckel sphere boundary conditions
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 2.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 1.264965939588E+04 kJ/mol
1869s   Calculating forces...
1869s [focusFillBound()]: WARNING:
1869s     Unusually large potential values
1869s     detected on the focusing boundary!
1869s     Convergence not guaranteed for NPBE/NRPBE calculations!
1869s 
1869s ----------------------------------------
1869s CALCULATION #4 (complex-ref-fine): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  4.87072 A
1869s   Current memory usage:  102.869 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 0.225 x 0.225 x 0.225
1869s   Grid lengths: 14.400 x 14.400 x 14.400
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 1
1869s   Linearized traditional PBE
1869s   Boundary conditions from focusing
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 2.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 4.301801664829E+04 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s CALCULATION #5 (dss-solv-coarse): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  30.4176 A
1869s   Current memory usage:  62.482 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 1.500 x 1.500 x 1.500
1869s   Grid lengths: 96.000 x 96.000 x 96.000
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 2
1869s   Linearized traditional PBE
1869s   Multiple Debye-Huckel sphere boundary conditions
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 78.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 7.942232645345E+01 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s CALCULATION #6 (dss-solv-fine): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  30.4176 A
1869s   Current memory usage:  62.482 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 0.225 x 0.225 x 0.225
1869s   Grid lengths: 14.400 x 14.400 x 14.400
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 2
1869s   Linearized traditional PBE
1869s   Boundary conditions from focusing
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 78.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 1.677798535473E+03 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s CALCULATION #7 (dss-ref-coarse): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  4.87072 A
1869s   Current memory usage:  62.482 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 1.500 x 1.500 x 1.500
1869s   Grid lengths: 96.000 x 96.000 x 96.000
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 2
1869s   Linearized traditional PBE
1869s   Multiple Debye-Huckel sphere boundary conditions
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 2.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 1.171079106781E+02 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s CALCULATION #8 (dss-ref-fine): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  4.87072 A
1869s   Current memory usage:  62.482 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 0.225 x 0.225 x 0.225
1869s   Grid lengths: 14.400 x 14.400 x 14.400
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 2
1869s   Linearized traditional PBE
1869s   Boundary conditions from focusing
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 2.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 1.697869784185E+03 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  30.4176 A
1869s   Current memory usage:  102.566 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 1.500 x 1.500 x 1.500
1869s   Grid lengths: 96.000 x 96.000 x 96.000
1869s   Grid center: (25.264, 18.988, 19.122)
1869s   Multigrid levels: 5
1869s   Molecule ID: 3
1869s   Linearized traditional PBE
1869s   Multiple Debye-Huckel sphere boundary conditions
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 78.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 9.507068451372E+03 kJ/mol
1869s   Calculating forces...
1869s [focusFillBound()]: WARNING:
1869s     Unusually large potential values
1869s     detected on the focusing boundary!
1869s     Convergence not guaranteed for NPBE/NRPBE calculations!
1869s 
1869s ----------------------------------------
1869s CALCULATION #10 (1d7i-solv-fine): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  30.4176 A
1869s   Current memory usage:  102.566 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 0.225 x 0.225 x 0.225
1869s   Grid lengths: 14.400 x 14.400 x 14.400
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 3
1869s   Linearized traditional PBE
1869s   Boundary conditions from focusing
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 78.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 3.835075772299E+04 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  4.87072 A
1869s   Current memory usage:  102.566 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 1.500 x 1.500 x 1.500
1869s   Grid lengths: 96.000 x 96.000 x 96.000
1869s   Grid center: (25.264, 18.988, 19.122)
1869s   Multigrid levels: 5
1869s   Molecule ID: 3
1869s   Linearized traditional PBE
1869s   Multiple Debye-Huckel sphere boundary conditions
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 2.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 1.252495566243E+04 kJ/mol
1869s   Calculating forces...
1869s [focusFillBound()]: WARNING:
1869s     Unusually large potential values
1869s     detected on the focusing boundary!
1869s     Convergence not guaranteed for NPBE/NRPBE calculations!
1869s 
1869s ----------------------------------------
1869s CALCULATION #12 (1d7i-ref-fine): MULTIGRID
1869s   Setting up problem...
1869s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1869s   Debye length:  4.87072 A
1869s   Current memory usage:  102.566 MB total, 183.200 MB high water
1869s   Using linear spline charge discretization.
1869s   Grid dimensions: 65 x 65 x 65
1869s   Grid spacings: 0.225 x 0.225 x 0.225
1869s   Grid lengths: 14.400 x 14.400 x 14.400
1869s   Grid center: (17.340, 19.211, 20.503)
1869s   Multigrid levels: 5
1869s   Molecule ID: 3
1869s   Linearized traditional PBE
1869s   Boundary conditions from focusing
1869s   2 ion species (0.010 M ionic strength):
1869s     2.000 A-radius, 1.000 e-charge, 0.010 M concentration
1869s     2.000 A-radius, -1.000 e-charge, 0.010 M concentration
1869s   Solute dielectric: 2.000
1869s   Solvent dielectric: 2.000
1869s   Using "molecular" surface definition;harmonic average smoothing
1869s   Solvent probe radius: 0.000 A
1869s   Temperature:  300.000 K
1869s   Electrostatic energies will be calculated
1869s   Total electrostatic energy = 4.133237922574E+04 kJ/mol
1869s   Calculating forces...
1869s ----------------------------------------
1869s PRINT STATEMENTS
1869s 
1869s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
1869s   Local net energy (PE 0) = -2.986241244040E+03 kJ/mol
1869s   Global net ELEC energy = -2.986241244040E+03 kJ/mol
1869s 
1869s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end
1869s   Local net energy (PE 0) = -2.007124871262E+01 kJ/mol
1869s   Global net ELEC energy = -2.007124871262E+01 kJ/mol
1869s 
1869s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end
1869s   Local net energy (PE 0) = -2.981621502756E+03 kJ/mol
1869s   Global net ELEC energy = -2.981621502756E+03 kJ/mol
1869s 
1869s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end
1869s   Local net energy (PE 0) = 1.545150742844E+01 kJ/mol
1869s   Global net ELEC energy = 1.545150742844E+01 kJ/mol
1869s ----------------------------------------
1869s CLEANING UP AND SHUTTING DOWN...
1869s Destroying force arrays.
1869s No energy arrays to destroy.
1869s Destroying multigrid structures.
1869s Destroying finite element structures.
1869s Destroying 3 molecules
1869s Final memory usage:  0.001 MB total, 183.200 MB high water
1869s 
1869s 
1869s Thanks for using APBS!
1869s 
1907s Checking for intermediate energies in input file 1d7i-dss-smol.out
1907s EXPECTED COMPUTED: 16
1907s EXPECTED EXPECTED: 16
1907s COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742844]
1907s EXPECTED: ['9.634884642408E+03', '4.003177540425E+04', '1.264965939588E+04', '4.301801664829E+04', '7.942232645345E+01', '1.677798535473E+03', '1.171079106781E+02', '1.697869784185E+03', '9.507068451372E+03', '3.835075772299E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.545150009785E+01']
1907s COMPUTED RESULT 9634.884642408
1907s COMPUTED RESULT 40031.77540425
1907s COMPUTED RESULT 12649.65939588
1907s COMPUTED RESULT 43018.01664829
1907s COMPUTED RESULT 79.42232645345
1907s COMPUTED RESULT 1677.798535473
1907s COMPUTED RESULT 117.1079106781
1907s COMPUTED RESULT 1697.869784185
1907s COMPUTED RESULT 9507.068451372
1907s COMPUTED RESULT 38350.75772299
1907s COMPUTED RESULT 12524.95566243
1907s COMPUTED RESULT 41332.37922574
1907s COMPUTED RESULT -2986.24124404
1907s COMPUTED RESULT -20.07124871262
1907s COMPUTED RESULT -2981.621502756
1907s COMPUTED RESULT 15.45150742844
1907s Running tests for hca-bind section
1907s BINARY:  /usr/bin/apbs
1907s INPUT:   apbs-mol.in
1907s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in']
1907s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02)
1907s *** PASSED ***
1907s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03)
1907s *** PASSED ***
1907s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03)
1907s *** PASSED ***
1907s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04)
1907s *** PASSED ***
1907s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05)
1907s *** PASSED ***
1907s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05)
1907s *** PASSED ***
1907s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04)
1907s *** PASSED ***
1907s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05)
1907s *** PASSED ***
1907s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05)
1907s *** PASSED ***
1907s Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01)
1907s *** PASSED ***
1907s Elapsed time: 38.199434 seconds
1907s --------------------------------------------------------------------------------
1907s --------------------------------------------------------------------------------
1907s Testing input file apbs-smol.in
1907s 
1907s asc_getToken: Error occurred (bailing out).
1907s Vio_scanf: Format problem with input.
1907s 
1907s 
1907s ----------------------------------------------------------------------
1907s     APBS -- Adaptive Poisson-Boltzmann Solver
1907s     Version APBS 3.4.1
1907s     
1907s     Nathan A. Baker (nathan.baker@pnnl.gov)
1907s     Pacific Northwest National Laboratory
1907s     
1907s     Additional contributing authors listed in the code documentation.
1907s     
1907s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1907s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1907s     Northwest Division for the U.S. Department of Energy.
1907s     
1907s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1907s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1907s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1907s     Portions Copyright (c) 1995, Michael Holst.
1907s     All rights reserved.
1907s     
1907s     Redistribution and use in source and binary forms, with or without
1907s     modification, are permitted provided that the following conditions are met:
1907s     
1907s     * Redistributions of source code must retain the above copyright notice, this
1907s       list of conditions and the following disclaimer.
1907s     
1907s     * Redistributions in binary form must reproduce the above copyright notice,
1907s       this list of conditions and the following disclaimer in the documentation
1907s       and/or other materials provided with the distribution.
1907s     
1907s     * Neither the name of the developer nor the names of its contributors may be
1907s       used to endorse or promote products derived from this software without
1907s       specific prior written permission.
1907s     
1907s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1907s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1907s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1907s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1907s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1907s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1907s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1907s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1907s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1907s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1907s ----------------------------------------------------------------------
1907s     APBS uses FETK (the Finite Element ToolKit) to solve the
1907s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1907s     of finite element modeling class libraries developed by the Michael Holst
1907s     research group and written in an object-oriented form of C.  FEtk is
1907s     designed to solve general coupled systems of nonlinear partial differential
1907s     equations using adaptive finite element methods, inexact Newton methods,
1907s     and algebraic multilevel methods.  More information about FEtk may be found
1907s     at <http://www.FEtk.ORG>.
1907s ----------------------------------------------------------------------
1907s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1907s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1907s     which has been modified by Patrice Koehl
1907s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1907s     memory usage when solving the Poisson-Boltzmann equation.
1907s ----------------------------------------------------------------------
1907s     Please cite your use of APBS as:
1907s 
1907s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1907s     nanosystems: application to microtubules and the ribosome. Proc.
1907s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1907s     
1907s 
1907s This executable compiled on Mar  2 2024 at 20:11:10
1907s 
1907s Parsing input file apbs-mol.in...
1907s rank 0 size 1...
1907s Parsed input file.
1907s Got paths for 3 molecules
1907s Reading PQR-format atom data from acet.pqr.
1907s asc_getToken: Error occurred (bailing out).
1907s Vio_scanf: Format problem with input.
1907s   18 atoms
1907s   Centered at (-6.028e+00, 3.898e+00, 1.518e+01)
1907s   Net charge -1.00e+00 e
1907s Reading PQR-format atom data from hca.pqr.
1907s asc_getToken: Error occurred (bailing out).
1907s Vio_scanf: Format problem with input.
1907s   2482 atoms
1907s   Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
1907s   Net charge 1.00e+00 e
1907s Reading PQR-format atom data from complex.pqr.
1907s   2500 atoms
1907s   Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
1907s   Net charge -1.02e-14 e
1907s Preparing to run 9 PBE calculations.
1907s ----------------------------------------
1907s CALCULATION #1 (acet): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  62.632 MB total, 62.632 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 1.500 x 1.500 x 1.500
1907s   Grid lengths: 96.000 x 96.000 x 96.000
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 1
1907s   Linearized traditional PBE
1907s   Single Debye-Huckel sphere boundary conditions
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 2.213600726771E+02 kJ/mol
1907s   Calculating forces...
1907s ----------------------------------------
1907s CALCULATION #2 (acet): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  62.632 MB total, 123.513 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 0.581 x 0.581 x 0.581
1907s   Grid lengths: 37.181 x 37.181 x 37.181
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 1
1907s   Linearized traditional PBE
1907s   Boundary conditions from focusing
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 1.825764811255E+03 kJ/mol
1907s   Calculating forces...
1907s ----------------------------------------
1907s CALCULATION #3 (acet): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  62.632 MB total, 123.513 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 0.225 x 0.225 x 0.225
1907s   Grid lengths: 14.400 x 14.400 x 14.400
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 1
1907s   Linearized traditional PBE
1907s   Boundary conditions from focusing
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 6.458471211905E+03 kJ/mol
1907s   Calculating forces...
1907s ----------------------------------------
1907s CALCULATION #4 (hca): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  127.616 MB total, 127.616 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 1.500 x 1.500 x 1.500
1907s   Grid lengths: 96.000 x 96.000 x 96.000
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 2
1907s   Linearized traditional PBE
1907s   Single Debye-Huckel sphere boundary conditions
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 2.093606095527E+04 kJ/mol
1907s   Calculating forces...
1907s [focusFillBound()]: WARNING:
1907s     Unusually large potential values
1907s     detected on the focusing boundary!
1907s     Convergence not guaranteed for NPBE/NRPBE calculations!
1907s 
1907s ----------------------------------------
1907s CALCULATION #5 (hca): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  127.616 MB total, 207.303 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 0.581 x 0.581 x 0.581
1907s   Grid lengths: 37.181 x 37.181 x 37.181
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 2
1907s   Linearized traditional PBE
1907s   Boundary conditions from focusing
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 1.515433544464E+05 kJ/mol
1907s   Calculating forces...
1907s [focusFillBound()]: WARNING:
1907s     Unusually large potential values
1907s     detected on the focusing boundary!
1907s     Convergence not guaranteed for NPBE/NRPBE calculations!
1907s 
1907s ----------------------------------------
1907s CALCULATION #6 (hca): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  127.616 MB total, 207.303 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 0.225 x 0.225 x 0.225
1907s   Grid lengths: 14.400 x 14.400 x 14.400
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 2
1907s   Linearized traditional PBE
1907s   Boundary conditions from focusing
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 1.786369323561E+05 kJ/mol
1907s   Calculating forces...
1907s ----------------------------------------
1907s CALCULATION #7 (complex): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  127.915 MB total, 207.303 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 1.500 x 1.500 x 1.500
1907s   Grid lengths: 96.000 x 96.000 x 96.000
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 3
1907s   Linearized traditional PBE
1907s   Single Debye-Huckel sphere boundary conditions
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 2.105322784838E+04 kJ/mol
1907s   Calculating forces...
1907s [focusFillBound()]: WARNING:
1907s     Unusually large potential values
1907s     detected on the focusing boundary!
1907s     Convergence not guaranteed for NPBE/NRPBE calculations!
1907s 
1907s ----------------------------------------
1907s CALCULATION #8 (complex): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  127.915 MB total, 207.713 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 0.581 x 0.581 x 0.581
1907s   Grid lengths: 37.181 x 37.181 x 37.181
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 3
1907s   Linearized traditional PBE
1907s   Boundary conditions from focusing
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 1.533304996252E+05 kJ/mol
1907s   Calculating forces...
1907s [focusFillBound()]: WARNING:
1907s     Unusually large potential values
1907s     detected on the focusing boundary!
1907s     Convergence not guaranteed for NPBE/NRPBE calculations!
1907s 
1907s ----------------------------------------
1907s CALCULATION #9 (complex): MULTIGRID
1907s   Setting up problem...
1907s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1907s   Debye length:  0 A
1907s   Current memory usage:  127.915 MB total, 207.713 MB high water
1907s   Using linear spline charge discretization.
1907s   Grid dimensions: 65 x 65 x 65
1907s   Grid spacings: 0.225 x 0.225 x 0.225
1907s   Grid lengths: 14.400 x 14.400 x 14.400
1907s   Grid center: (-6.028, 3.898, 15.179)
1907s   Multigrid levels: 5
1907s   Molecule ID: 3
1907s   Linearized traditional PBE
1907s   Boundary conditions from focusing
1907s   2 ion species (0.000 M ionic strength):
1907s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1907s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1907s   Solute dielectric: 2.000
1907s   Solvent dielectric: 78.540
1907s   Using "molecular" surface definition; no smoothing
1907s   Solvent probe radius: 0.000 A
1907s   Temperature:  298.150 K
1907s   Electrostatic energies will be calculated
1907s   Total electrostatic energy = 1.850429388099E+05 kJ/mol
1907s   Calculating forces...
1907s ----------------------------------------
1907s PRINT STATEMENTS
1907s 
1907s print energy 3 (complex) - 1 (acet) - 2 (hca) end
1907s   Local net energy (PE 0) = -5.246475812665E+01 kJ/mol
1907s   Global net ELEC energy = -5.246475812665E+01 kJ/mol
1907s ----------------------------------------
1907s CLEANING UP AND SHUTTING DOWN...
1907s Destroying force arrays.
1907s No energy arrays to destroy.
1907s Destroying multigrid structures.
1907s Destroying finite element structures.
1907s Destroying 3 molecules
1907s Final memory usage:  0.001 MB total, 207.713 MB high water
1907s 
1907s 
1907s Thanks for using APBS!
1907s 
1939s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02)
1939s *** PASSED ***
1939s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03)
1939s *** PASSED ***
1939s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03)
1939s *** PASSED ***
1939s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04)
1939s *** PASSED ***
1939s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05)
1939s *** PASSED ***
1939s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05)
1939s *** PASSED ***
1939s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04)
1939s *** PASSED ***
1939s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05)
1939s *** PASSED ***
1939s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05)
1939s *** PASSED ***
1939s Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01)
1939s *** PASSED ***
1939s Elapsed time: 32.025722 seconds
1939s --------------------------------------------------------------------------------
1939s Total elapsed time: 70.225156 seconds
1939s Test results have been logged
1939s --------------------------------------------------------------------------------
1939s --------------------------------------------------------------------------------
1939s Testing input file apbs-mol.in
1939s 
1939s Checking for intermediate energies in input file apbs-mol.out
1939s EXPECTED COMPUTED: 10
1939s EXPECTED EXPECTED: 10
1939s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665]
1939s EXPECTED: ['2.213600726771E+02', '1.825764811255E+03', '6.458471211905E+03', '2.093606095527E+04', '1.515433544464E+05', '1.786369323561E+05', '2.105322784838E+04', '1.533304996252E+05', '1.850429388099E+05', '-5.246475812665E+01']
1939s COMPUTED RESULT 221.3600726771
1939s COMPUTED RESULT 1825.764811255
1939s COMPUTED RESULT 6458.471211905
1939s COMPUTED RESULT 20936.06095527
1939s COMPUTED RESULT 151543.3544464
1939s COMPUTED RESULT 178636.9323561
1939s COMPUTED RESULT 21053.22784838
1939s COMPUTED RESULT 153330.4996252
1939s COMPUTED RESULT 185042.9388099
1939s COMPUTED RESULT -52.46475812665
1939s BINARY:  /usr/bin/apbs
1939s INPUT:   apbs-smol.in
1939s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in']
1939s asc_getToken: Error occurred (bailing out).
1939s Vio_scanf: Format problem with input.
1939s 
1939s 
1939s ----------------------------------------------------------------------
1939s     APBS -- Adaptive Poisson-Boltzmann Solver
1939s     Version APBS 3.4.1
1939s     
1939s     Nathan A. Baker (nathan.baker@pnnl.gov)
1939s     Pacific Northwest National Laboratory
1939s     
1939s     Additional contributing authors listed in the code documentation.
1939s     
1939s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1939s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1939s     Northwest Division for the U.S. Department of Energy.
1939s     
1939s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1939s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1939s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1939s     Portions Copyright (c) 1995, Michael Holst.
1939s     All rights reserved.
1939s     
1939s     Redistribution and use in source and binary forms, with or without
1939s     modification, are permitted provided that the following conditions are met:
1939s     
1939s     * Redistributions of source code must retain the above copyright notice, this
1939s       list of conditions and the following disclaimer.
1939s     
1939s     * Redistributions in binary form must reproduce the above copyright notice,
1939s       this list of conditions and the following disclaimer in the documentation
1939s       and/or other materials provided with the distribution.
1939s     
1939s     * Neither the name of the developer nor the names of its contributors may be
1939s       used to endorse or promote products derived from this software without
1939s       specific prior written permission.
1939s     
1939s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1939s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1939s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1939s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1939s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1939s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1939s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1939s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1939s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1939s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1939s ----------------------------------------------------------------------
1939s     APBS uses FETK (the Finite Element ToolKit) to solve the
1939s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1939s     of finite element modeling class libraries developed by the Michael Holst
1939s     research group and written in an object-oriented form of C.  FEtk is
1939s     designed to solve general coupled systems of nonlinear partial differential
1939s     equations using adaptive finite element methods, inexact Newton methods,
1939s     and algebraic multilevel methods.  More information about FEtk may be found
1939s     at <http://www.FEtk.ORG>.
1939s ----------------------------------------------------------------------
1939s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1939s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1939s     which has been modified by Patrice Koehl
1939s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1939s     memory usage when solving the Poisson-Boltzmann equation.
1939s ----------------------------------------------------------------------
1939s     Please cite your use of APBS as:
1939s 
1939s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1939s     nanosystems: application to microtubules and the ribosome. Proc.
1939s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1939s     
1939s 
1939s This executable compiled on Mar  2 2024 at 20:11:10
1939s 
1939s Parsing input file apbs-smol.in...
1939s rank 0 size 1...
1939s Parsed input file.
1939s Got paths for 3 molecules
1939s Reading PQR-format atom data from acet.pqr.
1939s asc_getToken: Error occurred (bailing out).
1939s Vio_scanf: Format problem with input.
1939s   18 atoms
1939s   Centered at (-6.028e+00, 3.898e+00, 1.518e+01)
1939s   Net charge -1.00e+00 e
1939s Reading PQR-format atom data from hca.pqr.
1939s asc_getToken: Error occurred (bailing out).
1939s Vio_scanf: Format problem with input.
1939s   2482 atoms
1939s   Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
1939s   Net charge 1.00e+00 e
1939s Reading PQR-format atom data from complex.pqr.
1939s   2500 atoms
1939s   Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
1939s   Net charge -1.02e-14 e
1939s Preparing to run 9 PBE calculations.
1939s ----------------------------------------
1939s CALCULATION #1 (acet): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  62.632 MB total, 62.632 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 1.500 x 1.500 x 1.500
1939s   Grid lengths: 96.000 x 96.000 x 96.000
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 1
1939s   Linearized traditional PBE
1939s   Single Debye-Huckel sphere boundary conditions
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 1.884888131017E+02 kJ/mol
1939s   Calculating forces...
1939s ----------------------------------------
1939s CALCULATION #2 (acet): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  62.632 MB total, 123.513 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 0.581 x 0.581 x 0.581
1939s   Grid lengths: 37.181 x 37.181 x 37.181
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 1
1939s   Linearized traditional PBE
1939s   Boundary conditions from focusing
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 1.820045922544E+03 kJ/mol
1939s   Calculating forces...
1939s ----------------------------------------
1939s CALCULATION #3 (acet): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  62.632 MB total, 123.513 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 0.225 x 0.225 x 0.225
1939s   Grid lengths: 14.400 x 14.400 x 14.400
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 1
1939s   Linearized traditional PBE
1939s   Boundary conditions from focusing
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 6.460002606908E+03 kJ/mol
1939s   Calculating forces...
1939s ----------------------------------------
1939s CALCULATION #4 (hca): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  127.616 MB total, 127.616 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 1.500 x 1.500 x 1.500
1939s   Grid lengths: 96.000 x 96.000 x 96.000
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 2
1939s   Linearized traditional PBE
1939s   Single Debye-Huckel sphere boundary conditions
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 2.189161497021E+04 kJ/mol
1939s   Calculating forces...
1939s [focusFillBound()]: WARNING:
1939s     Unusually large potential values
1939s     detected on the focusing boundary!
1939s     Convergence not guaranteed for NPBE/NRPBE calculations!
1939s 
1939s ----------------------------------------
1939s CALCULATION #5 (hca): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  127.616 MB total, 207.303 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 0.581 x 0.581 x 0.581
1939s   Grid lengths: 37.181 x 37.181 x 37.181
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 2
1939s   Linearized traditional PBE
1939s   Boundary conditions from focusing
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 1.520000494925E+05 kJ/mol
1939s   Calculating forces...
1939s [focusFillBound()]: WARNING:
1939s     Unusually large potential values
1939s     detected on the focusing boundary!
1939s     Convergence not guaranteed for NPBE/NRPBE calculations!
1939s 
1939s ----------------------------------------
1939s CALCULATION #6 (hca): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  127.616 MB total, 207.303 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 0.225 x 0.225 x 0.225
1939s   Grid lengths: 14.400 x 14.400 x 14.400
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 2
1939s   Linearized traditional PBE
1939s   Boundary conditions from focusing
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 1.790436191580E+05 kJ/mol
1939s   Calculating forces...
1939s ----------------------------------------
1939s CALCULATION #7 (complex): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  127.915 MB total, 207.303 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 1.500 x 1.500 x 1.500
1939s   Grid lengths: 96.000 x 96.000 x 96.000
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 3
1939s   Linearized traditional PBE
1939s   Single Debye-Huckel sphere boundary conditions
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 2.195842512312E+04 kJ/mol
1939s   Calculating forces...
1939s [focusFillBound()]: WARNING:
1939s     Unusually large potential values
1939s     detected on the focusing boundary!
1939s     Convergence not guaranteed for NPBE/NRPBE calculations!
1939s 
1939s ----------------------------------------
1939s CALCULATION #8 (complex): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  127.915 MB total, 207.713 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 0.581 x 0.581 x 0.581
1939s   Grid lengths: 37.181 x 37.181 x 37.181
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 3
1939s   Linearized traditional PBE
1939s   Boundary conditions from focusing
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 1.537771604355E+05 kJ/mol
1939s   Calculating forces...
1939s [focusFillBound()]: WARNING:
1939s     Unusually large potential values
1939s     detected on the focusing boundary!
1939s     Convergence not guaranteed for NPBE/NRPBE calculations!
1939s 
1939s ----------------------------------------
1939s CALCULATION #9 (complex): MULTIGRID
1939s   Setting up problem...
1939s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1939s   Debye length:  0 A
1939s   Current memory usage:  127.915 MB total, 207.713 MB high water
1939s   Using linear spline charge discretization.
1939s   Grid dimensions: 65 x 65 x 65
1939s   Grid spacings: 0.225 x 0.225 x 0.225
1939s   Grid lengths: 14.400 x 14.400 x 14.400
1939s   Grid center: (-6.028, 3.898, 15.179)
1939s   Multigrid levels: 5
1939s   Molecule ID: 3
1939s   Linearized traditional PBE
1939s   Boundary conditions from focusing
1939s   2 ion species (0.000 M ionic strength):
1939s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1939s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1939s   Solute dielectric: 2.000
1939s   Solvent dielectric: 78.540
1939s   Using "molecular" surface definition;harmonic average smoothing
1939s   Solvent probe radius: 0.000 A
1939s   Temperature:  298.150 K
1939s   Electrostatic energies will be calculated
1939s   Total electrostatic energy = 1.854495619747E+05 kJ/mol
1939s   Calculating forces...
1939s ----------------------------------------
1939s PRINT STATEMENTS
1939s 
1939s print energy 3 (complex) - 1 (acet) - 2 (hca) end
1939s   Local net energy (PE 0) = -5.405979017066E+01 kJ/mol
1939s   Global net ELEC energy = -5.405979017066E+01 kJ/mol
1939s ----------------------------------------
1939s CLEANING UP AND SHUTTING DOWN...
1939s Destroying force arrays.
1939s No energy arrays to destroy.
1939s Destroying multigrid structures.
1939s Destroying finite element structures.
1939s Destroying 3 molecules
1939s Final memory usage:  0.001 MB total, 207.713 MB high water
1939s 
1939s 
1939s Thanks for using APBS!
1939s 
1971s Checking for intermediate energies in input file apbs-smol.out
1971s EXPECTED COMPUTED: 10
1971s EXPECTED EXPECTED: 10
1971s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066]
1971s EXPECTED: ['1.884888131017E+02', '1.820045922544E+03', '6.460002606908E+03', '2.189161497021E+04', '1.520000494925E+05', '1.790436191580E+05', '2.195842512312E+04', '1.537771604355E+05', '1.854495619747E+05', '-5.405977880082E+01']
1971s COMPUTED RESULT 188.4888131017
1971s COMPUTED RESULT 1820.045922544
1971s COMPUTED RESULT 6460.002606908
1971s COMPUTED RESULT 21891.61497021
1971s COMPUTED RESULT 152000.0494925
1971s COMPUTED RESULT 179043.619158
1971s COMPUTED RESULT 21958.42512312
1971s COMPUTED RESULT 153777.1604355
1971s COMPUTED RESULT 185449.5619747
1971s COMPUTED RESULT -54.05979017066
1971s Running tests for ionize section
1971s BINARY:  /usr/bin/apbs
1971s INPUT:   apbs-mol.in
1971s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in']
1971s asc_getToken: Error occurred (bailing out).
1971s Vio_scanf: Format problem with input.
1971s 
1971s 
1971s ----------------------------------------------------------------------
1971s     APBS -- Adaptive Poisson-Boltzmann Solver
1971s     Version APBS 3.4.1
1971s     
1971s     Nathan A. Baker (nathan.baker@pnnl.gov)
1971s     Pacific Northwest National Laboratory
1971s     
1971s     Additional contributing authors listed in the code documentation.
1971s     
1971s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1971s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1971s     Northwest Division for the U.S. Department of Energy.
1971s     
1971s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1971s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1971s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1971s     Portions Copyright (c) 1995, Michael Holst.
1971s     All rights reserved.
1971s     
1971s     Redistribution and use in source and binary forms, with or without
1971s     modification, are permitted provided that the following conditions are met:
1971s     
1971s     * Redistributions of source code must retain the above copyright notice, this
1971s       list of conditions and the following disclaimer.
1971s     
1971s     * Redistributions in binary form must reproduce the above copyright notice,
1971s       this list of conditions and the following disclaimer in the documentation
1971s       and/or other materials provided with the distribution.
1971s     
1971s     * Neither the name of the developer nor the names of its contributors may be
1971s       used to endorse or promote products derived from this software without
1971s       specific prior written permission.
1971s     
1971s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1971s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1971s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1971s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1971s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1971s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1971s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1971s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1971s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1971s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1971s ----------------------------------------------------------------------
1971s     APBS uses FETK (the Finite Element ToolKit) to solve the
1971s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1971s     of finite element modeling class libraries developed by the Michael Holst
1971s     research group and written in an object-oriented form of C.  FEtk is
1971s     designed to solve general coupled systems of nonlinear partial differential
1971s     equations using adaptive finite element methods, inexact Newton methods,
1971s     and algebraic multilevel methods.  More information about FEtk may be found
1971s     at <http://www.FEtk.ORG>.
1971s ----------------------------------------------------------------------
1971s     APBS aTesting computed result against expected result (5.823898055191e+03, 5.823898055191e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04)
1971s *** PASSED ***
1971s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04)
1971s *** PASSED ***
1971s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03)
1971s *** PASSED ***
1971s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01)
1971s *** PASSED ***
1971s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02)
1971s *** PASSED ***
1971s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02)
1971s *** PASSED ***
1971s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02)
1971s *** PASSED ***
1971s Elapsed time: 31.964298 seconds
1971s --------------------------------------------------------------------------------
1971s --------------------------------------------------------------------------------
1971s Testing input file apbs-smol.in
1971s 
1971s lso uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1971s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1971s     which has been modified by Patrice Koehl
1971s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1971s     memory usage when solving the Poisson-Boltzmann equation.
1971s ----------------------------------------------------------------------
1971s     Please cite your use of APBS as:
1971s 
1971s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1971s     nanosystems: application to microtubules and the ribosome. Proc.
1971s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1971s     
1971s 
1971s This executable compiled on Mar  2 2024 at 20:11:10
1971s 
1971s Parsing input file apbs-mol.in...
1971s rank 0 size 1...
1971s Parsed input file.
1971s Got paths for 3 molecules
1971s Reading PQR-format atom data from acetic-acid.pqr.
1971s asc_getToken: Error occurred (bailing out).
1971s Vio_scanf: Format problem with input.
1971s   8 atoms
1971s   Centered at (0.000e+00, -1.535e-01, 1.287e+00)
1971s   Net charge -1.67e-16 e
1971s Reading PQR-format atom data from acetate.pqr.
1971s asc_getToken: Error occurred (bailing out).
1971s Vio_scanf: Format problem with input.
1971s   8 atoms
1971s   Centered at (0.000e+00, -1.535e-01, 1.287e+00)
1971s   Net charge -1.00e+00 e
1971s Reading PQR-format atom data from proton.pqr.
1971s   1 atoms
1971s   Centered at (1.780e-01, -1.286e+00, 2.937e+00)
1971s   Net charge 1.00e+00 e
1971s Preparing to run 12 PBE calculations.
1971s ----------------------------------------
1971s CALCULATION #1 (acetic-solv): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  7.76163 A
1971s   Current memory usage:  61.581 MB total, 61.581 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.188 x 0.188 x 0.188
1971s   Grid lengths: 12.000 x 12.000 x 12.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 1
1971s   Linearized traditional PBE
1971s   Multiple Debye-Huckel sphere boundary conditions
1971s   2 ion species (0.150 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 78.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 5.823898055191E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #2 (acetic-solv): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  7.76163 A
1971s   Current memory usage:  61.581 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.094 x 0.094 x 0.094
1971s   Grid lengths: 6.000 x 6.000 x 6.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 1
1971s   Linearized traditional PBE
1971s   Boundary conditions from focusing
1971s   2 ion species (0.150 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 78.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 9.793274462353E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #3 (acetic-ref): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  0 A
1971s   Current memory usage:  61.405 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.188 x 0.188 x 0.188
1971s   Grid lengths: 12.000 x 12.000 x 12.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 1
1971s   Linearized traditional PBE
1971s   Multiple Debye-Huckel sphere boundary conditions
1971s   2 ion species (0.000 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 2.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 5.846917564309E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #4 (acetic-ref): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  0 A
1971s   Current memory usage:  61.405 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.094 x 0.094 x 0.094
1971s   Grid lengths: 6.000 x 6.000 x 6.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 1
1971s   Linearized traditional PBE
1971s   Boundary conditions from focusing
1971s   2 ion species (0.000 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 2.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 9.815953282539E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #5 (acetate-solv): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  7.76163 A
1971s   Current memory usage:  61.581 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.188 x 0.188 x 0.188
1971s   Grid lengths: 12.000 x 12.000 x 12.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 2
1971s   Linearized traditional PBE
1971s   Multiple Debye-Huckel sphere boundary conditions
1971s   2 ion species (0.150 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 78.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 8.219846763777E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #6 (acetate-solv): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  7.76163 A
1971s   Current memory usage:  61.581 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.094 x 0.094 x 0.094
1971s   Grid lengths: 6.000 x 6.000 x 6.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 2
1971s   Linearized traditional PBE
1971s   Boundary conditions from focusing
1971s   2 ion species (0.150 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 78.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 1.392741988698E+04 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #7 (acetate-ref): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  0 A
1971s   Current memory usage:  61.405 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.188 x 0.188 x 0.188
1971s   Grid lengths: 12.000 x 12.000 x 12.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 2
1971s   Linearized traditional PBE
1971s   Multiple Debye-Huckel sphere boundary conditions
1971s   2 ion species (0.000 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 2.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 8.420373979905E+03 kJ/mol
1971s   Calculating forces...
1971s [focusFillBound()]: WARNING:
1971s     Unusually large potential values
1971s     detected on the focusing boundary!
1971s     Convergence not guaranteed for NPBE/NRPBE calculations!
1971s 
1971s ----------------------------------------
1971s CALCULATION #8 (acetate-ref): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  0 A
1971s   Current memory usage:  61.405 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.094 x 0.094 x 0.094
1971s   Grid lengths: 6.000 x 6.000 x 6.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 2
1971s   Linearized traditional PBE
1971s   Boundary conditions from focusing
1971s   2 ion species (0.000 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 2.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 1.412716615065E+04 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #9 (proton-solv): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  7.76163 A
1971s   Current memory usage:  61.410 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.188 x 0.188 x 0.188
1971s   Grid lengths: 12.000 x 12.000 x 12.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 3
1971s   Linearized traditional PBE
1971s   Multiple Debye-Huckel sphere boundary conditions
1971s   2 ion species (0.150 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 78.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 3.862359524598E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #10 (proton-solv): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  7.76163 A
1971s   Current memory usage:  61.410 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.094 x 0.094 x 0.094
1971s   Grid lengths: 6.000 x 6.000 x 6.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 3
1971s   Linearized traditional PBE
1971s   Boundary conditions from focusing
1971s   2 ion species (0.150 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 78.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 6.288156251610E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s CALCULATION #11 (proton-ref): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  0 A
1971s   Current memory usage:  61.371 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.188 x 0.188 x 0.188
1971s   Grid lengths: 12.000 x 12.000 x 12.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 3
1971s   Linearized traditional PBE
1971s   Multiple Debye-Huckel sphere boundary conditions
1971s   2 ion species (0.000 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 2.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 4.162533113906E+03 kJ/mol
1971s   Calculating forces...
1971s [focusFillBound()]: WARNING:
1971s     Unusually large potential values
1971s     detected on the focusing boundary!
1971s     Convergence not guaranteed for NPBE/NRPBE calculations!
1971s 
1971s ----------------------------------------
1971s CALCULATION #12 (proton-ref): MULTIGRID
1971s   Setting up problem...
1971s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1971s   Debye length:  0 A
1971s   Current memory usage:  61.371 MB total, 122.371 MB high water
1971s   Using linear spline charge discretization.
1971s   Grid dimensions: 65 x 65 x 65
1971s   Grid spacings: 0.094 x 0.094 x 0.094
1971s   Grid lengths: 6.000 x 6.000 x 6.000
1971s   Grid center: (0.000, -0.154, 1.287)
1971s   Multigrid levels: 5
1971s   Molecule ID: 3
1971s   Linearized traditional PBE
1971s   Boundary conditions from focusing
1971s   2 ion species (0.000 M ionic strength):
1971s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1971s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1971s   Solute dielectric: 2.000
1971s   Solvent dielectric: 2.000
1971s   Using "molecular" surface definition; no smoothing
1971s   Solvent probe radius: 0.000 A
1971s   Temperature:  293.000 K
1971s   Electrostatic energies will be calculated
1971s   Total electrostatic energy = 6.585616091973E+03 kJ/mol
1971s   Calculating forces...
1971s ----------------------------------------
1971s PRINT STATEMENTS
1971s 
1971s print energy 1 (acetic-solv) - 2 (acetic-ref) end
1971s   Local net energy (PE 0) = -2.267882018629E+01 kJ/mol
1971s   Global net ELEC energy = -2.267882018629E+01 kJ/mol
1971s 
1971s print energy 3 (acetate-solv) - 4 (acetate-ref) end
1971s   Local net energy (PE 0) = -1.997462636633E+02 kJ/mol
1971s   Global net ELEC energy = -1.997462636633E+02 kJ/mol
1971s 
1971s print energy 5 (proton-solv) - 6 (proton-ref) end
1971s   Local net energy (PE 0) = -2.974598403628E+02 kJ/mol
1971s   Global net ELEC energy = -2.974598403628E+02 kJ/mol
1971s 
1971s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end
1971s   Local net energy (PE 0) = -4.745272838398E+02 kJ/mol
1971s   Global net ELEC energy = -4.745272838398E+02 kJ/mol
1971s ----------------------------------------
1971s CLEANING UP AND SHUTTING DOWN...
1971s Destroying force arrays.
1971s No energy arrays to destroy.
1971s Destroying multigrid structures.
1971s Destroying finite element structures.
1971s Destroying 3 molecules
1971s Final memory usage:  0.001 MB total, 122.371 MB high water
1971s 
1971s 
1971s Thanks for using APBS!
1971s 
1995s Checking for intermediate energies in input file apbs-mol.out
1995s EXPECTED COMPUTED: 16
1995s EXPECTED EXPECTED: 16
1995s COMPUTED: [5823.898055191, 9793.274462353, 5846.917564309, 9815.953282539, 8219.846763777, 13927.41988698, 8420.373979905, 14127.16615065, 3862.359524598, 6288.15625161, 4162.533113906, 6585.616091973, -22.67882018629, -199.7462636633, -297.4598403628, -474.5272838398]
1995s EXPECTED: ['5.823898055191E+03', '9.793274462353E+03', '5.846917564309E+03', '9.815953282539E+03', '8.219846763777E+03', '1.392741988698E+04', '8.420373979905E+03', '1.412716615065E+04', '3.862359524598E+03', '6.288156251610E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.267881997628E+01', '-1.997462580204E+02', '-2.974598331751E+02', '-4.745272868358E+02']
1995s COMPUTED RESULT 5823.898055191
1995s COMPUTED RESULT 9793.274462353
1995s COMPUTED RESULT 5846.917564309
1995s COMPUTED RESULT 9815.953282539
1995s COMPUTED RESULT 8219.846763777
1995s COMPUTED RESULT 13927.41988698
1995s COMPUTED RESULT 8420.373979905
1995s COMPUTED RESULT 14127.16615065
1995s COMPUTED RESULT 3862.359524598
1995s COMPUTED RESULT 6288.15625161
1995s COMPUTED RESULT 4162.533113906
1995s COMPUTED RESULT 6585.616091973
1995s COMPUTED RESULT -22.67882018629
1995s COMPUTED RESULT -199.7462636633
1995s COMPUTED RESULT -297.4598403628
1995s COMPUTED RESULT -474.5272838398
1995s BINARY:  /usr/bin/apbs
1995s INPUT:   apbs-smol.in
1995s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in']
1995s asc_getToken: Error occurred (bailing out).
1995s Vio_scanf: Format problem with input.
1995s 
1995s 
1995s ----------------------------------------------------------------------
1995s     APBS -- Adaptive Poisson-Boltzmann Solver
1995s     Version APBS 3.4.1
1995s     
1995s     Nathan A. Baker (nathan.baker@pnnl.gov)
1995s     Pacific Northwest National Laboratory
1995s     
1995s     Additional contributing authors listed in the code documentation.
1995s     
1995s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
1995s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
1995s     Northwest Division for the U.S. Department of Energy.
1995s     
1995s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
1995s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
1995s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
1995s     Portions Copyright (c) 1995, Michael Holst.
1995s     All rights reserved.
1995s     
1995s     Redistribution and use in source and binary forms, with or without
1995s     modification, are permitted provided that the following conditions are met:
1995s     
1995s     * Redistributions of source code must retain the above copyright notice, this
1995s       list of conditions and the following disclaimer.
1995s     
1995s     * Redistributions in binary form must reproduce the above copyright notice,
1995s       this list of conditions and the following disclaimer in the documentation
1995s       and/or other materials provided with the distribution.
1995s     
1995s     * Neither the name of the developer nor the names of its contributors may be
1995s       used to endorse or promote products derived from this software without
1995s       specific prior written permission.
1995s     
1995s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
1995s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
1995s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
1995s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
1995s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
1995s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
1995s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
1995s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
1995s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
1995s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1995s ----------------------------------------------------------------------
1995s     APBS uses FETK (the Finite Element ToolKit) to solve the
1995s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
1995s     of finite element modeling class libraries developed by the Michael Holst
1995s     research group and writtenTesting computed result against expected result (5.824172730822e+03, 5.824172730822e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04)
1995s *** PASSED ***
1995s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04)
1995s *** PASSED ***
1995s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03)
1995s *** PASSED ***
1995s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01)
1995s *** PASSED ***
1995s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02)
1995s *** PASSED ***
1995s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02)
1995s *** PASSED ***
1995s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02)
1995s *** PASSED ***
1995s Elapsed time: 24.402776 seconds
1995s --------------------------------------------------------------------------------
1995s Total elapsed time: 56.367074 seconds
1995s Test results have been logged
1995s --------------------------------------------------------------------------------
1995s --------------------------------------------------------------------------------
1995s Testing input file ion-pmf.in
1995s 
1995s  in an object-oriented form of C.  FEtk is
1995s     designed to solve general coupled systems of nonlinear partial differential
1995s     equations using adaptive finite element methods, inexact Newton methods,
1995s     and algebraic multilevel methods.  More information about FEtk may be found
1995s     at <http://www.FEtk.ORG>.
1995s ----------------------------------------------------------------------
1995s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
1995s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
1995s     which has been modified by Patrice Koehl
1995s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
1995s     memory usage when solving the Poisson-Boltzmann equation.
1995s ----------------------------------------------------------------------
1995s     Please cite your use of APBS as:
1995s 
1995s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
1995s     nanosystems: application to microtubules and the ribosome. Proc.
1995s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
1995s     
1995s 
1995s This executable compiled on Mar  2 2024 at 20:11:10
1995s 
1995s Parsing input file apbs-smol.in...
1995s rank 0 size 1...
1995s Parsed input file.
1995s Got paths for 3 molecules
1995s Reading PQR-format atom data from acetic-acid.pqr.
1995s asc_getToken: Error occurred (bailing out).
1995s Vio_scanf: Format problem with input.
1995s   8 atoms
1995s   Centered at (0.000e+00, -1.535e-01, 1.287e+00)
1995s   Net charge -1.67e-16 e
1995s Reading PQR-format atom data from acetate.pqr.
1995s asc_getToken: Error occurred (bailing out).
1995s Vio_scanf: Format problem with input.
1995s   8 atoms
1995s   Centered at (0.000e+00, -1.535e-01, 1.287e+00)
1995s   Net charge -1.00e+00 e
1995s Reading PQR-format atom data from proton.pqr.
1995s   1 atoms
1995s   Centered at (1.780e-01, -1.286e+00, 2.937e+00)
1995s   Net charge 1.00e+00 e
1995s Preparing to run 12 PBE calculations.
1995s ----------------------------------------
1995s CALCULATION #1 (acetic-solv): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  7.76163 A
1995s   Current memory usage:  61.581 MB total, 61.581 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.188 x 0.188 x 0.188
1995s   Grid lengths: 12.000 x 12.000 x 12.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 1
1995s   Linearized traditional PBE
1995s   Multiple Debye-Huckel sphere boundary conditions
1995s   2 ion species (0.150 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 78.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 5.824172730822E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #2 (acetic-solv): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  7.76163 A
1995s   Current memory usage:  61.581 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.094 x 0.094 x 0.094
1995s   Grid lengths: 6.000 x 6.000 x 6.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 1
1995s   Linearized traditional PBE
1995s   Boundary conditions from focusing
1995s   2 ion species (0.150 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 78.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 9.793622759239E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #3 (acetic-ref): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  0 A
1995s   Current memory usage:  61.405 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.188 x 0.188 x 0.188
1995s   Grid lengths: 12.000 x 12.000 x 12.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 1
1995s   Linearized traditional PBE
1995s   Multiple Debye-Huckel sphere boundary conditions
1995s   2 ion species (0.000 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 2.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 5.846917564309E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #4 (acetic-ref): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  0 A
1995s   Current memory usage:  61.405 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.094 x 0.094 x 0.094
1995s   Grid lengths: 6.000 x 6.000 x 6.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 1
1995s   Linearized traditional PBE
1995s   Boundary conditions from focusing
1995s   2 ion species (0.000 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 2.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 9.815953282539E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #5 (acetate-solv): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  7.76163 A
1995s   Current memory usage:  61.581 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.188 x 0.188 x 0.188
1995s   Grid lengths: 12.000 x 12.000 x 12.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 2
1995s   Linearized traditional PBE
1995s   Multiple Debye-Huckel sphere boundary conditions
1995s   2 ion species (0.150 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 78.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 8.221328580569E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #6 (acetate-solv): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  7.76163 A
1995s   Current memory usage:  61.581 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.094 x 0.094 x 0.094
1995s   Grid lengths: 6.000 x 6.000 x 6.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 2
1995s   Linearized traditional PBE
1995s   Boundary conditions from focusing
1995s   2 ion species (0.150 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 78.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 1.392867783119E+04 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #7 (acetate-ref): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  0 A
1995s   Current memory usage:  61.405 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.188 x 0.188 x 0.188
1995s   Grid lengths: 12.000 x 12.000 x 12.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 2
1995s   Linearized traditional PBE
1995s   Multiple Debye-Huckel sphere boundary conditions
1995s   2 ion species (0.000 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 2.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 8.420373979905E+03 kJ/mol
1995s   Calculating forces...
1995s [focusFillBound()]: WARNING:
1995s     Unusually large potential values
1995s     detected on the focusing boundary!
1995s     Convergence not guaranteed for NPBE/NRPBE calculations!
1995s 
1995s ----------------------------------------
1995s CALCULATION #8 (acetate-ref): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  0 A
1995s   Current memory usage:  61.405 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.094 x 0.094 x 0.094
1995s   Grid lengths: 6.000 x 6.000 x 6.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 2
1995s   Linearized traditional PBE
1995s   Boundary conditions from focusing
1995s   2 ion species (0.000 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 2.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 1.412716615065E+04 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #9 (proton-solv): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  7.76163 A
1995s   Current memory usage:  61.410 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.188 x 0.188 x 0.188
1995s   Grid lengths: 12.000 x 12.000 x 12.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 3
1995s   Linearized traditional PBE
1995s   Multiple Debye-Huckel sphere boundary conditions
1995s   2 ion species (0.150 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 78.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 3.863066835285E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #10 (proton-solv): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  7.76163 A
1995s   Current memory usage:  61.410 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.094 x 0.094 x 0.094
1995s   Grid lengths: 6.000 x 6.000 x 6.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 3
1995s   Linearized traditional PBE
1995s   Boundary conditions from focusing
1995s   2 ion species (0.150 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.150 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 78.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 6.289649216644E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s CALCULATION #11 (proton-ref): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  0 A
1995s   Current memory usage:  61.371 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.188 x 0.188 x 0.188
1995s   Grid lengths: 12.000 x 12.000 x 12.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 3
1995s   Linearized traditional PBE
1995s   Multiple Debye-Huckel sphere boundary conditions
1995s   2 ion species (0.000 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 2.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 4.162533113906E+03 kJ/mol
1995s   Calculating forces...
1995s [focusFillBound()]: WARNING:
1995s     Unusually large potential values
1995s     detected on the focusing boundary!
1995s     Convergence not guaranteed for NPBE/NRPBE calculations!
1995s 
1995s ----------------------------------------
1995s CALCULATION #12 (proton-ref): MULTIGRID
1995s   Setting up problem...
1995s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
1995s   Debye length:  0 A
1995s   Current memory usage:  61.371 MB total, 122.371 MB high water
1995s   Using linear spline charge discretization.
1995s   Grid dimensions: 65 x 65 x 65
1995s   Grid spacings: 0.094 x 0.094 x 0.094
1995s   Grid lengths: 6.000 x 6.000 x 6.000
1995s   Grid center: (0.000, -0.154, 1.287)
1995s   Multigrid levels: 5
1995s   Molecule ID: 3
1995s   Linearized traditional PBE
1995s   Boundary conditions from focusing
1995s   2 ion species (0.000 M ionic strength):
1995s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
1995s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
1995s   Solute dielectric: 2.000
1995s   Solvent dielectric: 2.000
1995s   Using "molecular" surface definition;harmonic average smoothing
1995s   Solvent probe radius: 0.000 A
1995s   Temperature:  293.000 K
1995s   Electrostatic energies will be calculated
1995s   Total electrostatic energy = 6.585616091973E+03 kJ/mol
1995s   Calculating forces...
1995s ----------------------------------------
1995s PRINT STATEMENTS
1995s 
1995s print energy 1 (acetic-solv) - 2 (acetic-ref) end
1995s   Local net energy (PE 0) = -2.233052329981E+01 kJ/mol
1995s   Global net ELEC energy = -2.233052329981E+01 kJ/mol
1995s 
1995s print energy 3 (acetate-solv) - 4 (acetate-ref) end
1995s   Local net energy (PE 0) = -1.984883194538E+02 kJ/mol
1995s   Global net ELEC energy = -1.984883194538E+02 kJ/mol
1995s 
1995s print energy 5 (proton-solv) - 6 (proton-ref) end
1995s   Local net energy (PE 0) = -2.959668753288E+02 kJ/mol
1995s   Global net ELEC energy = -2.959668753288E+02 kJ/mol
1995s 
1995s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end
1995s   Local net energy (PE 0) = -4.721246714828E+02 kJ/mol
1995s   Global net ELEC energy = -4.721246714828E+02 kJ/mol
1995s ----------------------------------------
1995s CLEANING UP AND SHUTTING DOWN...
1995s Destroying force arrays.
1995s No energy arrays to destroy.
1995s Destroying multigrid structures.
1995s Destroying finite element structures.
1995s Destroying 3 molecules
1995s Final memory usage:  0.001 MB total, 122.371 MB high water
1995s 
1995s 
1995s Thanks for using APBS!
1995s 
2026s Checking for intermediate energies in input file apbs-smol.out
2026s EXPECTED COMPUTED: 16
2026s EXPECTED EXPECTED: 16
2026s COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828]
2026s EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02']
2026s COMPUTED RESULT 5824.172730822
2026s COMPUTED RESULT 9793.622759239
2026s COMPUTED RESULT 5846.917564309
2026s COMPUTED RESULT 9815.953282539
2026s COMPUTED RESULT 8221.328580569
2026s COMPUTED RESULT 13928.67783119
2026s COMPUTED RESULT 8420.373979905
2026s COMPUTED RESULT 14127.16615065
2026s COMPUTED RESULT 3863.066835285
2026s COMPUTED RESULT 6289.649216644
2026s COMPUTED RESULT 4162.533113906
2026s COMPUTED RESULT 6585.616091973
2026s COMPUTED RESULT -22.33052329981
2026s COMPUTED RESULT -198.4883194538
2026s COMPUTED RESULT -295.9668753288
2026s COMPUTED RESULT -472.1246714828
2026s Running tests for ion-pmf section
2026s BINARY:  /usr/bin/apbs
2026s INPUT:   ion-pmf.in
2026s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in']
2026s asc_getToken: Error occurred (bailing out).
2026s Vio_scanf: Format problem with input.
2026s asc_getToken: Error occurred (bailing out).
2026s Vio_scanf: Format problem with input.
2026s 
2026s 
2026s ----------------------------------------------------------------------
2026s     APBS -- Adaptive Poisson-Boltzmann Solver
2026s     Version APBS 3.4.1
2026s     
2026s     Nathan A. Baker (nathan.baker@pnnl.gov)
2026s     Pacific Northwest National Laboratory
2026s     
2026s     Additional contributing authors listed in the code documentation.
2026s     
2026s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2026s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2026s     Northwest Division for the U.S. Department of Energy.
2026s     
2026s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2026s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2026s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2026s     Portions Copyright (c) 1995, Michael Holst.
2026s     All rights reserved.
2026s     
2026s     Redistribution and use in source and binary forms, with or without
2026s     modification, are permitted provided that the following conditions are met:
2026s     
2026s     * Redistributions of source code must retain the above copyright notice, this
2026s       list of conditions and the following disclaimer.
2026s     
2026s     * Redistributions in binary form must reproduce the above copyright notice,
2026s       this list of conditions and the following disclaimer in the documentation
2026s       and/or other materials provided with the distribution.
2026s     
2026s     * Neither the name of the developer nor the names of its contributors may be
2026s       used to endorse or promote products derived from this software without
2026s       specific prior written permission.
2026s     
2026s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2026s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2026s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2026s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2026s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2026s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2026s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2026s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2026s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2026s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2026s ----------------------------------------------------------------------
2026s     APBS uses FETK (the Finite Element ToolKit) to solve the
2026s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2026s     of finite element modeling class libraries developed by the Michael Holst
2026s     research group and written in an object-oriented form of C.  FEtk is
2026s     designed to solve general coupled systems of nonlinear partial differential
2026s     equations using adaptive finite element methods, inexact Newton methods,
2026s     and algebraic multilevel methods.  More information about FEtk may be found
2026s     at <http://www.FEtk.ORG>.
2026s ----------------------------------------------------------------------
2026s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2026s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2026s     which has been modified by Patrice Koehl
2026s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2026s     memory usage when solving the Poisson-Boltzmann equation.
2026s ----------------------------------------------------------------------
2026s     Please cite your use of APBS as:
2026s 
2026s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2026s     nanosystems: application to microtubules and the ribosome. Proc.
2026s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2026s     
2026s 
2026s This executable compiled on Mar  2 2024 at 20:11:10
2026s 
2026s Parsing input file ion-pmf.in...
2026s rank 0 size 1...
2026s Parsed input file.
2026s Reading parameter data from parm.dat.
2026s Got paths for 1 molecules
2026s Reading PDB-format atom data from ion-pmf.pdb.
2026s Vpmg_ibForce:  No force for zero ionic strength!
2026s Vpmg_ibForce:  No force for zero ionic strength!
2026s   2 atoms
2026s   Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
2026s   Net charge 2.00e+00 e
2026s Preparing to run 3 PBE calculations.
2026s ----------------------------------------
2026s CALCULATION #1 (solv): MULTIGRID
2026s   Setting up problem...
2026s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2026s   Debye length:  0 A
2026s   Current memory usage:  61.094 MB total, 61.094 MB high water
2026s   Using cubic spline charge discretization.
2026s   Grid dimensions: 65 x 65 x 65
2026s   Grid spacings: 0.210 x 0.210 x 0.210
2026s   Grid lengths: 13.440 x 13.440 x 13.440
2026s   Grid center: (0.000, 0.000, 0.000)
2026s   Multigrid levels: 5
2026s   Molecule ID: 1
2026s   Linearized traditional PBE
2026s   Multiple Debye-Huckel sphere boundary conditions
2026s   0 ion species (0.000 M ionic strength):
2026s   Solute dielectric: 1.000
2026s   Solvent dielectric: 78.540
2026s   Using spline-based surface definition;window = 0.300
2026s   Temperature:  298.150 K
2026s   Electrostatic energies will be calculated
2026s   All-atom solvent forces will be calculated
2026s   Total electrostatic energy = 7.839535983197E+03 kJ/mol
2026s   Calculating forces...
2026s   Printing per-atom forces for molecule 1 (kJ/mol/A)
2026s   Legend:
2026s     tot n -- total force for atom n
2026s     qf  n -- fixed charge force for atom n
2026s     db  n -- dielectric boundary force for atom n
2026s     ib  n -- ionic boundary force for atom n
2026s mgF  tot 0  -3.760e+03  -4.398e-05  -7.763e-05
2026s mgF  qf  0  -3.767e+03  -1.730e-05  -2.384e-05
2026s mgF  ib  0  0.000e+00  0.000e+00  0.000e+00
2026s mgF  db  0  6.148e+00  -2.668e-05  -5.379e-05
2026s mgF  tot 1  -3.596e+03  -5.403e-05  -1.012e-04
2026s mgF  qf  1  -3.598e+03  -2.253e-05  -3.831e-05
2026s mgF  ib  1  0.000e+00  0.000e+00  0.000e+00
2026s mgF  db  1  2.883e+00  -3.150e-05  -6.291e-05
2026s Vpmg_ibForce:  No force for zero ionic strength!
2026s Vpmg_ibForce:  No force for zero ionic strength!
2026s ----------------------------------------
2026s CALCULATION #2 (ref): MULTIGRID
2026s   Setting up problem...
2026s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2026s   Debye length:  0 A
2026s   Current memory usage:  61.095 MB total, 61.134 MB high water
2026s   Using cubic spline charge discretization.
2026s   Grid dimensions: 65 x 65 x 65
2026s   Grid spacings: 0.210 x 0.210 x 0.210
2026s   Grid lengths: 13.440 x 13.440 x 13.440
2026s   Grid center: (0.000, 0.000, 0.000)
2026s   Multigrid levels: 5
2026s   Molecule ID: 1
2026s   Linearized traditional PBE
2026s   Multiple Debye-Huckel sphere boundary conditions
2026s   0 ion species (0.000 M ionic strength):
2026s   Solute dielectric: 1.000
2026s   Solvent dielectric: 1.000
2026s   Using spline-based surface definition;window = 0.300
2026s   Temperature:  298.150 K
2026s   Electrostatic energies will be calculated
2026s   All-atom solvent forces will be calculated
2026s   Total electrostatic energy = 8.964727588811E+03 kJ/mol
2026s   Calculating forces...
2026s   Printing per-atom forces for molecule 1 (kJ/mol/A)
2026s   Legend:
2026s     tot n -- total force for atom n
2026s     qf  n -- fixed charge force for atom n
2026s     db  n -- dielectric boundary force for atom n
2026s     ib  n -- ionic boundary force for atom n
2026s mgF  tot 0  -3.850e+03  -4.055e-06  -7.703e-06
2026s mgF  qf  0  -3.850e+03  -4.055e-06  -7.703e-06
2026s mgF  ib  0  0.000e+00  0.000e+00  0.000e+00
2026s mgF  db  0  0.000e+00  0.000e+00  0.000e+00
2026s mgF  tot 1  -3.514e+03  -4.163e-06  -7.690e-06
2026s mgF  qf  1  -3.514e+03  -4.163e-06  -7.690e-06
2026s mgF  ib  1  0.000e+00  0.000e+00  0.000e+00
2026s mgF  db  1  0.000e+00  0.000e+00  0.000e+00
2026s ----------------------------------------
2026s CALCULATION #3 (asolv): APOLAR
2026s   Printing per atom forces (kJ/mol/A)
2026s   Legend:
2026s     tot  n -- Total force for atom n
2026s     sasa n -- SASA force for atom n
2026s     sav  n -- SAV force for atom n
2026s     wca  n -- WCA force for atom n
2026s 
2026s     gamma    0.000720
2026s     pressure 0.000000
2026s     bconc    0.033000 
2026s 
2026s   tot  0 2.715e-02 9.130e-07 9.130e-07
2026s   sasa 0 -1.100e+01 0.000e+00 0.000e+00
2026s   sav  0 0.000e+00 0.000e+00 0.000e+00
2026s   wca  0 -5.827e-01 -2.767e-05 -2.767e-05
2026s   tot  1 -2.723e-02 9.133e-07 9.133e-07
2026s   sasa 1 1.112e+01 0.000e+00 0.000e+00
2026s   sav  1 0.000e+00 0.000e+00 0.000e+00
2026s   wca  1 5.827e-01 -2.767e-05 -2.767e-05
2026s 
2026s 
2026s Solvent Accessible Surface Area (SASA) for each atom:
2026s   SASA for atom 0: 1.153275282828E+02
2026s   SASA for atom 1: 1.153114143344E+02
2026s 
2026s Total solvent accessible surface area: 230.639 A^2
2026s 
2026s Surface tension*area energies (gamma * SASA) for each atom:
2026s   Surface tension*area energy for atom 0: 8.303582036361E-02
2026s   Surface tension*area energy for atom 1: 8.302421832080E-02
2026s 
2026s Total surface tension energy: 0.16606 kJ/mol
2026s 
2026s Total solvent accessible volume: 0 A^3
2026s 
2026s Total pressure*volume energy: 0 kJ/mol
2026s 
2026s WCA dispersion Energies for each atom:
2026s   WCA energy for atom 0: -6.909718359932E+00
2026s   WCA energy for atom 1: -6.909422551724E+00
2026s 
2026s Total WCA energy: -13.8191 kJ/mol
2026s 
2026s Total non-polar energy = -1.365308087297E+01 kJ/mol
2026s ----------------------------------------
2026s PRINT STATEMENTS
2026s 
2026s print energy 1 (solv) - 2 (ref) end
2026s   Local net energy (PE 0) = -1.125191605614E+03 kJ/mol
2026s   Global net ELEC energy = -1.125191605614E+03 kJ/mol
2026s print force 1 (solv) - 2 (ref) end
2026s   Printing per-atom forces (kJ/mol/A).
2026s   Legend:
2026s     tot n -- Total force for atom n
2026s     qf  n -- Fixed charge force for atom n
2026s     db  n -- Dielectric boundary force for atom n
2026s     ib  n -- Ionic boundary force for atom n
2026s     tot all -- Total force for system
2026s   qf  0  8.398642197666E+01  -1.324564548552E-05  -1.613435632529E-05
2026s   ib  0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
2026s   db  0  6.148357059184E+00  -2.667517425897E-05  -5.378919678211E-05
2026s   tot 0  9.013477903584E+01  -3.992081974449E-05  -6.992355310740E-05
2026s   qf  1  -8.466423642736E+01  -1.836748045969E-05  -3.062224428458E-05
2026s   ib  1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
2026s   db  1  2.882739230548E+00  -3.149946357588E-05  -6.291495506459E-05
2026s   tot 1  -8.178149719681E+01  -4.986694403557E-05  -9.353719934917E-05
2026s   tot all 8.353281839029E+00  -8.978776378007E-05  -1.634607524566E-04
2026s 
2026s print APOL energy 1 (asolv) end
2026s   Global net APOL energy = -1.365308087297E+01 kJ/mol
2026s 
2026s print APOL force 1 (asolv) end
2026s   Printing per atom forces (kJ/mol/A)
2026s   Legend:
2026s     tot   n -- Total force for atom n
2026s     sasa  n -- SASA force for atom n
2026s     sav   n -- SAV force for atom n
2026s     wca   n -- WCA force for atom n
2026s     tot all -- Total force for system
2026s   sasa  0  -1.099776974333E+01  0.000000000000E+00  0.000000000000E+00
2026s   sav   0  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
2026s   wca   0  -5.826577086437E-01  -2.766670515801E-05  -2.766670515838E-05
2026s   tot   0  -1.158042745197E+01  -2.766670515801E-05  -2.766670515838E-05
2026s   sasa  1  1.111862435589E+01  0.000000000000E+00  0.000000000000E+00
2026s   sav   1  0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
2026s   wca   1  5.826560767576E-01  -2.767485007141E-05  -2.767485007183E-05
2026s   tot   1  1.170128043265E+01  -2.767485007141E-05  -2.767485007183E-05
2026s   tot all  1.208529806779E-01  -5.534155522943E-05  -5.534155523021E-05
2026s ----------------------------------------
2026s CLEANING UP AND SHUTTING DOWN...
2026s Destroying force arrays.
2026s No energy arrays to destroy.
2026s Destroying multigrid structures.
2026s Destroying finite element structures.
2026s Destroying 1 molecules
2026s Final memory usage:  60.711 MB total, 62.228 MB high water
2026s 
2026s 
2026s Thanks for using APBS!
2026s 
2026s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03)
2026s *** PASSED ***
2026s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03)
2026s *** PASSED ***
2026s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03)
2026s *** PASSED ***
2026s Elapsed time: 30.733384 seconds
2026s --------------------------------------------------------------------------------
2026s Total elapsed time: 30.733384 seconds
2026s Test results have been logged
2026s --------------------------------------------------------------------------------
2026s --------------------------------------------------------------------------------
2026s Testing input file apbs-mol-vdw.in
2026s 
2088s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03)
2088s *** PASSED ***
2088s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04)
2088s *** PASSED ***
2088s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05)
2088s *** PASSED ***
2088s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05)
2088s *** PASSED ***
2088s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05)
2088s *** PASSED ***
2088s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05)
2088s *** PASSED ***
2088s Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00)
2088s *** PASSED ***
2088s Elapsed time: 61.871865 seconds
2088s --------------------------------------------------------------------------------
2088s --------------------------------------------------------------------------------
2088s Testing input file apbs-smol-vdw.in
2088s 
2088s Checking for intermediate energies in input file ion-pmf.out
2088s EXPECTED COMPUTED: 4
2088s EXPECTED EXPECTED: 4
2088s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297]
2088s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*']
2088s COMPUTED RESULT 7839.535983197
2088s COMPUTED RESULT 8964.727588811
2088s COMPUTED RESULT -1125.191605614
2088s COMPUTED RESULT -13.65308087297
2088s Running tests for pka-lig section
2088s BINARY:  /usr/bin/apbs
2088s INPUT:   apbs-mol-vdw.in
2088s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in']
2088s asc_getToken: Error occurred (bailing out).
2088s Vio_scanf: Format problem with input.
2088s 
2088s 
2088s ----------------------------------------------------------------------
2088s     APBS -- Adaptive Poisson-Boltzmann Solver
2088s     Version APBS 3.4.1
2088s     
2088s     Nathan A. Baker (nathan.baker@pnnl.gov)
2088s     Pacific Northwest National Laboratory
2088s     
2088s     Additional contributing authors listed in the code documentation.
2088s     
2088s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2088s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2088s     Northwest Division for the U.S. Department of Energy.
2088s     
2088s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2088s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2088s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2088s     Portions Copyright (c) 1995, Michael Holst.
2088s     All rights reserved.
2088s     
2088s     Redistribution and use in source and binary forms, with or without
2088s     modification, are permitted provided that the following conditions are met:
2088s     
2088s     * Redistributions of source code must retain the above copyright notice, this
2088s       list of conditions and the following disclaimer.
2088s     
2088s     * Redistributions in binary form must reproduce the above copyright notice,
2088s       this list of conditions and the following disclaimer in the documentation
2088s       and/or other materials provided with the distribution.
2088s     
2088s     * Neither the name of the developer nor the names of its contributors may be
2088s       used to endorse or promote products derived from this software without
2088s       specific prior written permission.
2088s     
2088s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2088s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2088s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2088s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2088s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2088s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2088s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2088s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2088s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2088s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2088s ----------------------------------------------------------------------
2088s     APBS uses FETK (the Finite Element ToolKit) to solve the
2088s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2088s     of finite element modeling class libraries developed by the Michael Holst
2088s     research group and written in an object-oriented form of C.  FEtk is
2088s     designed to solve general coupled systems of nonlinear partial differential
2088s     equations using adaptive finite element methods, inexact Newton methods,
2088s     and algebraic multilevel methods.  More information about FEtk may be found
2088s     at <http://www.FEtk.ORG>.
2088s ----------------------------------------------------------------------
2088s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2088s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2088s     which has been modified by Patrice Koehl
2088s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2088s     memory usage when solving the Poisson-Boltzmann equation.
2088s ----------------------------------------------------------------------
2088s     Please cite your use of APBS as:
2088s 
2088s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2088s     nanosystems: application to microtubules and the ribosome. Proc.
2088s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2088s     
2088s 
2088s This executable compiled on Mar  2 2024 at 20:11:10
2088s 
2088s Parsing input file apbs-mol-vdw.in...
2088s rank 0 size 1...
2088s Parsed input file.
2088s Got paths for 3 molecules
2088s Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
2088s asc_getToken: Error occurred (bailing out).
2088s Vio_scanf: Format problem with input.
2088s   47 atoms
2088s   Centered at (2.482e+01, -3.315e+01, 2.154e+01)
2088s   Net charge 1.11e-16 e
2088s Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
2088s asc_getToken: Error occurred (bailing out).
2088s Vio_scanf: Format problem with input.
2088s   3423 atoms
2088s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2088s   Net charge 1.00e+00 e
2088s Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
2088s   3470 atoms
2088s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2088s   Net charge 1.00e+00 e
2088s Preparing to run 6 PBE calculations.
2088s ----------------------------------------
2088s CALCULATION #1 (lig-coarse): MULTIGRID
2088s   Setting up problem...
2088s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2088s   Debye length:  0 A
2088s   Current memory usage:  203.811 MB total, 203.811 MB high water
2088s   Using linear spline charge discretization.
2088s   Grid dimensions: 97 x 97 x 97
2088s   Grid spacings: 0.729 x 0.729 x 0.729
2088s   Grid lengths: 70.000 x 70.000 x 70.000
2088s   Grid center: (28.969, -32.507, 27.022)
2088s   Multigrid levels: 4
2088s   Molecule ID: 1
2088s   Linearized traditional PBE
2088s   Single Debye-Huckel sphere boundary conditions
2088s   2 ion species (0.000 M ionic strength):
2088s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2088s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2088s   Solute dielectric: 2.000
2088s   Solvent dielectric: 78.000
2088s   Using "molecular" surface definition; no smoothing
2088s   Solvent probe radius: 0.000 A
2088s   Temperature:  298.150 K
2088s   Electrostatic energies will be calculated
2088s   Total electrostatic energy = 2.224988750664E+03 kJ/mol
2088s   Calculating forces...
2088s ----------------------------------------
2088s CALCULATION #2 (lig-fine): MULTIGRID
2088s   Setting up problem...
2088s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2088s   Debye length:  0 A
2088s   Current memory usage:  203.811 MB total, 405.040 MB high water
2088s   Using linear spline charge discretization.
2088s   Grid dimensions: 97 x 97 x 97
2088s   Grid spacings: 0.250 x 0.250 x 0.250
2088s   Grid lengths: 24.000 x 24.000 x 24.000
2088s   Grid center: (24.822, -33.153, 21.545)
2088s   Multigrid levels: 4
2088s   Molecule ID: 1
2088s   Linearized traditional PBE
2088s   Boundary conditions from focusing
2088s   2 ion species (0.000 M ionic strength):
2088s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2088s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2088s   Solute dielectric: 2.000
2088s   Solvent dielectric: 78.000
2088s   Using "molecular" surface definition; no smoothing
2088s   Solvent probe radius: 0.000 A
2088s   Temperature:  298.150 K
2088s   Electrostatic energies will be calculated
2088s   Total electrostatic energy = 1.049695084686E+04 kJ/mol
2088s   Calculating forces...
2088s ----------------------------------------
2088s CALCULATION #3 (pka-coarse): MULTIGRID
2088s   Setting up problem...
2088s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2088s   Debye length:  0 A
2088s   Current memory usage:  270.381 MB total, 405.040 MB high water
2088s   Using linear spline charge discretization.
2088s   Grid dimensions: 97 x 97 x 97
2088s   Grid spacings: 0.729 x 0.729 x 0.729
2088s   Grid lengths: 70.000 x 70.000 x 70.000
2088s   Grid center: (28.969, -32.507, 27.022)
2088s   Multigrid levels: 4
2088s   Molecule ID: 2
2088s   Linearized traditional PBE
2088s   Single Debye-Huckel sphere boundary conditions
2088s   2 ion species (0.000 M ionic strength):
2088s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2088s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2088s   Solute dielectric: 2.000
2088s   Solvent dielectric: 78.000
2088s   Using "molecular" surface definition; no smoothing
2088s   Solvent probe radius: 0.000 A
2088s   Temperature:  298.150 K
2088s   Electrostatic energies will be calculated
2088s   Total electrostatic energy = 1.818450789522E+05 kJ/mol
2088s   Calculating forces...
2088s [focusFillBound()]: WARNING:
2088s     Unusually large potential values
2088s     detected on the focusing boundary!
2088s     Convergence not guaranteed for NPBE/NRPBE calculations!
2088s 
2088s ----------------------------------------
2088s CALCULATION #4 (pka-fine): MULTIGRID
2088s   Setting up problem...
2088s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2088s   Debye length:  0 A
2088s   Current memory usage:  270.381 MB total, 491.899 MB high water
2088s   Using linear spline charge discretization.
2088s   Grid dimensions: 97 x 97 x 97
2088s   Grid spacings: 0.250 x 0.250 x 0.250
2088s   Grid lengths: 24.000 x 24.000 x 24.000
2088s   Grid center: (24.822, -33.153, 21.545)
2088s   Multigrid levels: 4
2088s   Molecule ID: 2
2088s   Linearized traditional PBE
2088s   Boundary conditions from focusing
2088s   2 ion species (0.000 M ionic strength):
2088s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2088s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2088s   Solute dielectric: 2.000
2088s   Solvent dielectric: 78.000
2088s   Using "molecular" surface definition; no smoothing
2088s   Solvent probe radius: 0.000 A
2088s   Temperature:  298.150 K
2088s   Electrostatic energies will be calculated
2088s   Total electrostatic energy = 3.008254338259E+05 kJ/mol
2088s   Calculating forces...
2088s ----------------------------------------
2088s CALCULATION #5 (complex-coarse): MULTIGRID
2088s   Setting up problem...
2088s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2088s   Debye length:  0 A
2088s   Current memory usage:  271.059 MB total, 491.899 MB high water
2088s   Using linear spline charge discretization.
2088s   Grid dimensions: 97 x 97 x 97
2088s   Grid spacings: 0.729 x 0.729 x 0.729
2088s   Grid lengths: 70.000 x 70.000 x 70.000
2088s   Grid center: (28.969, -32.507, 27.022)
2088s   Multigrid levels: 4
2088s   Molecule ID: 3
2088s   Linearized traditional PBE
2088s   Single Debye-Huckel sphere boundary conditions
2088s   2 ion species (0.000 M ionic strength):
2088s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2088s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2088s   Solute dielectric: 2.000
2088s   Solvent dielectric: 78.000
2088s   Using "molecular" surface definition; no smoothing
2088s   Solvent probe radius: 0.000 A
2088s   Temperature:  298.150 K
2088s   Electrostatic energies will be calculated
2088s   Total electrostatic energy = 1.840918409896E+05 kJ/mol
2088s   Calculating forces...
2088s [focusFillBound()]: WARNING:
2088s     Unusually large potential values
2088s     detected on the focusing boundary!
2088s     Convergence not guaranteed for NPBE/NRPBE calculations!
2088s 
2088s ----------------------------------------
2088s CALCULATION #6 (complex-fine): MULTIGRID
2088s   Setting up problem...
2088s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2088s   Debye length:  0 A
2088s   Current memory usage:  271.059 MB total, 492.811 MB high water
2088s   Using linear spline charge discretization.
2088s   Grid dimensions: 97 x 97 x 97
2088s   Grid spacings: 0.250 x 0.250 x 0.250
2088s   Grid lengths: 24.000 x 24.000 x 24.000
2088s   Grid center: (24.822, -33.153, 21.545)
2088s   Multigrid levels: 4
2088s   Molecule ID: 3
2088s   Linearized traditional PBE
2088s   Boundary conditions from focusing
2088s   2 ion species (0.000 M ionic strength):
2088s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2088s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2088s   Solute dielectric: 2.000
2088s   Solvent dielectric: 78.000
2088s   Using "molecular" surface definition; no smoothing
2088s   Solvent probe radius: 0.000 A
2088s   Temperature:  298.150 K
2088s   Electrostatic energies will be calculated
2088s   Total electrostatic energy = 3.113304681884E+05 kJ/mol
2088s   Calculating forces...
2088s ----------------------------------------
2088s PRINT STATEMENTS
2088s 
2088s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
2088s   Local net energy (PE 0) = 8.083515648730E+00 kJ/mol
2088s   Global net ELEC energy = 8.083515648730E+00 kJ/mol
2088s ----------------------------------------
2088s CLEANING UP AND SHUTTING DOWN...
2088s Destroying force arrays.
2088s No energy arrays to destroy.
2088s Destroying multigrid structures.
2088s Destroying finite element structures.
2088s Destroying 3 molecules
2088s Final memory usage:  0.001 MB total, 492.811 MB high water
2088s 
2088s 
2088s Thanks for using APBS!
2088s 
2129s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03)
2129s *** PASSED ***
2129s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04)
2129s *** PASSED ***
2129s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05)
2129s *** PASSED ***
2129s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05)
2129s *** PASSED ***
2129s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05)
2129s *** PASSED ***
2129s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05)
2129s *** PASSED ***
2129s Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01)
2129s *** PASSED ***
2129s Elapsed time: 41.494695 seconds
2129s --------------------------------------------------------------------------------
2129s --------------------------------------------------------------------------------
2129s Testing input file apbs-mol-surf.in
2129s 
2129s Checking for intermediate energies in input file apbs-mol-vdw.out
2129s EXPECTED COMPUTED: 7
2129s EXPECTED EXPECTED: 7
2129s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873]
2129s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00']
2129s COMPUTED RESULT 2224.988750664
2129s COMPUTED RESULT 10496.95084686
2129s COMPUTED RESULT 181845.0789522
2129s COMPUTED RESULT 300825.4338259
2129s COMPUTED RESULT 184091.8409896
2129s COMPUTED RESULT 311330.4681884
2129s COMPUTED RESULT 8.08351564873
2129s BINARY:  /usr/bin/apbs
2129s INPUT:   apbs-smol-vdw.in
2129s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in']
2129s asc_getToken: Error occurred (bailing out).
2129s Vio_scanf: Format problem with input.
2129s 
2129s 
2129s ----------------------------------------------------------------------
2129s     APBS -- Adaptive Poisson-Boltzmann Solver
2129s     Version APBS 3.4.1
2129s     
2129s     Nathan A. Baker (nathan.baker@pnnl.gov)
2129s     Pacific Northwest National Laboratory
2129s     
2129s     Additional contributing authors listed in the code documentation.
2129s     
2129s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2129s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2129s     Northwest Division for the U.S. Department of Energy.
2129s     
2129s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2129s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2129s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2129s     Portions Copyright (c) 1995, Michael Holst.
2129s     All rights reserved.
2129s     
2129s     Redistribution and use in source and binary forms, with or without
2129s     modification, are permitted provided that the following conditions are met:
2129s     
2129s     * Redistributions of source code must retain the above copyright notice, this
2129s       list of conditions and the following disclaimer.
2129s     
2129s     * Redistributions in binary form must reproduce the above copyright notice,
2129s       this list of conditions and the following disclaimer in the documentation
2129s       and/or other materials provided with the distribution.
2129s     
2129s     * Neither the name of the developer nor the names of its contributors may be
2129s       used to endorse or promote products derived from this software without
2129s       specific prior written permission.
2129s     
2129s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2129s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2129s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2129s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2129s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2129s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2129s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2129s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2129s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2129s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2129s ----------------------------------------------------------------------
2129s     APBS uses FETK (the Finite Element ToolKit) to solve the
2129s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2129s     of finite element modeling class libraries developed by the Michael Holst
2129s     research group and written in an object-oriented form of C.  FEtk is
2129s     designed to solve general coupled systems of nonlinear partial differential
2129s     equations using adaptive finite element methods, inexact Newton methods,
2129s     and algebraic multilevel methods.  More information about FEtk may be found
2129s     at <http://www.FEtk.ORG>.
2129s ----------------------------------------------------------------------
2129s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2129s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2129s     which has been modified by Patrice Koehl
2129s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2129s     memory usage when solving the Poisson-Boltzmann equation.
2129s ----------------------------------------------------------------------
2129s     Please cite your use of APBS as:
2129s 
2129s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2129s     nanosystems: application to microtubules and the ribosome. Proc.
2129s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2129s     
2129s 
2129s This executable compiled on Mar  2 2024 at 20:11:10
2129s 
2129s Parsing input file apbs-smol-vdw.in...
2129s rank 0 size 1...
2129s Parsed input file.
2129s Got paths for 3 molecules
2129s Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
2129s asc_getToken: Error occurred (bailing out).
2129s Vio_scanf: Format problem with input.
2129s   47 atoms
2129s   Centered at (2.482e+01, -3.315e+01, 2.154e+01)
2129s   Net charge 1.11e-16 e
2129s Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
2129s asc_getToken: Error occurred (bailing out).
2129s Vio_scanf: Format problem with input.
2129s   3423 atoms
2129s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2129s   Net charge 1.00e+00 e
2129s Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
2129s   3470 atoms
2129s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2129s   Net charge 1.00e+00 e
2129s Preparing to run 6 PBE calculations.
2129s ----------------------------------------
2129s CALCULATION #1 (lig-coarse): MULTIGRID
2129s   Setting up problem...
2129s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2129s   Debye length:  0 A
2129s   Current memory usage:  203.811 MB total, 203.811 MB high water
2129s   Using linear spline charge discretization.
2129s   Grid dimensions: 97 x 97 x 97
2129s   Grid spacings: 0.729 x 0.729 x 0.729
2129s   Grid lengths: 70.000 x 70.000 x 70.000
2129s   Grid center: (28.969, -32.507, 27.022)
2129s   Multigrid levels: 4
2129s   Molecule ID: 1
2129s   Linearized traditional PBE
2129s   Single Debye-Huckel sphere boundary conditions
2129s   2 ion species (0.000 M ionic strength):
2129s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2129s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2129s   Solute dielectric: 2.000
2129s   Solvent dielectric: 78.000
2129s   Using "molecular" surface definition;harmonic average smoothing
2129s   Solvent probe radius: 0.000 A
2129s   Temperature:  298.150 K
2129s   Electrostatic energies will be calculated
2129s   Total electrostatic energy = 2.226793167046E+03 kJ/mol
2129s   Calculating forces...
2129s ----------------------------------------
2129s CALCULATION #2 (lig-fine): MULTIGRID
2129s   Setting up problem...
2129s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2129s   Debye length:  0 A
2129s   Current memory usage:  203.811 MB total, 405.040 MB high water
2129s   Using linear spline charge discretization.
2129s   Grid dimensions: 97 x 97 x 97
2129s   Grid spacings: 0.250 x 0.250 x 0.250
2129s   Grid lengths: 24.000 x 24.000 x 24.000
2129s   Grid center: (24.822, -33.153, 21.545)
2129s   Multigrid levels: 4
2129s   Molecule ID: 1
2129s   Linearized traditional PBE
2129s   Boundary conditions from focusing
2129s   2 ion species (0.000 M ionic strength):
2129s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2129s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2129s   Solute dielectric: 2.000
2129s   Solvent dielectric: 78.000
2129s   Using "molecular" surface definition;harmonic average smoothing
2129s   Solvent probe radius: 0.000 A
2129s   Temperature:  298.150 K
2129s   Electrostatic energies will be calculated
2129s   Total electrostatic energy = 1.050504485887E+04 kJ/mol
2129s   Calculating forces...
2129s ----------------------------------------
2129s CALCULATION #3 (pka-coarse): MULTIGRID
2129s   Setting up problem...
2129s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2129s   Debye length:  0 A
2129s   Current memory usage:  270.381 MB total, 405.040 MB high water
2129s   Using linear spline charge discretization.
2129s   Grid dimensions: 97 x 97 x 97
2129s   Grid spacings: 0.729 x 0.729 x 0.729
2129s   Grid lengths: 70.000 x 70.000 x 70.000
2129s   Grid center: (28.969, -32.507, 27.022)
2129s   Multigrid levels: 4
2129s   Molecule ID: 2
2129s   Linearized traditional PBE
2129s   Single Debye-Huckel sphere boundary conditions
2129s   2 ion species (0.000 M ionic strength):
2129s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2129s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2129s   Solute dielectric: 2.000
2129s   Solvent dielectric: 78.000
2129s   Using "molecular" surface definition;harmonic average smoothing
2129s   Solvent probe radius: 0.000 A
2129s   Temperature:  298.150 K
2129s   Electrostatic energies will be calculated
2129s   Total electrostatic energy = 1.827976621645E+05 kJ/mol
2129s   Calculating forces...
2129s [focusFillBound()]: WARNING:
2129s     Unusually large potential values
2129s     detected on the focusing boundary!
2129s     Convergence not guaranteed for NPBE/NRPBE calculations!
2129s 
2129s ----------------------------------------
2129s CALCULATION #4 (pka-fine): MULTIGRID
2129s   Setting up problem...
2129s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2129s   Debye length:  0 A
2129s   Current memory usage:  270.381 MB total, 491.899 MB high water
2129s   Using linear spline charge discretization.
2129s   Grid dimensions: 97 x 97 x 97
2129s   Grid spacings: 0.250 x 0.250 x 0.250
2129s   Grid lengths: 24.000 x 24.000 x 24.000
2129s   Grid center: (24.822, -33.153, 21.545)
2129s   Multigrid levels: 4
2129s   Molecule ID: 2
2129s   Linearized traditional PBE
2129s   Boundary conditions from focusing
2129s   2 ion species (0.000 M ionic strength):
2129s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2129s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2129s   Solute dielectric: 2.000
2129s   Solvent dielectric: 78.000
2129s   Using "molecular" surface definition;harmonic average smoothing
2129s   Solvent probe radius: 0.000 A
2129s   Temperature:  298.150 K
2129s   Electrostatic energies will be calculated
2129s   Total electrostatic energy = 3.017228546773E+05 kJ/mol
2129s   Calculating forces...
2129s ----------------------------------------
2129s CALCULATION #5 (complex-coarse): MULTIGRID
2129s   Setting up problem...
2129s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2129s   Debye length:  0 A
2129s   Current memory usage:  271.059 MB total, 491.899 MB high water
2129s   Using linear spline charge discretization.
2129s   Grid dimensions: 97 x 97 x 97
2129s   Grid spacings: 0.729 x 0.729 x 0.729
2129s   Grid lengths: 70.000 x 70.000 x 70.000
2129s   Grid center: (28.969, -32.507, 27.022)
2129s   Multigrid levels: 4
2129s   Molecule ID: 3
2129s   Linearized traditional PBE
2129s   Single Debye-Huckel sphere boundary conditions
2129s   2 ion species (0.000 M ionic strength):
2129s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2129s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2129s   Solute dielectric: 2.000
2129s   Solvent dielectric: 78.000
2129s   Using "molecular" surface definition;harmonic average smoothing
2129s   Solvent probe radius: 0.000 A
2129s   Temperature:  298.150 K
2129s   Electrostatic energies will be calculated
2129s   Total electrostatic energy = 1.850819075387E+05 kJ/mol
2129s   Calculating forces...
2129s [focusFillBound()]: WARNING:
2129s     Unusually large potential values
2129s     detected on the focusing boundary!
2129s     Convergence not guaranteed for NPBE/NRPBE calculations!
2129s 
2129s ----------------------------------------
2129s CALCULATION #6 (complex-fine): MULTIGRID
2129s   Setting up problem...
2129s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2129s   Debye length:  0 A
2129s   Current memory usage:  271.059 MB total, 492.811 MB high water
2129s   Using linear spline charge discretization.
2129s   Grid dimensions: 97 x 97 x 97
2129s   Grid spacings: 0.250 x 0.250 x 0.250
2129s   Grid lengths: 24.000 x 24.000 x 24.000
2129s   Grid center: (24.822, -33.153, 21.545)
2129s   Multigrid levels: 4
2129s   Molecule ID: 3
2129s   Linearized traditional PBE
2129s   Boundary conditions from focusing
2129s   2 ion species (0.000 M ionic strength):
2129s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2129s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2129s   Solute dielectric: 2.000
2129s   Solvent dielectric: 78.000
2129s   Using "molecular" surface definition;harmonic average smoothing
2129s   Solvent probe radius: 0.000 A
2129s   Temperature:  298.150 K
2129s   Electrostatic energies will be calculated
2129s   Total electrostatic energy = 3.122488625388E+05 kJ/mol
2129s   Calculating forces...
2129s ----------------------------------------
2129s PRINT STATEMENTS
2129s 
2129s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
2129s   Local net energy (PE 0) = 2.096300255723E+01 kJ/mol
2129s   Global net ELEC energy = 2.096300255723E+01 kJ/mol
2129s ----------------------------------------
2129s CLEANING UP AND SHUTTING DOWN...
2129s Destroying force arrays.
2129s No energy arrays to destroy.
2129s Destroying multigrid structures.
2129s Destroying finite element structures.
2129s Destroying 3 molecules
2129s Final memory usage:  0.001 MB total, 492.811 MB high water
2129s 
2129s 
2129s Thanks for using APBS!
2129s 
2170s Checking for intermediate energies in input file apbs-smol-vdw.out
2170s EXPECTED COMPUTED: 7
2170s EXPECTED EXPECTED: 7
2170s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723]
2170s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01']
2170s COMPUTED RESULT 2226.793167046
2170s COMPUTED RESULT 10505.04485887
2170s COMPUTED RESULT 182797.6621645
2170s COMPUTED RESULT 301722.8546773
2170s COMPUTED RESULT 185081.9075387
2170s COMPUTED RESULT 312248.8625388
2170s COMPUTED RESULT 20.96300255723
2170s BINARY:  /usr/bin/apbs
2170s INPUT:   apbs-mol-surf.in
2170s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in']
2170s asc_getToken: Error occurred (bailing out).
2170s Vio_scanf: Format problem with input.
2170s 
2170s 
2170s ----------------------------------------------------------------------
2170s     APBS -- Adaptive Poisson-Boltzmann Solver
2170s     Version APBS 3.4.1
2170s     
2170s     Nathan A. Baker (nathan.baker@pnnl.gov)
2170s     Pacific Northwest National Laboratory
2170s     
2170s     Additional contributing authors listed in the code documentation.
2170s     
2170s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2170s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2170s     Northwest Division for the U.S. Department of Energy.
2170s     
2170s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2170s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2170s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2170s     Portions Copyright (c) 1995, Michael Holst.
2170s     All rights reserved.
2170s     
2170s     Redistribution and use in source and binary forms, with or without
2170s     modification, are permitted provided that the following conditions are met:
2170s     
2170s     * Redistributions of source code must retain the above copyright notice, this
2170s       list of conditions and the following disclaimer.
2170s     
2170s     * Redistributions in binary form must reproduce the above copyright notice,
2170s       this list of conditions and the following disclaimer in the documentation
2170s       and/or other materials provided with the distribution.
2170s     
2170s     * Neither the name of the developer nor the names of its contributors may be
2170s       used to endorse or promote products derived from this software without
2170s       specific prior written permission.
2170s     
2170s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2170s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2170s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2170s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2170s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2170s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2170s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2170s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2170s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2170s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2170s ----------------------------------------------------------------------
2170s     APBS uses FETK (the Finite Element ToolKit) to solve the
2170s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2170s     of finite element modeling class libraries developed by the Michael Holst
2170s     research group and written in an object-oriented form of C.  FEtk is
2170s     designed to solve general coupled systems of nonlinear partial differential
2170s     equations using adaptive finite element methods, inexact Newton methods,
2170s     and algebraic multilevel methods.  More information about FEtk may be found
2170s     at <http://www.FEtk.ORG>.
2170s ----------------------------------------------------------------------
2170s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2170s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2170s     which has been modified by Patrice Koehl
2170s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2170s     memory usage when solving the Poisson-Boltzmann equation.
2170s ----------------------------------------------------------------------
2170s     Please cite your use of APBS as:
2170s 
2170s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2170s     nanosystems: application to microtubules and the ribosome. Proc.
2170s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2170s     
2170s 
2170s This executable compiled on Mar  2 2024 at 20:11:10
2170s 
2170s Parsing input file apbs-mol-surf.in...
2170s rank 0 size 1...
2170s Parsed input file.
2170s Got paths for 3 molecules
2170s Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
2170s asc_getToken: Error occurred (bailing out).
2170s Vio_scanf: Format problem with input.
2170s   47 atoms
2170s   Centered at (2.482e+01, -3.315e+01, 2.154e+01)
2170s   Net charge 1.11e-16 e
2170s Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
2170s asc_getToken: Error occurred (bailing out).
2170s Vio_scanf: Format problem with input.
2170s   3423 atoms
2170s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2170s   Net charge 1.00e+00 e
2170s Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
2170s   3470 atoms
2170s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2170s   Net charge 1.00e+00 e
2170s Preparing to run 6 PBE calculations.
2170s ----------------------------------------
2170s CALCULATION #1 (lig-coarse): MULTIGRID
2170s   Setting up problem...
2170s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2170s   Debye length:  0 A
2170s   Current memory usage:  203.396 MB total, 203.396 MB high water
2170s   Using linear spline charge discretization.
2170s   Grid dimensions: 97 x 97 x 97
2170s   Grid spacings: 0.729 x 0.729 x 0.729
2170s   Grid lengths: 70.000 x 70.000 x 70.000
2170s   Grid center: (28.969, -32.507, 27.022)
2170s   Multigrid levels: 4
2170s   Molecule ID: 1
2170s   Linearized traditional PBE
2170s   Single Debye-Huckel sphere boundary conditions
2170s   2 ion species (0.000 M ionic strength):
2170s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2170s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2170s   Solute dielectric: 2.000
2170s   Solvent dielectric: 78.000
2170s   Using "molecular" surface definition; no smoothing
2170s   Solvent probe radius: 1.400 A
2170s   Temperature:  298.150 K
2170s   Electrostatic energies will be calculated
2170s   Total electrostatic energy = 2.244350164274E+03 kJ/mol
2170s   Calculating forces...
2170s ----------------------------------------
2170s CALCULATION #2 (lig-fine): MULTIGRID
2170s   Setting up problem...
2170s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2170s   Debye length:  0 A
2170s   Current memory usage:  203.396 MB total, 404.625 MB high water
2170s   Using linear spline charge discretization.
2170s   Grid dimensions: 97 x 97 x 97
2170s   Grid spacings: 0.250 x 0.250 x 0.250
2170s   Grid lengths: 24.000 x 24.000 x 24.000
2170s   Grid center: (24.822, -33.153, 21.545)
2170s   Multigrid levels: 4
2170s   Molecule ID: 1
2170s   Linearized traditional PBE
2170s   Boundary conditions from focusing
2170s   2 ion species (0.000 M ionic strength):
2170s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2170s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2170s   Solute dielectric: 2.000
2170s   Solvent dielectric: 78.000
2170s   Using "molecular" surface definition; no smoothing
2170s   Solvent probe radius: 1.400 A
2170s   Temperature:  298.150 K
2170s   Electrostatic energies will be calculated
2170s   Total electrostatic energy = 1.052149475373E+04 kJ/mol
2170s   Calculating forces...
2170s ----------------------------------------
2170s CALCULATION #3 (pka-coarse): MULTIGRID
2170s   Setting up problem...
2170s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2170s   Debye length:  0 A
2170s   Current memory usage:  230.750 MB total, 404.625 MB high water
2170s   Using linear spline charge discretization.
2170s   Grid dimensions: 97 x 97 x 97
2170s   Grid spacings: 0.729 x 0.729 x 0.729
2170s   Grid lengths: 70.000 x 70.000 x 70.000
2170s   Grid center: (28.969, -32.507, 27.022)
2170s   Multigrid levels: 4
2170s   Molecule ID: 2
2170s   Linearized traditional PBE
2170s   Single Debye-Huckel sphere boundary conditions
2170s   2 ion species (0.000 M ionic strength):
2170s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2170s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2170s   Solute dielectric: 2.000
2170s   Solvent dielectric: 78.000
2170s   Using "molecular" surface definition; no smoothing
2170s   Solvent probe radius: 1.400 A
2170s   Temperature:  298.150 K
2170s   Electrostatic energies will be calculated
2170s   Total electrostatic energy = 1.862615690066E+05 kJ/mol
2170s   Calculating forces...
2170s [focusFillBound()]: WARNING:
2170s     Unusually large potential values
2170s     detected on the focusing boundary!
2170s     Convergence not guaranteed for NPBE/NRPBE calculations!
2170s 
2170s ----------------------------------------
2170s CALCULATION #4 (pka-fine): MULTIGRID
2170s   Setting up problem...
2170s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2170s   Debye length:  0 A
2170s   Current memory usage:  230.750 MB total, 452.268 MB high water
2170s   Using linear spline charge discretization.
2170s   Grid dimensions: 97 x 97 x 97
2170s   Grid spacings: 0.250 x 0.250 x 0.250
2170s   Grid lengths: 24.000 x 24.000 x 24.000
2170s   Grid center: (24.822, -33.153, 21.545)
2170s   Multigrid levels: 4
2170s   Molecule ID: 2
2170s   Linearized traditional PBE
2170s   Boundary conditions from focusing
2170s   2 ion species (0.000 M ionic strength):
2170s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2170s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2170s   Solute dielectric: 2.000
2170s   Solvent dielectric: 78.000
2170s   Using "molecular" surface definition; no smoothing
2170s   Solvent probe radius: 1.400 A
2170s   Temperature:  298.150 K
2170s   Electrostatic energies will be calculated
2170s   Total electrostatic energy = 3.051810884053E+05 kJ/mol
2170s   Calculating forces...
2170s ----------------------------------------
2170s CALCULATION #5 (complex-coarse): MULTIGRID
2170s   Setting up problem...
2170s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2170s   Debye length:  0 A
2170s   Current memory usage:  230.854 MB total, 452.268 MB high water
2170s   Using linear spline charge discretization.
2170s   Grid dimensions: 97 x 97 x 97
2170s   Grid spacings: 0.729 x 0.729 x 0.729
2170s   Grid lengths: 70.000 x 70.000 x 70.000
2170s   Grid center: (28.969, -32.507, 27.022)
2170s   Multigrid levels: 4
2170s   Molecule ID: 3
2170s   Linearized traditional PBE
2170s   Single Debye-Huckel sphere boundary conditions
2170s   2 ion species (0.000 M ionic strength):
2170s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2170s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2170s   Solute dielectric: 2.000
2170s   Solvent dielectric: 78.000
2170s   Using "molecular" surface definition; no smoothing
2170s   Solvent probe radius: 1.400 A
2170s   Temperature:  298.150 K
2170s   Electrostatic energies will be calculated
2170s   Total electrostatic energy = 1.886625455219E+05 kJ/mol
2170s   Calculating forces...
2170s [focusFillBound()]: WARNING:
2170s     Unusually large potential values
2170s     detected on the focusing boundary!
2170s     Convergence not guaranteed for NPBE/NRPBE calculations!
2170s 
2170s ----------------------------------------
2170s CALCULATION #6 (complex-fine): MULTIGRID
2170s   Setting up problem...
2170s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2170s   Debye length:  0 A
2170s   Current memory usage:  230.854 MB total, 452.606 MB high water
2170s   Using linear spline charge discretization.
2170s   Grid dimensions: 97 x 97 x 97
2170s   Grid spacings: 0.250 x 0.250 x 0.250
2170s   Grid lengths: 24.000 x 24.000 x 24.000
2170s   Grid center: (24.822, -33.153, 21.545)
2170s   Multigrid levels: 4
2170s   Molecule ID: 3
2170s   Linearized traditional PBE
2170s   Boundary conditions from focusing
2170s   2 ion species (0.000 M ionic strength):
2170s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2170s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2170s   Solute dielectric: 2.000
2170s   Solvent dielectric: 78.000
2170s   Using "molecular" surface definition; no smoothing
2170s   Solvent probe radius: 1.400 A
2170s   Temperature:  298.150 K
2170s   Electrostatic energies will be calculated
2170s   Total electrostatic energy = 3.158218439277E+05 kJ/mol
2170s   Calculating forces...
2170s ----------------------------------------
2170s PRINT STATEMENTS
2170s 
2170s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
2170s   Local net energy (PE 0) = 1.192607686581E+02 kJ/mol
2170s   Global net ELEC energy = 1.192607686581E+02 kJ/mol
2170s ----------------------------------------
2170s CLEANING UP AND SHUTTING DOWN...
2170s Destroying force arrays.
2170s No energy arrays to destroy.
2170s Destroying multigrid structures.
2170s Destroying finite element structures.
2170s Destroying 3 molecules
2170s Final memory usage:  0.001 MB total, 452.606 MB high water
2170s 
2170s 
2170s Thanks for using APBS!
2170s 
2170s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03)
2170s *** PASSED ***
2170s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04)
2170s *** PASSED ***
2170s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05)
2170s *** PASSED ***
2170s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05)
2170s *** PASSED ***
2170s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05)
2170s *** PASSED ***
2170s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05)
2170s *** PASSED ***
2170s Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02)
2170s *** PASSED ***
2170s Elapsed time: 40.380189 seconds
2170s --------------------------------------------------------------------------------
2170s --------------------------------------------------------------------------------
2170s Testing input file apbs-smol-surf.in
2170s 
2206s Checking for intermediate energies in input file apbs-mol-surf.out
2206s EXPECTED COMPUTED: 7
2206s EXPECTED EXPECTED: 7
2206s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581]
2206s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02']
2206s COMPUTED RESULT 2244.350164274
2206s COMPUTED RESULT 10521.49475373
2206s COMPUTED RESULT 186261.5690066
2206s COMPUTED RESULT 305181.0884053
2206s COMPUTED RESULT 188662.5455219
2206s COMPUTED RESULT 315821.8439277
2206s COMPUTED RESULT 119.2607686581
2206s BINARY:  /usr/bin/apbs
2206s INPUT:   apbs-smol-surf.in
2206s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in']
2206s asc_getToken: Error occurred (bailing out).
2206s Vio_scanf: Format problem with input.
2206s 
2206s 
2206s ----------------------------------------------------------------------
2206s     APBS -- Adaptive Poisson-Boltzmann Solver
2206s     Version APBS 3.4.1
2206s     
2206s     Nathan A. Baker (nathan.baker@pnnl.gov)
2206s     Pacific Northwest National Laboratory
2206s     
2206s     Additional contributing authors listed in the code documentation.
2206s     
2206s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2206s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2206s     Northwest Division for the U.S. Department of Energy.
2206s     
2206s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2206s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2206s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2206s     Portions Copyright (c) 1995, Michael Holst.
2206s     All rights reserved.
2206s     
2206s     Redistribution and use in source and binary forms, with or without
2206s     modification, are permitted provided that the following conditions are met:
2206s     
2206s     * Redistributions of source code must retain the above copyright notice, this
2206s       list of conditions and the following disclaimer.
2206s     
2206s     * Redistributions in binary form must reproduce the above copyright notice,
2206s       this list of conditions and the following disclaimer in the documentation
2206s       and/or other materials provided with the distribution.
2206s     
2206s     * Neither the name of the developer nor the names of its contributors may be
2206s       used to endorse or promote products derived from this software without
2206s       specific prior written permission.
2206s     
2206s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2206s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2206s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2206s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2206s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2206s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2206s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2206s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2206s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2206s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2206s ----------------------------------------------------------------------
2206s     APBS uses FETK (the Finite Element ToolKit) to solve the
2206s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2206s     of finite element modeling class libraries developed by the Michael Holst
2206s     research group and written in an object-oriented form of C.  FEtk is
2206s     designed to solve general coupled systems of nonlinear partial differential
2206s     equations using adaptive finite element methods, inexact Newton methods,
2206s     and algebraic multilevel methods.  More information about FEtk may be found
2206s     at <http://www.FEtk.ORG>.
2206s ----------------------------------------------------------------------
2206s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2206s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2206s     which has been modified by Patrice Koehl
2206s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2206s     memory usage when solving the Poisson-Boltzmann equation.
2206s ----------------------------------------------------------------------
2206s     Please cite your use of APBS as:
2206s 
2206s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2206s     nanosystems: application to microtubules and the ribosome. Proc.
2206s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2206s     
2206s 
2206s This executable compiled on Mar  2 2024 at 20:11:10
2206s 
2206s Parsing input file apbs-smol-surf.in...
2206s rank 0 size 1...
2206s Parsed input file.
2206s Got paths for 3 molecules
2206s Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
2206s asc_getToken: Error occurred (bailing out).
2206s Vio_scanf: Format problem with input.
2206s   47 atoms
2206s   Centered at (2.482e+01, -3.315e+01, 2.154e+01)
2206s   Net charge 1.11e-16 e
2206s Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
2206s asc_getToken: Error occurred (bailing out).
2206s Vio_scanf: Format problem with input.
2206s   3423 atoms
2206s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2206s   Net charge 1.00e+00 e
2206s Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
2206s   3470 atoms
2206s   Centered at (2.897e+01, -3.251e+01, 2.702e+01)
2206s   Net charge 1.00e+00 e
2206s Preparing to run 6 PBE calculations.
2206s ----------------------------------------
2206s CALCULATION #1 (lig-coarse): MULTIGRID
2206s   Setting up problem...
2206s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2206s   Debye length:  0 A
2206s   Current memory usage:  203.396 MB total, 203.396 MB high water
2206s   Using linear spline charge discretization.
2206s   Grid dimensions: 97 x 97 x 97
2206s   Grid spacings: 0.729 x 0.729 x 0.729
2206s   Grid lengths: 70.000 x 70.000 x 70.000
2206s   Grid center: (28.969, -32.507, 27.022)
2206s   Multigrid levels: 4
2206s   Molecule ID: 1
2206s   Linearized traditional PBE
2206s   Single Debye-Huckel sphere boundary conditions
2206s   2 ion species (0.000 M ionic strength):
2206s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2206s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2206s   Solute dielectric: 2.000
2206s   Solvent dielectric: 78.000
2206s   Using "molecular" surface definition;harmonic average smoothing
2206s   Solvent probe radius: 1.400 A
2206s   Temperature:  298.150 K
2206s   Electrostatic energies will be calculated
2206s   Total electrostatic energy = 2.251466789420E+03 kJ/mol
2206s   Calculating forces...
2206s ----------------------------------------
2206s CALCULATION #2 (lig-fine): MULTIGRID
2206s   Setting up problem...
2206s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2206s   Debye length:  0 A
2206s   Current memory usage:  203.396 MB total, 404.625 MB high water
2206s   Using linear spline charge discretization.
2206s   Grid dimensions: 97 x 97 x 97
2206s   Grid spacings: 0.250 x 0.250 x 0.250
2206s   Grid lengths: 24.000 x 24.000 x 24.000
2206s   Grid center: (24.822, -33.153, 21.545)
2206s   Multigrid levels: 4
2206s   Molecule ID: 1
2206s   Linearized traditional PBE
2206s   Boundary conditions from focusing
2206s   2 ion species (0.000 M ionic strength):
2206s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2206s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2206s   Solute dielectric: 2.000
2206s   Solvent dielectric: 78.000
2206s   Using "molecular" surface definition;harmonic average smoothing
2206s   Solvent probe radius: 1.400 A
2206s   Temperature:  298.150 K
2206s   Electrostatic energies will be calculated
2206s   Total electrostatic energy = 1.052814502873E+04 kJ/mol
2206s   Calculating forces...
2206s ----------------------------------------
2206s CALCULATION #3 (pka-coarse): MULTIGRID
2206s   Setting up problem...
2206s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2206s   Debye length:  0 A
2206s   Current memory usage:  230.750 MB total, 404.625 MB high water
2206s   Using linear spline charge discretization.
2206s   Grid dimensions: 97 x 97 x 97
2206s   Grid spacings: 0.729 x 0.729 x 0.729
2206s   Grid lengths: 70.000 x 70.000 x 70.000
2206s   Grid center: (28.969, -32.507, 27.022)
2206s   Multigrid levels: 4
2206s   Molecule ID: 2
2206s   Linearized traditional PBE
2206s   Single Debye-Huckel sphere boundary conditions
2206s   2 ion species (0.000 M ionic strength):
2206s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2206s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2206s   Solute dielectric: 2.000
2206s   Solvent dielectric: 78.000
2206s   Using "molecular" surface definition;harmonic average smoothing
2206s   Solvent probe radius: 1.400 A
2206s   Temperature:  298.150 K
2206s   Electrostatic energies will be calculated
2206s   Total electrostatic energy = 1.864071689626E+05 kJ/mol
2206s   Calculating forces...
2206s [focusFillBound()]: WARNING:
2206s     Unusually large potential values
2206s     detected on the focusing boundary!
2206s     Convergence not guaranteed for NPBE/NRPBE calculations!
2206s 
2206s ----------------------------------------
2206s CALCULATION #4 (pka-fine): MULTIGRID
2206s   Setting up problem...
2206s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2206s   Debye length:  0 A
2206s   Current memory usage:  230.750 MB total, 452.268 MB high water
2206s   Using linear spline charge discretization.
2206s   Grid dimensions: 97 x 97 x 97
2206s   Grid spacings: 0.250 x 0.250 x 0.250
2206s   Grid lengths: 24.000 x 24.000 x 24.000
2206s   Grid center: (24.822, -33.153, 21.545)
2206s   Multigrid levels: 4
2206s   Molecule ID: 2
2206s   Linearized traditional PBE
2206s   Boundary conditions from focusing
2206s   2 ion species (0.000 M ionic strength):
2206s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2206s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2206s   Solute dielectric: 2.000
2206s   Solvent dielectric: 78.000
2206s   Using "molecular" surface definition;harmonic average smoothing
2206s   Solvent probe radius: 1.400 A
2206s   Temperature:  298.150 K
2206s   Electrostatic energies will be calculated
2206s   Total electrostatic energy = 3.053319953673E+05 kJ/mol
2206s   Calculating forces...
2206s ----------------------------------------
2206s CALCULATION #5 (complex-coarse): MULTIGRID
2206s   Setting up problem...
2206s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2206s   Debye length:  0 A
2206s   Current memory usage:  230.854 MB total, 452.268 MB high water
2206s   Using linear spline charge discretization.
2206s   Grid dimensions: 97 x 97 x 97
2206s   Grid spacings: 0.729 x 0.729 x 0.729
2206s   Grid lengths: 70.000 x 70.000 x 70.000
2206s   Grid center: (28.969, -32.507, 27.022)
2206s   Multigrid levels: 4
2206s   Molecule ID: 3
2206s   Linearized traditional PBE
2206s   Single Debye-Huckel sphere boundary conditions
2206s   2 ion species (0.000 M ionic strength):
2206s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2206s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2206s   Solute dielectric: 2.000
2206s   Solvent dielectric: 78.000
2206s   Using "molecular" surface definition;harmonic average smoothing
2206s   Solvent probe radius: 1.400 A
2206s   Temperature:  298.150 K
2206s   Electrostatic energies will be calculated
2206s   Total electrostatic energy = 1.888027142979E+05 kJ/mol
2206s   Calculating forces...
2206s [focusFillBound()]: WARNING:
2206s     Unusually large potential values
2206s     detected on the focusing boundary!
2206s     Convergence not guaranteed for NPBE/NRPBE calculations!
2206s 
2206s ----------------------------------------
2206s CALCULATION #6 (complex-fine): MULTIGRID
2206s   Setting up problem...
2206s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2206s   Debye length:  0 A
2206s   Current memory usage:  230.854 MB total, 452.606 MB high water
2206s   Using linear spline charge discretization.
2206s   Grid dimensions: 97 x 97 x 97
2206s   Grid spacings: 0.250 x 0.250 x 0.250
2206s   Grid lengths: 24.000 x 24.000 x 24.000
2206s   Grid center: (24.822, -33.153, 21.545)
2206s   Multigrid levels: 4
2206s   Molecule ID: 3
2206s   Linearized traditional PBE
2206s   Boundary conditions from focusing
2206s   2 ion species (0.000 M ionic strength):
2206s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2206s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2206s   Solute dielectric: 2.000
2206s   Solvent dielectric: 78.000
2206s   Using "molecular" surface definition;harmonic average smoothing
2206s   Solvent probe radius: 1.400 A
2206s   Temperature:  298.150 K
2206s   Electrostatic energies will be calculated
2206s   Total electrostatic energy = 3.159690177241E+05 kJ/mol
2206s   Calculating forces...
2206s ----------------------------------------
2206s PRINT STATEMENTS
2206s 
2206s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
2206s   Local net energy (PE 0) = 1.088773280806E+02 kJ/mol
2206s   Global net ELEC energy = 1.088773280806E+02 kJ/mol
2206s ----------------------------------------
2206s CLEANING UP AND SHUTTING DOWN...
2206s Destroying force arrays.
2206s No energy arrays to destroy.
2206s Destroying multigrid structures.
2206s Destroying finite element structures.
2206s Destroying 3 molecules
2206s Final memory usage:  0.001 MB total, 452.606 MB high water
2206s 
2206s 
2206s Thanks for using APBS!
2206s 
2206s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03)
2206s *** PASSED ***
2206s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04)
2206s *** PASSED ***
2206s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05)
2206s *** PASSED ***
2206s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05)
2206s *** PASSED ***
2206s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05)
2206s *** PASSED ***
2206s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05)
2206s *** PASSED ***
2206s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02)
2206s *** PASSED ***
2206s Elapsed time: 36.56353 seconds
2206s --------------------------------------------------------------------------------
2206s Total elapsed time: 180.310279 seconds
2206s Test results have been logged
2206s --------------------------------------------------------------------------------
2206s --------------------------------------------------------------------------------
2206s Testing input file complex-0_1.in
2206s 
2210s Checking for intermediate energies in input file apbs-smol-surf.out
2210s EXPECTED COMPUTED: 7
2210s EXPECTED EXPECTED: 7
2210s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806]
2210s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02']
2210s COMPUTED RESULT 2251.46678942
2210s COMPUTED RESULT 10528.14502873
2210s COMPUTED RESULT 186407.1689626
2210s COMPUTED RESULT 305331.9953673
2210s COMPUTED RESULT 188802.7142979
2210s COMPUTED RESULT 315969.0177241
2210s COMPUTED RESULT 108.8773280806
2210s Running tests for point-pmf section
2210s BINARY:  /usr/bin/apbs
2210s INPUT:   complex-0_1.in
2210s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in']
2210s asc_getToken: Error occurred (bailing out).
2210s Vio_scanf: Format problem with input.
2210s 
2210s 
2210s ----------------------------------------------------------------------
2210s     APBS -- Adaptive Poisson-Boltzmann Solver
2210s     Version APBS 3.4.1
2210s     
2210s     Nathan A. Baker (nathan.baker@pnnl.gov)
2210s     Pacific Northwest National Laboratory
2210s     
2210s     Additional contributing authors listed in the code documentation.
2210s     
2210s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2210s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2210s     Northwest Division for the U.S. Department of Energy.
2210s     
2210s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2210s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2210s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2210s     Portions Copyright (c) 1995, Michael Holst.
2210s     All rights reserved.
2210s     
2210s     Redistribution and use in source and binary forms, with or without
2210s     modification, are permitted provided that the following conditions are met:
2210s     
2210s     * Redistributions of source code must retain the above copyright notice, this
2210s       list of conditions and the following disclaimer.
2210s     
2210s     * Redistributions in binary form must reproduce the above copyright notice,
2210s       this list of conditions and the following disclaimer in the documentation
2210s       and/or other materials provided with the distribution.
2210s     
2210s     * Neither the name of the developer nor the names of its contributors may be
2210s       used to endorse or promote products derived from this software without
2210s       specific prior written permission.
2210s     
2210s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2210s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2210s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2210s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2210s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2210s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2210s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2210s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2210s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2210s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2210s ----------------------------------------------------------------------
2210s     APBS uses FETK (the Finite Element ToolKit) to solve the
2210s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2210s     of finite element modeling class libraries developed by the Michael Holst
2210s     research group and written in an object-oriented form of C.  FEtk is
2210s     designed to solve general coupled systems of nonlinear partial differential
2210s     equations using adaptive finite element methods, inexact Newton methods,
2210s     and algebraic multilevel methods.  More information about FEtk may be found
2210s     at <http://www.FEtk.ORG>.
2210s ----------------------------------------------------------------------
2210s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2210s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2210s     which has been modified by Patrice Koehl
2210s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2210s     memory usage when solving the Poisson-Boltzmann equation.
2210s ----------------------------------------------------------------------
2210s     Please cite your use of APBS as:
2210s 
2210s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2210s     nanosystems: application to microtubules and the ribosome. Proc.
2210s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2210s     
2210s 
2210s This executable compiled on Mar  2 2024 at 20:11:10
2210s 
2210s Parsing input file complex-0_1.in...
2210s rank 0 size 1...
2210s Parsed input file.
2210s Got paths for 3 molecules
2210s Reading PQR-format atom data from mol0.pqr.
2210s asc_getToken: Error occurred (bailing out).
2210s Vio_scanf: Format problem with input.
2210s   1 atoms
2210s   Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
2210s   Net charge 1.00e+00 e
2210s Reading PQR-format atom data from mol1.pqr.
2210s asc_getToken: Error occurred (bailing out).
2210s Vio_scanf: Format problem with input.
2210s   1 atoms
2210s   Centered at (-2.000e+00, 0.000e+00, 0.000e+00)
2210s   Net charge 1.00e+00 e
2210s Reading PQR-format atom data from complex-0_1.pqr.
2210s   2 atoms
2210s   Centered at (-2.500e+00, 0.000e+00, 0.000e+00)
2210s   Net charge 2.00e+00 e
2210s Preparing to run 3 PBE calculations.
2210s ----------------------------------------
2210s CALCULATION #1 (point1): MULTIGRID
2210s   Setting up problem...
2210s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2210s   Debye length:  0 A
2210s   Current memory usage:  61.059 MB total, 61.059 MB high water
2210s   Using linear spline charge discretization.
2210s   Grid dimensions: 65 x 65 x 65
2210s   Grid spacings: 0.210 x 0.210 x 0.210
2210s   Grid lengths: 13.440 x 13.440 x 13.440
2210s   Grid center: (0.000, 0.000, 0.000)
2210s   Multigrid levels: 5
2210s   Molecule ID: 1
2210s   Linearized traditional PBE
2210s   Multiple Debye-Huckel sphere boundary conditions
2210s   0 ion species (0.000 M ionic strength):
2210s   Solute dielectric: 78.540
2210s   Solvent dielectric: 78.540
2210s   Using spline-based surface definition;window = 0.300
2210s   Temperature:  298.150 K
2210s   Electrostatic energies will be calculated
2210s   Total electrostatic energy = 9.776035707281E+01 kJ/mol
2210s   Fixed charge energy = 97.7604 kJ/mol
2210s   Mobile charge energy = 0 kJ/mol
2210s   Dielectric energy = 96.5336 kJ/mol
2210s   Per-atom energies:
2210s       Atom 0:  9.776035707281E+01 kJ/mol
2210s   Calculating forces...
2210s ----------------------------------------
2210s CALCULATION #2 (point2): MULTIGRID
2210s   Setting up problem...
2210s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2210s   Debye length:  0 A
2210s   Current memory usage:  61.059 MB total, 61.066 MB high water
2210s   Using linear spline charge discretization.
2210s   Grid dimensions: 65 x 65 x 65
2210s   Grid spacings: 0.210 x 0.210 x 0.210
2210s   Grid lengths: 13.440 x 13.440 x 13.440
2210s   Grid center: (0.000, 0.000, 0.000)
2210s   Multigrid levels: 5
2210s   Molecule ID: 2
2210s   Linearized traditional PBE
2210s   Multiple Debye-Huckel sphere boundary conditions
2210s   0 ion species (0.000 M ionic strength):
2210s   Solute dielectric: 78.540
2210s   Solvent dielectric: 78.540
2210s   Using spline-based surface definition;window = 0.300
2210s   Temperature:  298.150 K
2210s   Electrostatic energies will be calculated
2210s   Total electrostatic energy = 8.975920687031E+01 kJ/mol
2210s   Fixed charge energy = 89.7592 kJ/mol
2210s   Mobile charge energy = 0 kJ/mol
2210s   Dielectric energy = 88.6151 kJ/mol
2210s   Per-atom energies:
2210s       Atom 0:  8.975920687031E+01 kJ/mol
2210s   Calculating forces...
2210s ----------------------------------------
2210s CALCULATION #3 (complex): MULTIGRID
2210s   Setting up problem...
2210s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2210s   Debye length:  0 A
2210s   Current memory usage:  61.059 MB total, 61.066 MB high water
2210s   Using linear spline charge discretization.
2210s   Grid dimensions: 65 x 65 x 65
2210s   Grid spacings: 0.210 x 0.210 x 0.210
2210s   Grid lengths: 13.440 x 13.440 x 13.440
2210s   Grid center: (0.000, 0.000, 0.000)
2210s   Multigrid levels: 5
2210s   Molecule ID: 3
2210s   Linearized traditional PBE
2210s   Multiple Debye-Huckel sphere boundary conditions
2210s   0 ion species (0.000 M ionic strength):
2210s   Solute dielectric: 78.540
2210s   Solvent dielectric: 78.540
2210s   Using spline-based surface definition;window = 0.300
2210s   Temperature:  298.150 K
2210s   Electrostatic energies will be calculated
2210s   Total electrostatic energy = 2.058277719334E+02 kJ/mol
2210s   Fixed charge energy = 205.828 kJ/mol
2210s   Mobile charge energy = 0 kJ/mol
2210s   Dielectric energy = 201.106 kJ/mol
2210s   Per-atom energies:
2210s       Atom 0:  1.069144350786E+02 kJ/mol
2210s       Atom 1:  9.891333685475E+01 kJ/mol
2210s   Calculating forces...
2210s ----------------------------------------
2210s PRINT STATEMENTS
2210s 
2210s print energy 3 (complex) - 1 (point1) - 2 (point2) end
2210s   Local net energy (PE 0) = 1.830820799027E+01 kJ/mol
2210s   Global net ELEC energy = 1.830820799027E+01 kJ/mol
2210s ----------------------------------------
2210s CLEANING UP AND SHUTTING DOWN...
2210s Destroying force arrays.
2210s No energy arrays to destroy.
2210s Destroying multigrid structures.
2210s Destroying finite element structures.
2210s Destroying 3 molecules
2210s Final memory usage:  0.001 MB total, 61.066 MB high water
2210s 
2210s 
2210s Thanks for using APBS!
2210s 
2210s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
2210s *** PASSED ***
2210s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01)
2210s *** PASSED ***
2210s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02)
2210s *** PASSED ***
2210s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
2210s *** PASSED ***
2210s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01)
2210s *** PASSED ***
2210s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02)
2210s *** PASSED ***
2210s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
2210s *** PASSED ***
2210s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01)
2210s *** PASSED ***
2210s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02)
2210s *** PASSED ***
2210s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01)
2210s *** PASSED ***
2210s Elapsed time: 3.51671 seconds
2210s --------------------------------------------------------------------------------
2210s --------------------------------------------------------------------------------
2210s Testing input file complex-0_2.in
2210s 
2214s Checking for intermediate energies in input file complex-0_1.out
2214s EXPECTED COMPUTED: 13
2214s EXPECTED EXPECTED: 13
2214s COMPUTED: [97.76035707281, 89.75920687031, 205.8277719334, 0.0, 0.0, 0.0, 97.7604, 89.7592, 205.828, 96.5336, 88.6151, 201.106, 18.30820799027]
2214s EXPECTED: ['9.776035707281E+01', '8.975920687031E+01', '2.058277719334E+02', '*', '*', '*', '97.7604', '89.7592', '205.828', '96.5336', '88.6151', '201.106', '1.830820799027E+01']
2214s COMPUTED RESULT 97.76035707281
2214s COMPUTED RESULT 89.75920687031
2214s COMPUTED RESULT 205.8277719334
2214s COMPUTED RESULT 0.0
2214s COMPUTED RESULT 0.0
2214s COMPUTED RESULT 0.0
2214s COMPUTED RESULT 97.7604
2214s COMPUTED RESULT 89.7592
2214s COMPUTED RESULT 205.828
2214s COMPUTED RESULT 96.5336
2214s COMPUTED RESULT 88.6151
2214s COMPUTED RESULT 201.106
2214s COMPUTED RESULT 18.30820799027
2214s BINARY:  /usr/bin/apbs
2214s INPUT:   complex-0_2.in
2214s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in']
2214s asc_getToken: Error occurred (bailing out).
2214s Vio_scanf: Format problem with input.
2214s 
2214s 
2214s ----------------------------------------------------------------------
2214s     APBS -- Adaptive Poisson-Boltzmann Solver
2214s     Version APBS 3.4.1
2214s     
2214s     Nathan A. Baker (nathan.baker@pnnl.gov)
2214s     Pacific Northwest National Laboratory
2214s     
2214s     Additional contributing authors listed in the code documentation.
2214s     
2214s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2214s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2214s     Northwest Division for the U.S. Department of Energy.
2214s     
2214s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2214s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2214s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2214s     Portions Copyright (c) 1995, Michael Holst.
2214s     All rights reserved.
2214s     
2214s     Redistribution and use in source and binary forms, with or without
2214s     modification, are permitted provided that the following conditions are met:
2214s     
2214s     * Redistributions of source code must retain the above copyright notice, this
2214s       list of conditions and the following disclaimer.
2214s     
2214s     * Redistributions in binary form must reproduce the above copyright notice,
2214s       this list of conditions and the following disclaimer in the documentation
2214s       and/or other materials provided with the distribution.
2214s     
2214s     * Neither the name of the developer nor the names of its contributors may be
2214s       used to endorse or promote products derived from this software without
2214s       specific prior written permission.
2214s     
2214s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2214s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2214s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2214s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2214s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2214s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2214s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2214s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2214s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2214s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2214s ----------------------------------------------------------------------
2214s     APBS uses FETK (the Finite Element ToolKit) to solve the
2214s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2214s     of finite element modeling class libraries developed by the Michael Holst
2214s     research group and written in an object-oriented form of C.  FEtk is
2214s     designed to solve general coupled systems of nonlinear partial differential
2214s     equations using adaptive finite element methods, inexact Newton methods,
2214s     and algebraic multilevel methods.  More information about FEtk may be found
2214s     at <http://www.FEtk.ORG>.
2214s ----------------------------------------------------------------------
2214s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2214s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2214s     which has been modified by Patrice Koehl
2214s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2214s     memory usage when solving the Poisson-Boltzmann equation.
2214s ----------------------------------------------------------------------
2214s     Please cite your use of APBS as:
2214s 
2214s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2214s     nanosystems: application to microtubules and the ribosome. Proc.
2214s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2214s     
2214s 
2214s This executable compiled on Mar  2 2024 at 20:11:10
2214s 
2214s Parsing input file complex-0_2.in...
2214s rank 0 size 1...
2214s Parsed input file.
2214s Got paths for 3 molecules
2214s Reading PQR-format atom data from mol0.pqr.
2214s asc_getToken: Error occurred (bailing out).
2214s Vio_scanf: Format problem with input.
2214s   1 atoms
2214s   Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
2214s   Net charge 1.00e+00 e
2214s Reading PQR-format atom data from mol2.pqr.
2214s asc_getToken: Error occurred (bailing out).
2214s Vio_scanf: Format problem with input.
2214s   1 atoms
2214s   Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
2214s   Net charge 1.00e+00 e
2214s Reading PQR-format atom data from complex-0_2.pqr.
2214s   2 atoms
2214s   Centered at (-2.000e+00, 0.000e+00, 0.000e+00)
2214s   Net charge 2.00e+00 e
2214s Preparing to run 3 PBE calculations.
2214s ----------------------------------------
2214s CALCULATION #1 (point1): MULTIGRID
2214s   Setting up problem...
2214s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2214s   Debye length:  0 A
2214s   Current memory usage:  61.059 MB total, 61.059 MB high water
2214s   Using linear spline charge discretization.
2214s   Grid dimensions: 65 x 65 x 65
2214s   Grid spacings: 0.210 x 0.210 x 0.210
2214s   Grid lengths: 13.440 x 13.440 x 13.440
2214s   Grid center: (0.000, 0.000, 0.000)
2214s   Multigrid levels: 5
2214s   Molecule ID: 1
2214s   Linearized traditional PBE
2214s   Multiple Debye-Huckel sphere boundary conditions
2214s   0 ion species (0.000 M ionic strength):
2214s   Solute dielectric: 78.540
2214s   Solvent dielectric: 78.540
2214s   Using spline-based surface definition;window = 0.300
2214s   Temperature:  298.150 K
2214s   Electrostatic energies will be calculated
2214s   Total electrostatic energy = 9.776035707281E+01 kJ/mol
2214s   Fixed charge energy = 97.7604 kJ/mol
2214s   Mobile charge energy = 0 kJ/mol
2214s   Dielectric energy = 96.5336 kJ/mol
2214s   Per-atom energies:
2214s       Atom 0:  9.776035707281E+01 kJ/mol
2214s   Calculating forces...
2214s ----------------------------------------
2214s CALCULATION #2 (point2): MULTIGRID
2214s   Setting up problem...
2214s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2214s   Debye length:  0 A
2214s   Current memory usage:  61.059 MB total, 61.066 MB high water
2214s   Using linear spline charge discretization.
2214s   Grid dimensions: 65 x 65 x 65
2214s   Grid spacings: 0.210 x 0.210 x 0.210
2214s   Grid lengths: 13.440 x 13.440 x 13.440
2214s   Grid center: (0.000, 0.000, 0.000)
2214s   Multigrid levels: 5
2214s   Molecule ID: 2
2214s   Linearized traditional PBE
2214s   Multiple Debye-Huckel sphere boundary conditions
2214s   0 ion species (0.000 M ionic strength):
2214s   Solute dielectric: 78.540
2214s   Solvent dielectric: 78.540
2214s   Using spline-based surface definition;window = 0.300
2214s   Temperature:  298.150 K
2214s   Electrostatic energies will be calculated
2214s   Total electrostatic energy = 1.017611498797E+02 kJ/mol
2214s   Fixed charge energy = 101.761 kJ/mol
2214s   Mobile charge energy = 0 kJ/mol
2214s   Dielectric energy = 100.656 kJ/mol
2214s   Per-atom energies:
2214s       Atom 0:  1.017611498797E+02 kJ/mol
2214s   Calculating forces...
2214s ----------------------------------------
2214s CALCULATION #3 (complex): MULTIGRID
2214s   Setting up problem...
2214s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2214s   Debye length:  0 A
2214s   Current memory usage:  61.059 MB total, 61.066 MB high water
2214s   Using linear spline charge discretization.
2214s   Grid dimensions: 65 x 65 x 65
2214s   Grid spacings: 0.210 x 0.210 x 0.210
2214s   Grid lengths: 13.440 x 13.440 x 13.440
2214s   Grid center: (0.000, 0.000, 0.000)
2214s   Multigrid levels: 5
2214s   Molecule ID: 3
2214s   Linearized traditional PBE
2214s   Multiple Debye-Huckel sphere boundary conditions
2214s   0 ion species (0.000 M ionic strength):
2214s   Solute dielectric: 78.540
2214s   Solvent dielectric: 78.540
2214s   Using spline-based surface definition;window = 0.300
2214s   Temperature:  298.150 K
2214s   Electrostatic energies will be calculated
2214s   Total electrostatic energy = 2.084282010393E+02 kJ/mol
2214s   Fixed charge energy = 208.428 kJ/mol
2214s   Mobile charge energy = 0 kJ/mol
2214s   Dielectric energy = 203.83 kJ/mol
2214s   Per-atom energies:
2214s       Atom 0:  1.022136878480E+02 kJ/mol
2214s       Atom 1:  1.062145131913E+02 kJ/mol
2214s   Calculating forces...
2214s ----------------------------------------
2214s PRINT STATEMENTS
2214s 
2214s print energy 3 (complex) - 1 (point1) - 2 (point2) end
2214s   Local net energy (PE 0) = 8.906694086750E+00 kJ/mol
2214s   Global net ELEC energy = 8.906694086750E+00 kJ/mol
2214s ----------------------------------------
2214s CLEANING UP AND SHUTTING DOWN...
2214s Destroying force arrays.
2214s No energy arrays to destroy.
2214s Destroying multigrid structures.
2214s Destroying finite element structures.
2214s Destroying 3 molecules
2214s Final memory usage:  0.001 MB total, 61.066 MB high water
2214s 
2214s 
2214s Thanks for using APBS!
2214s 
2214s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
2214s *** PASSED ***
2214s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02)
2214s *** PASSED ***
2214s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02)
2214s *** PASSED ***
2214s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
2214s *** PASSED ***
2214s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02)
2214s *** PASSED ***
2214s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02)
2214s *** PASSED ***
2214s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
2214s *** PASSED ***
2214s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02)
2214s *** PASSED ***
2214s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02)
2214s *** PASSED ***
2214s Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00)
2214s *** PASSED ***
2214s Elapsed time: 3.77313 seconds
2214s --------------------------------------------------------------------------------
2214s --------------------------------------------------------------------------------
2214s Testing input file complex-0_3.in
2214s 
2219s Checking for intermediate energies in input file complex-0_2.out
2219s EXPECTED COMPUTED: 13
2219s EXPECTED EXPECTED: 13
2219s COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.90669408675]
2219s EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.084282010393E+02', '*', '*', '*', '97.7604', '101.761', '208.428', '96.5336', '100.656', '203.83', '8.906694086750E+00']
2219s COMPUTED RESULT 97.76035707281
2219s COMPUTED RESULT 101.7611498797
2219s COMPUTED RESULT 208.4282010393
2219s COMPUTED RESULT 0.0
2219s COMPUTED RESULT 0.0
2219s COMPUTED RESULT 0.0
2219s COMPUTED RESULT 97.7604
2219s COMPUTED RESULT 101.761
2219s COMPUTED RESULT 208.428
2219s COMPUTED RESULT 96.5336
2219s COMPUTED RESULT 100.656
2219s COMPUTED RESULT 203.83
2219s COMPUTED RESULT 8.90669408675
2219s BINARY:  /usr/bin/apbs
2219s INPUT:   complex-0_3.in
2219s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in']
2219s asc_getToken: Error occurred (bailing out).
2219s Vio_scanf: Format problem with input.
2219s 
2219s 
2219s ----------------------------------------------------------------------
2219s     APBS -- Adaptive Poisson-Boltzmann Solver
2219s     Version APBS 3.4.1
2219s     
2219s     Nathan A. Baker (nathan.baker@pnnl.gov)
2219s     Pacific Northwest National Laboratory
2219s     
2219s     Additional contributing authors listed in the code documentation.
2219s     
2219s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2219s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2219s     Northwest Division for the U.S. Department of Energy.
2219s     
2219s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2219s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2219s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2219s     Portions Copyright (c) 1995, Michael Holst.
2219s     All rights reserved.
2219s     
2219s     Redistribution and use in source and binary forms, with or without
2219s     modification, are permitted provided that the following conditions are met:
2219s     
2219s     * Redistributions of source code must retain the above copyright notice, this
2219s       list of conditions and the following disclaimer.
2219s     
2219s     * Redistributions in binary form must reproduce the above copyright notice,
2219s       this list of conditions and the following disclaimer in the documentation
2219s       and/or other materials provided with the distribution.
2219s     
2219s     * Neither the name of the developer nor the names of its contributors may be
2219s       used to endorse or promote products derived from this software without
2219s       specific prior written permission.
2219s     
2219s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2219s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2219s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2219s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2219s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2219s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2219s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2219s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2219s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2219s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2219s ----------------------------------------------------------------------
2219s     APBS uses FETK (the Finite Element ToolKit) to solve the
2219s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2219s     of finite element modeling class libraries developed by the Michael Holst
2219s     research group and written in an object-oriented form of C.  FEtk is
2219s     designed to solve general coupled systems of nonlinear partial differential
2219s     equations using adaptive finite element methods, inexact Newton methods,
2219s     and algebraic multilevel methods.  More information about FEtk may be found
2219s     at <http://www.FEtk.ORG>.
2219s ----------------------------------------------------------------------
2219s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2219s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2219s     which has been modified by Patrice Koehl
2219s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2219s     memory usage when solving the Poisson-Boltzmann equation.
2219s ----------------------------------------------------------------------
2219s     Please cite your use of APBS as:
2219s 
2219s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2219s     nanosystems: application to microtubules and the ribosome. Proc.
2219s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2219s     
2219s 
2219s This executable compiled on Mar  2 2024 at 20:11:10
2219s 
2219s Parsing input file complex-0_3.in...
2219s rank 0 size 1...
2219s Parsed input file.
2219s Got paths for 3 molecules
2219s Reading PQR-format atom data from mol0.pqr.
2219s asc_getToken: Error occurred (bailing out).
2219s Vio_scanf: Format problem with input.
2219s   1 atoms
2219s   Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
2219s   Net charge 1.00e+00 e
2219s Reading PQR-format atom data from mol3.pqr.
2219s asc_getToken: Error occurred (bailing out).
2219s Vio_scanf: Format problem with input.
2219s   1 atoms
2219s   Centered at (0.000e+00, 0.000e+00, 0.000e+00)
2219s   Net charge 1.00e+00 e
2219s Reading PQR-format atom data from complex-0_3.pqr.
2219s   2 atoms
2219s   Centered at (-1.500e+00, 0.000e+00, 0.000e+00)
2219s   Net charge 2.00e+00 e
2219s Preparing to run 3 PBE calculations.
2219s ----------------------------------------
2219s CALCULATION #1 (point1): MULTIGRID
2219s   Setting up problem...
2219s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2219s   Debye length:  0 A
2219s   Current memory usage:  61.059 MB total, 61.059 MB high water
2219s   Using linear spline charge discretization.
2219s   Grid dimensions: 65 x 65 x 65
2219s   Grid spacings: 0.210 x 0.210 x 0.210
2219s   Grid lengths: 13.440 x 13.440 x 13.440
2219s   Grid center: (0.000, 0.000, 0.000)
2219s   Multigrid levels: 5
2219s   Molecule ID: 1
2219s   Linearized traditional PBE
2219s   Multiple Debye-Huckel sphere boundary conditions
2219s   0 ion species (0.000 M ionic strength):
2219s   Solute dielectric: 78.540
2219s   Solvent dielectric: 78.540
2219s   Using spline-based surface definition;window = 0.300
2219s   Temperature:  298.150 K
2219s   Electrostatic energies will be calculated
2219s   Total electrostatic energy = 9.776035707281E+01 kJ/mol
2219s   Fixed charge energy = 97.7604 kJ/mol
2219s   Mobile charge energy = 0 kJ/mol
2219s   Dielectric energy = 96.5336 kJ/mol
2219s   Per-atom energies:
2219s       Atom 0:  9.776035707281E+01 kJ/mol
2219s   Calculating forces...
2219s ----------------------------------------
2219s CALCULATION #2 (point2): MULTIGRID
2219s   Setting up problem...
2219s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2219s   Debye length:  0 A
2219s   Current memory usage:  61.059 MB total, 61.066 MB high water
2219s   Using linear spline charge discretization.
2219s   Grid dimensions: 65 x 65 x 65
2219s   Grid spacings: 0.210 x 0.210 x 0.210
2219s   Grid lengths: 13.440 x 13.440 x 13.440
2219s   Grid center: (0.000, 0.000, 0.000)
2219s   Multigrid levels: 5
2219s   Molecule ID: 2
2219s   Linearized traditional PBE
2219s   Multiple Debye-Huckel sphere boundary conditions
2219s   0 ion species (0.000 M ionic strength):
2219s   Solute dielectric: 78.540
2219s   Solvent dielectric: 78.540
2219s   Using spline-based surface definition;window = 0.300
2219s   Temperature:  298.150 K
2219s   Electrostatic energies will be calculated
2219s   Total electrostatic energy = 1.337661883222E+02 kJ/mol
2219s   Fixed charge energy = 133.766 kJ/mol
2219s   Mobile charge energy = 0 kJ/mol
2219s   Dielectric energy = 132.672 kJ/mol
2219s   Per-atom energies:
2219s       Atom 0:  1.337661883222E+02 kJ/mol
2219s   Calculating forces...
2219s ----------------------------------------
2219s CALCULATION #3 (complex): MULTIGRID
2219s   Setting up problem...
2219s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2219s   Debye length:  0 A
2219s   Current memory usage:  61.059 MB total, 61.066 MB high water
2219s   Using linear spline charge discretization.
2219s   Grid dimensions: 65 x 65 x 65
2219s   Grid spacings: 0.210 x 0.210 x 0.210
2219s   Grid lengths: 13.440 x 13.440 x 13.440
2219s   Grid center: (0.000, 0.000, 0.000)
2219s   Multigrid levels: 5
2219s   Molecule ID: 3
2219s   Linearized traditional PBE
2219s   Multiple Debye-Huckel sphere boundary conditions
2219s   0 ion species (0.000 M ionic strength):
2219s   Solute dielectric: 78.540
2219s   Solvent dielectric: 78.540
2219s   Using spline-based surface definition;window = 0.300
2219s   Temperature:  298.150 K
2219s   Electrostatic energies will be calculated
2219s   Total electrostatic energy = 2.374361452120E+02 kJ/mol
2219s   Fixed charge energy = 237.436 kJ/mol
2219s   Mobile charge energy = 0 kJ/mol
2219s   Dielectric energy = 232.924 kJ/mol
2219s   Per-atom energies:
2219s       Atom 0:  1.007151570480E+02 kJ/mol
2219s       Atom 1:  1.367209881640E+02 kJ/mol
2219s   Calculating forces...
2219s ----------------------------------------
2219s PRINT STATEMENTS
2219s 
2219s print energy 3 (complex) - 1 (point1) - 2 (point2) end
2219s   Local net energy (PE 0) = 5.909599816984E+00 kJ/mol
2219s   Global net ELEC energy = 5.909599816984E+00 kJ/mol
2219s ----------------------------------------
2219s CLEANING UP AND SHUTTING DOWN...
2219s Destroying force arrays.
2219s No energy arrays to destroy.
2219s Destroying multigrid structures.
2219s Destroying finite element structures.
2219s Destroying 3 molecules
2219s Final memory usage:  0.001 MB total, 61.066 MB high water
2219s 
2219s 
2219s Thanks for using APBS!
2219s 
2219s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
2219s *** PASSED ***
2219s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02)
2219s *** PASSED ***
2219s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02)
2219s *** PASSED ***
2219s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
2219s *** PASSED ***
2219s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02)
2219s *** PASSED ***
2219s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02)
2219s *** PASSED ***
2219s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
2219s *** PASSED ***
2219s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02)
2219s *** PASSED ***
2219s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02)
2219s *** PASSED ***
2219s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00)
2219s *** PASSED ***
2219s Elapsed time: 5.046395 seconds
2219s --------------------------------------------------------------------------------
2219s --------------------------------------------------------------------------------
2219s Testing input file complex-0_4.in
2219s 
2222s Checking for intermediate energies in input file complex-0_3.out
2222s EXPECTED COMPUTED: 13
2222s EXPECTED EXPECTED: 13
2222s COMPUTED: [97.76035707281, 133.7661883222, 237.436145212, 0.0, 0.0, 0.0, 97.7604, 133.766, 237.436, 96.5336, 132.672, 232.924, 5.909599816984]
2222s EXPECTED: ['9.776035707281E+01', '1.337661883222E+02', '2.374361452120E+02', '*', '*', '*', '97.7604', '133.766', '237.436', '96.5336', '132.672', '232.924', '5.909599816984E+00']
2222s COMPUTED RESULT 97.76035707281
2222s COMPUTED RESULT 133.7661883222
2222s COMPUTED RESULT 237.436145212
2222s COMPUTED RESULT 0.0
2222s COMPUTED RESULT 0.0
2222s COMPUTED RESULT 0.0
2222s COMPUTED RESULT 97.7604
2222s COMPUTED RESULT 133.766
2222s COMPUTED RESULT 237.436
2222s COMPUTED RESULT 96.5336
2222s COMPUTED RESULT 132.672
2222s COMPUTED RESULT 232.924
2222s COMPUTED RESULT 5.909599816984
2222s BINARY:  /usr/bin/apbs
2222s INPUT:   complex-0_4.in
2222s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in']
2222s asc_getToken: Error occurred (bailing out).
2222s Vio_scanf: Format problem with input.
2222s 
2222s 
2222s ----------------------------------------------------------------------
2222s     APBS -- Adaptive Poisson-Boltzmann Solver
2222s     Version APBS 3.4.1
2222s     
2222s     Nathan A. Baker (nathan.baker@pnnl.gov)
2222s     Pacific Northwest National Laboratory
2222s     
2222s     Additional contributing authors listed in the code documentation.
2222s     
2222s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2222s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2222s     Northwest Division for the U.S. Department of Energy.
2222s     
2222s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2222s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2222s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2222s     Portions Copyright (c) 1995, Michael Holst.
2222s     All rights reserved.
2222s     
2222s     Redistribution and use in source and binary forms, with or without
2222s     modification, are permitted provided that the following conditions are met:
2222s     
2222s     * Redistributions of source code must retain the above copyright notice, this
2222s       list of conditions and the following disclaimer.
2222s     
2222s     * Redistributions in binary form must reproduce the above copyright notice,
2222s       this list of conditions and the following disclaimer in the documentation
2222s       and/or other materials provided with the distribution.
2222s     
2222s     * Neither the name of the developer nor the names of its contributors may be
2222s       used to endorse or promote products derived from this software without
2222s       specific prior written permission.
2222s     
2222s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2222s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2222s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2222s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2222s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2222s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2222s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2222s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2222s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2222s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2222s ----------------------------------------------------------------------
2222s     APBS uses FETK (the Finite Element ToolKit) to solve the
2222s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2222s     of finite element modeling class libraries developed by the Michael Holst
2222s     research group and written in an object-oriented form of C.  FEtk is
2222s     designed to solve general coupled systems of nonlinear partial differential
2222s     equations using adaptive finite element methods, inexact Newton methods,
2222s     and algebraic multilevel methods.  More information about FEtk may be found
2222s     at <http://www.FEtk.ORG>.
2222s ----------------------------------------------------------------------
2222s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2222s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2222s     which has been modified by Patrice Koehl
2222s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2222s     memory usage when solving the Poisson-Boltzmann equation.
2222s ----------------------------------------------------------------------
2222s     Please cite your use of APBS as:
2222s 
2222s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2222s     nanosystems: application to microtubules and the ribosome. Proc.
2222s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2222s     
2222s 
2222s This executable compiled on Mar  2 2024 at 20:11:10
2222s 
2222s Parsing input file complex-0_4.in...
2222s rank 0 size 1...
2222s Parsed input file.
2222s Got paths for 3 molecules
2222s Reading PQR-format atom data from mol0.pqr.
2222s asc_getToken: Error occurred (bailing out).
2222s Vio_scanf: Format problem with input.
2222s   1 atoms
2222s   Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
2222s   Net charge 1.00e+00 e
2222s Reading PQR-format atom data from mol4.pqr.
2222s asc_getToken: Error occurred (bailing out).
2222s Vio_scanf: Format problem with input.
2222s   1 atoms
2222s   Centered at (1.000e+00, 0.000e+00, 0.000e+00)
2222s   Net charge 1.00e+00 e
2222s Reading PQR-format atom data from complex-0_4.pqr.
2222s   2 atoms
2222s   Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
2222s   Net charge 2.00e+00 e
2222s Preparing to run 3 PBE calculations.
2222s ----------------------------------------
2222s CALCULATION #1 (point1): MULTIGRID
2222s   Setting up problem...
2222s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2222s   Debye length:  0 A
2222s   Current memory usage:  61.059 MB total, 61.059 MB high water
2222s   Using linear spline charge discretization.
2222s   Grid dimensions: 65 x 65 x 65
2222s   Grid spacings: 0.210 x 0.210 x 0.210
2222s   Grid lengths: 13.440 x 13.440 x 13.440
2222s   Grid center: (0.000, 0.000, 0.000)
2222s   Multigrid levels: 5
2222s   Molecule ID: 1
2222s   Linearized traditional PBE
2222s   Multiple Debye-Huckel sphere boundary conditions
2222s   0 ion species (0.000 M ionic strength):
2222s   Solute dielectric: 78.540
2222s   Solvent dielectric: 78.540
2222s   Using spline-based surface definition;window = 0.300
2222s   Temperature:  298.150 K
2222s   Electrostatic energies will be calculated
2222s   Total electrostatic energy = 9.776035707281E+01 kJ/mol
2222s   Fixed charge energy = 97.7604 kJ/mol
2222s   Mobile charge energy = 0 kJ/mol
2222s   Dielectric energy = 96.5336 kJ/mol
2222s   Per-atom energies:
2222s       Atom 0:  9.776035707281E+01 kJ/mol
2222s   Calculating forces...
2222s ----------------------------------------
2222s CALCULATION #2 (point2): MULTIGRID
2222s   Setting up problem...
2222s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2222s   Debye length:  0 A
2222s   Current memory usage:  61.059 MB total, 61.066 MB high water
2222s   Using linear spline charge discretization.
2222s   Grid dimensions: 65 x 65 x 65
2222s   Grid spacings: 0.210 x 0.210 x 0.210
2222s   Grid lengths: 13.440 x 13.440 x 13.440
2222s   Grid center: (0.000, 0.000, 0.000)
2222s   Multigrid levels: 5
2222s   Molecule ID: 2
2222s   Linearized traditional PBE
2222s   Multiple Debye-Huckel sphere boundary conditions
2222s   0 ion species (0.000 M ionic strength):
2222s   Solute dielectric: 78.540
2222s   Solvent dielectric: 78.540
2222s   Using spline-based surface definition;window = 0.300
2222s   Temperature:  298.150 K
2222s   Electrostatic energies will be calculated
2222s   Total electrostatic energy = 1.017611498797E+02 kJ/mol
2222s   Fixed charge energy = 101.761 kJ/mol
2222s   Mobile charge energy = 0 kJ/mol
2222s   Dielectric energy = 100.654 kJ/mol
2222s   Per-atom energies:
2222s       Atom 0:  1.017611498797E+02 kJ/mol
2222s   Calculating forces...
2222s ----------------------------------------
2222s CALCULATION #3 (complex): MULTIGRID
2222s   Setting up problem...
2222s   Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
2222s   Debye length:  0 A
2222s   Current memory usage:  61.059 MB total, 61.066 MB high water
2222s   Using linear spline charge discretization.
2222s   Grid dimensions: 65 x 65 x 65
2222s   Grid spacings: 0.210 x 0.210 x 0.210
2222s   Grid lengths: 13.440 x 13.440 x 13.440
2222s   Grid center: (0.000, 0.000, 0.000)
2222s   Multigrid levels: 5
2222s   Molecule ID: 3
2222s   Linearized traditional PBE
2222s   Multiple Debye-Huckel sphere boundary conditions
2222s   0 ion species (0.000 M ionic strength):
2222s   Solute dielectric: 78.540
2222s   Solvent dielectric: 78.540
2222s   Using spline-based surface definition;window = 0.300
2222s   Temperature:  298.150 K
2222s   Electrostatic energies will be calculated
2222s   Total electrostatic energy = 2.039516519000E+02 kJ/mol
2222s   Fixed charge energy = 203.952 kJ/mol
2222s   Mobile charge energy = 0 kJ/mol
2222s   Dielectric energy = 199.493 kJ/mol
2222s   Per-atom energies:
2222s       Atom 0:  9.997541697022E+01 kJ/mol
2222s       Atom 1:  1.039762349297E+02 kJ/mol
2222s   Calculating forces...
2222s ----------------------------------------
2222s PRINT STATEMENTS
2222s 
2222s print energy 3 (complex) - 1 (point1) - 2 (point2) end
2222s   Local net energy (PE 0) = 4.430144947418E+00 kJ/mol
2222s   Global net ELEC energy = 4.430144947418E+00 kJ/mol
2222s ----------------------------------------
2222s CLEANING UP AND SHUTTING DOWN...
2222s Destroying force arrays.
2222s No energy arrays to destroy.
2222s Destroying multigrid structures.
2222s Destroying finite element structures.
2222s Destroying 3 molecules
2222s Final memory usage:  0.001 MB total, 61.066 MB high water
2222s 
2222s 
2222s Thanks for using APBS!
2222s 
2222s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
2222s *** PASSED ***
2222s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02)
2222s *** PASSED ***
2222s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02)
2222s *** PASSED ***
2222s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
2222s *** PASSED ***
2222s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02)
2222s *** PASSED ***
2222s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02)
2222s *** PASSED ***
2222s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
2222s *** PASSED ***
2222s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02)
2222s *** PASSED ***
2222s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02)
2222s *** PASSED ***
2222s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00)
2222s *** PASSED ***
2222s Elapsed time: 3.736335 seconds
2222s --------------------------------------------------------------------------------
2222s Total elapsed time: 16.07257 seconds
2222s Test results have been logged
2222s --------------------------------------------------------------------------------
2222s --------------------------------------------------------------------------------
2222s Testing input file apbs-mol.in
2222s 
2229s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03)
2229s *** PASSED ***
2229s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03)
2229s *** PASSED ***
2229s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03)
2229s *** PASSED ***
2229s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03)
2229s *** PASSED ***
2229s Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01)
2229s *** PASSED ***
2229s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02)
2229s *** PASSED ***
2229s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02)
2229s *** PASSED ***
2229s Elapsed time: 6.712296 seconds
2229s --------------------------------------------------------------------------------
2229s --------------------------------------------------------------------------------
2229s Testing input file apbs-smol.in
2229s 
2229s Checking for intermediate energies in input file complex-0_4.out
2229s EXPECTED COMPUTED: 13
2229s EXPECTED EXPECTED: 13
2229s COMPUTED: [97.76035707281, 101.7611498797, 203.9516519, 0.0, 0.0, 0.0, 97.7604, 101.761, 203.952, 96.5336, 100.654, 199.493, 4.430144947418]
2229s EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.039516519000E+02', '*', '*', '*', '97.7604', '101.761', '203.952', '96.5336', '100.654', '199.493', '4.430144947418E+00']
2229s COMPUTED RESULT 97.76035707281
2229s COMPUTED RESULT 101.7611498797
2229s COMPUTED RESULT 203.9516519
2229s COMPUTED RESULT 0.0
2229s COMPUTED RESULT 0.0
2229s COMPUTED RESULT 0.0
2229s COMPUTED RESULT 97.7604
2229s COMPUTED RESULT 101.761
2229s COMPUTED RESULT 203.952
2229s COMPUTED RESULT 96.5336
2229s COMPUTED RESULT 100.654
2229s COMPUTED RESULT 199.493
2229s COMPUTED RESULT 4.430144947418
2229s Running tests for solv section
2229s BINARY:  /usr/bin/apbs
2229s INPUT:   apbs-mol.in
2229s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in']
2229s asc_getToken: Error occurred (bailing out).
2229s Vio_scanf: Format problem with input.
2229s 
2229s 
2229s ----------------------------------------------------------------------
2229s     APBS -- Adaptive Poisson-Boltzmann Solver
2229s     Version APBS 3.4.1
2229s     
2229s     Nathan A. Baker (nathan.baker@pnnl.gov)
2229s     Pacific Northwest National Laboratory
2229s     
2229s     Additional contributing authors listed in the code documentation.
2229s     
2229s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2229s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2229s     Northwest Division for the U.S. Department of Energy.
2229s     
2229s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2229s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2229s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2229s     Portions Copyright (c) 1995, Michael Holst.
2229s     All rights reserved.
2229s     
2229s     Redistribution and use in source and binary forms, with or without
2229s     modification, are permitted provided that the following conditions are met:
2229s     
2229s     * Redistributions of source code must retain the above copyright notice, this
2229s       list of conditions and the following disclaimer.
2229s     
2229s     * Redistributions in binary form must reproduce the above copyright notice,
2229s       this list of conditions and the following disclaimer in the documentation
2229s       and/or other materials provided with the distribution.
2229s     
2229s     * Neither the name of the developer nor the names of its contributors may be
2229s       used to endorse or promote products derived from this software without
2229s       specific prior written permission.
2229s     
2229s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2229s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2229s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2229s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2229s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2229s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2229s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2229s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2229s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2229s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2229s ----------------------------------------------------------------------
2229s     APBS uses FETK (the Finite Element ToolKit) to solve the
2229s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2229s     of finite element modeling class libraries developed by the Michael Holst
2229s     research group and written in an object-oriented form of C.  FEtk is
2229s     designed to solve general coupled systems of nonlinear partial differential
2229s     equations using adaptive finite element methods, inexact Newton methods,
2229s     and algebraic multilevel methods.  More information about FEtk may be found
2229s     at <http://www.FEtk.ORG>.
2229s ----------------------------------------------------------------------
2229s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2229s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2229s     which has been modified by Patrice Koehl
2229s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2229s     memory usage when solving the Poisson-Boltzmann equation.
2229s ----------------------------------------------------------------------
2229s     Please cite your use of APBS as:
2229s 
2229s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2229s     nanosystems: application to microtubules and the ribosome. Proc.
2229s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2229s     
2229s 
2229s This executable compiled on Mar  2 2024 at 20:11:10
2229s 
2229s Parsing input file apbs-mol.in...
2229s rank 0 size 1...
2229s Parsed input file.
2229s Got paths for 2 molecules
2229s Reading PQR-format atom data from methanol.pqr.
2229s asc_getToken: Error occurred (bailing out).
2229s Vio_scanf: Format problem with input.
2229s   3 atoms
2229s   Centered at (3.086e-01, 0.000e+00, -2.417e-01)
2229s   Net charge 5.55e-17 e
2229s Reading PQR-format atom data from methoxide.pqr.
2229s   2 atoms
2229s   Centered at (0.000e+00, 0.000e+00, -1.279e-01)
2229s   Net charge -1.00e+00 e
2229s Preparing to run 4 PBE calculations.
2229s ----------------------------------------
2229s CALCULATION #1 (methanol-solv): MULTIGRID
2229s   Setting up problem...
2229s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2229s   Debye length:  0 A
2229s   Current memory usage:  61.247 MB total, 61.247 MB high water
2229s   Using linear spline charge discretization.
2229s   Grid dimensions: 65 x 65 x 65
2229s   Grid spacings: 0.250 x 0.250 x 0.250
2229s   Grid lengths: 16.000 x 16.000 x 16.000
2229s   Grid center: (0.309, 0.000, -0.242)
2229s   Multigrid levels: 5
2229s   Molecule ID: 1
2229s   Linearized traditional PBE
2229s   Multiple Debye-Huckel sphere boundary conditions
2229s   2 ion species (0.000 M ionic strength):
2229s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2229s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2229s   Solute dielectric: 2.000
2229s   Solvent dielectric: 78.000
2229s   Using "molecular" surface definition; no smoothing
2229s   Solvent probe radius: 0.000 A
2229s   Temperature:  300.000 K
2229s   Electrostatic energies will be calculated
2229s   Total electrostatic energy = 1.847663548071E+03 kJ/mol
2229s   Calculating forces...
2229s ----------------------------------------
2229s CALCULATION #2 (methanol-ref): MULTIGRID
2229s   Setting up problem...
2229s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2229s   Debye length:  0 A
2229s   Current memory usage:  61.247 MB total, 61.316 MB high water
2229s   Using linear spline charge discretization.
2229s   Grid dimensions: 65 x 65 x 65
2229s   Grid spacings: 0.250 x 0.250 x 0.250
2229s   Grid lengths: 16.000 x 16.000 x 16.000
2229s   Grid center: (0.309, 0.000, -0.242)
2229s   Multigrid levels: 5
2229s   Molecule ID: 1
2229s   Linearized traditional PBE
2229s   Multiple Debye-Huckel sphere boundary conditions
2229s   2 ion species (0.000 M ionic strength):
2229s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2229s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2229s   Solute dielectric: 2.000
2229s   Solvent dielectric: 1.000
2229s   Using "molecular" surface definition; no smoothing
2229s   Solvent probe radius: 0.000 A
2229s   Temperature:  300.000 K
2229s   Electrostatic energies will be calculated
2229s   Total electrostatic energy = 1.883912182952E+03 kJ/mol
2229s   Calculating forces...
2229s ----------------------------------------
2229s CALCULATION #3 (methoxide-solv): MULTIGRID
2229s   Setting up problem...
2229s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2229s   Debye length:  0 A
2229s   Current memory usage:  61.243 MB total, 61.316 MB high water
2229s   Using linear spline charge discretization.
2229s   Grid dimensions: 65 x 65 x 65
2229s   Grid spacings: 0.250 x 0.250 x 0.250
2229s   Grid lengths: 16.000 x 16.000 x 16.000
2229s   Grid center: (0.000, 0.000, -0.128)
2229s   Multigrid levels: 5
2229s   Molecule ID: 2
2229s   Linearized traditional PBE
2229s   Multiple Debye-Huckel sphere boundary conditions
2229s   2 ion species (0.000 M ionic strength):
2229s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2229s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2229s   Solute dielectric: 2.000
2229s   Solvent dielectric: 78.000
2229s   Using "molecular" surface definition; no smoothing
2229s   Solvent probe radius: 0.000 A
2229s   Temperature:  300.000 K
2229s   Electrostatic energies will be calculated
2229s   Total electrostatic energy = 2.732623683321E+03 kJ/mol
2229s   Calculating forces...
2229s ----------------------------------------
2229s CALCULATION #4 (methoxide-ref): MULTIGRID
2229s   Setting up problem...
2229s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2229s   Debye length:  0 A
2229s   Current memory usage:  61.243 MB total, 61.316 MB high water
2229s   Using linear spline charge discretization.
2229s   Grid dimensions: 65 x 65 x 65
2229s   Grid spacings: 0.250 x 0.250 x 0.250
2229s   Grid lengths: 16.000 x 16.000 x 16.000
2229s   Grid center: (0.000, 0.000, -0.128)
2229s   Multigrid levels: 5
2229s   Molecule ID: 2
2229s   Linearized traditional PBE
2229s   Multiple Debye-Huckel sphere boundary conditions
2229s   2 ion species (0.000 M ionic strength):
2229s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2229s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2229s   Solute dielectric: 2.000
2229s   Solvent dielectric: 1.000
2229s   Using "molecular" surface definition; no smoothing
2229s   Solvent probe radius: 0.000 A
2229s   Temperature:  300.000 K
2229s   Electrostatic energies will be calculated
2229s   Total electrostatic energy = 3.123035854133E+03 kJ/mol
2229s   Calculating forces...
2229s ----------------------------------------
2229s PRINT STATEMENTS
2229s 
2229s print energy 1 (methanol-solv) - 2 (methanol-ref) end
2229s   Local net energy (PE 0) = -3.624863488074E+01 kJ/mol
2229s   Global net ELEC energy = -3.624863488074E+01 kJ/mol
2229s 
2229s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end
2229s   Local net energy (PE 0) = -3.904121708125E+02 kJ/mol
2229s   Global net ELEC energy = -3.904121708125E+02 kJ/mol
2229s 
2229s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end
2229s   Local net energy (PE 0) = -3.541635359318E+02 kJ/mol
2229s   Global net ELEC energy = -3.541635359318E+02 kJ/mol
2229s ----------------------------------------
2229s CLEANING UP AND SHUTTING DOWN...
2229s Destroying force arrays.
2229s No energy arrays to destroy.
2229s Destroying multigrid structures.
2229s Destroying finite element structures.
2229s Destroying 2 molecules
2229s Final memory usage:  0.001 MB total, 61.316 MB high water
2229s 
2229s 
2229s Thanks for using APBS!
2229s 
2234s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03)
2234s *** PASSED ***
2234s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03)
2234s *** PASSED ***
2234s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03)
2234s *** PASSED ***
2234s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03)
2234s *** PASSED ***
2234s Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01)
2234s *** PASSED ***
2234s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02)
2234s *** PASSED ***
2234s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02)
2234s *** PASSED ***
2234s Elapsed time: 5.068256 seconds
2234s --------------------------------------------------------------------------------
2234s Total elapsed time: 11.780552 seconds
2234s Test results have been logged
2234s --------------------------------------------------------------------------------
2234s Checking for intermediate energies in input file apbs-mol.out
2234s EXPECTED COMPUTED: 7
2234s EXPECTED EXPECTED: 7
2234s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318]
2234s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02']
2234s COMPUTED RESULT 1847.663548071
2234s COMPUTED RESULT 1883.912182952
2234s COMPUTED RESULT 2732.623683321
2234s COMPUTED RESULT 3123.035854133
2234s COMPUTED RESULT -36.24863488074
2234s COMPUTED RESULT -390.4121708125
2234s COMPUTED RESULT -354.1635359318
2234s BINARY:  /usr/bin/apbs
2234s INPUT:   apbs-smol.in
2234s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in']
2234s asc_getToken: Error occurred (bailing out).
2234s Vio_scanf: Format problem with input.
2234s 
2234s 
2234s ----------------------------------------------------------------------
2234s     APBS -- Adaptive Poisson-Boltzmann Solver
2234s     Version APBS 3.4.1
2234s     
2234s     Nathan A. Baker (nathan.baker@pnnl.gov)
2234s     Pacific Northwest National Laboratory
2234s     
2234s     Additional contributing authors listed in the code documentation.
2234s     
2234s     Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
2234s     Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
2234s     Northwest Division for the U.S. Department of Energy.
2234s     
2234s     Portions Copyright (c) 2002-2010, Washington University in St. Louis.
2234s     Portions Copyright (c) 2002-2020, Nathan A. Baker.
2234s     Portions Copyright (c) 1999-2002, The Regents of the University of California.
2234s     Portions Copyright (c) 1995, Michael Holst.
2234s     All rights reserved.
2234s     
2234s     Redistribution and use in source and binary forms, with or without
2234s     modification, are permitted provided that the following conditions are met:
2234s     
2234s     * Redistributions of source code must retain the above copyright notice, this
2234s       list of conditions and the following disclaimer.
2234s     
2234s     * Redistributions in binary form must reproduce the above copyright notice,
2234s       this list of conditions and the following disclaimer in the documentation
2234s       and/or other materials provided with the distribution.
2234s     
2234s     * Neither the name of the developer nor the names of its contributors may be
2234s       used to endorse or promote products derived from this software without
2234s       specific prior written permission.
2234s     
2234s     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
2234s     ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
2234s     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
2234s     DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
2234s     ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
2234s     (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
2234s     LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
2234s     ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
2234s     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
2234s     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2234s ----------------------------------------------------------------------
2234s     APBS uses FETK (the Finite Element ToolKit) to solve the
2234s     Poisson-Boltzmann equation numerically.  FETK is a portable collection
2234s     of finite element modeling class libraries developed by the Michael Holst
2234s     research group and written in an object-oriented form of C.  FEtk is
2234s     designed to solve general coupled systems of nonlinear partial differential
2234s     equations using adaptive finite element methods, inexact Newton methods,
2234s     and algebraic multilevel methods.  More information about FEtk may be found
2234s     at <http://www.FEtk.ORG>.
2234s ----------------------------------------------------------------------
2234s     APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
2234s     Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
2234s     which has been modified by Patrice Koehl
2234s     <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
2234s     memory usage when solving the Poisson-Boltzmann equation.
2234s ----------------------------------------------------------------------
2234s     Please cite your use of APBS as:
2234s 
2234s     Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
2234s     nanosystems: application to microtubules and the ribosome. Proc.
2234s     Natl. Acad. Sci. USA 98, 10037-10041 2001.
2234s     
2234s 
2234s This executable compiled on Mar  2 2024 at 20:11:10
2234s 
2234s Parsing input file apbs-smol.in...
2234s rank 0 size 1...
2234s Parsed input file.
2234s Got paths for 2 molecules
2234s Reading PQR-format atom data from methanol.pqr.
2234s asc_getToken: Error occurred (bailing out).
2234s Vio_scanf: Format problem with input.
2234s   3 atoms
2234s   Centered at (3.086e-01, 0.000e+00, -2.417e-01)
2234s   Net charge 5.55e-17 e
2234s Reading PQR-format atom data from methoxide.pqr.
2234s   2 atoms
2234s   Centered at (0.000e+00, 0.000e+00, -1.279e-01)
2234s   Net charge -1.00e+00 e
2234s Preparing to run 4 PBE calculations.
2234s ----------------------------------------
2234s CALCULATION #1 (methanol-solv): MULTIGRID
2234s   Setting up problem...
2234s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2234s   Debye length:  0 A
2234s   Current memory usage:  61.247 MB total, 61.247 MB high water
2234s   Using linear spline charge discretization.
2234s   Grid dimensions: 65 x 65 x 65
2234s   Grid spacings: 0.250 x 0.250 x 0.250
2234s   Grid lengths: 16.000 x 16.000 x 16.000
2234s   Grid center: (0.309, 0.000, -0.242)
2234s   Multigrid levels: 5
2234s   Molecule ID: 1
2234s   Linearized traditional PBE
2234s   Multiple Debye-Huckel sphere boundary conditions
2234s   2 ion species (0.000 M ionic strength):
2234s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2234s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2234s   Solute dielectric: 2.000
2234s   Solvent dielectric: 78.000
2234s   Using "molecular" surface definition;harmonic average smoothing
2234s   Solvent probe radius: 0.000 A
2234s   Temperature:  300.000 K
2234s   Electrostatic energies will be calculated
2234s   Total electrostatic energy = 1.847860440020E+03 kJ/mol
2234s   Calculating forces...
2234s ----------------------------------------
2234s CALCULATION #2 (methanol-ref): MULTIGRID
2234s   Setting up problem...
2234s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2234s   Debye length:  0 A
2234s   Current memory usage:  61.247 MB total, 61.316 MB high water
2234s   Using linear spline charge discretization.
2234s   Grid dimensions: 65 x 65 x 65
2234s   Grid spacings: 0.250 x 0.250 x 0.250
2234s   Grid lengths: 16.000 x 16.000 x 16.000
2234s   Grid center: (0.309, 0.000, -0.242)
2234s   Multigrid levels: 5
2234s   Molecule ID: 1
2234s   Linearized traditional PBE
2234s   Multiple Debye-Huckel sphere boundary conditions
2234s   2 ion species (0.000 M ionic strength):
2234s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2234s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2234s   Solute dielectric: 2.000
2234s   Solvent dielectric: 1.000
2234s   Using "molecular" surface definition;harmonic average smoothing
2234s   Solvent probe radius: 0.000 A
2234s   Temperature:  300.000 K
2234s   Electrostatic energies will be calculated
2234s   Total electrostatic energy = 1.885436377745E+03 kJ/mol
2234s   Calculating forces...
2234s ----------------------------------------
2234s CALCULATION #3 (methoxide-solv): MULTIGRID
2234s   Setting up problem...
2234s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2234s   Debye length:  0 A
2234s   Current memory usage:  61.243 MB total, 61.316 MB high water
2234s   Using linear spline charge discretization.
2234s   Grid dimensions: 65 x 65 x 65
2234s   Grid spacings: 0.250 x 0.250 x 0.250
2234s   Grid lengths: 16.000 x 16.000 x 16.000
2234s   Grid center: (0.000, 0.000, -0.128)
2234s   Multigrid levels: 5
2234s   Molecule ID: 2
2234s   Linearized traditional PBE
2234s   Multiple Debye-Huckel sphere boundary conditions
2234s   2 ion species (0.000 M ionic strength):
2234s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2234s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2234s   Solute dielectric: 2.000
2234s   Solvent dielectric: 78.000
2234s   Using "molecular" surface definition;harmonic average smoothing
2234s   Solvent probe radius: 0.000 A
2234s   Temperature:  300.000 K
2234s   Electrostatic energies will be calculated
2234s   Total electrostatic energy = 2.734040568569E+03 kJ/mol
2234s   Calculating forces...
2234s ----------------------------------------
2234s CALCULATION #4 (methoxide-ref): MULTIGRID
2234s   Setting up problem...
2234s   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
2234s   Debye length:  0 A
2234s   Current memory usage:  61.243 MB total, 61.316 MB high water
2234s   Using linear spline charge discretization.
2234s   Grid dimensions: 65 x 65 x 65
2234s   Grid spacings: 0.250 x 0.250 x 0.250
2234s   Grid lengths: 16.000 x 16.000 x 16.000
2234s   Grid center: (0.000, 0.000, -0.128)
2234s   Multigrid levels: 5
2234s   Molecule ID: 2
2234s   Linearized traditional PBE
2234s   Multiple Debye-Huckel sphere boundary conditions
2234s   2 ion species (0.000 M ionic strength):
2234s     2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2234s     2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2234s   Solute dielectric: 2.000
2234s   Solvent dielectric: 1.000
2234s   Using "molecular" surface definition;harmonic average smoothing
2234s   Solvent probe radius: 0.000 A
2234s   Temperature:  300.000 K
2234s   Electrostatic energies will be calculated
2234s   Total electrostatic energy = 3.125279428954E+03 kJ/mol
2234s   Calculating forces...
2234s ----------------------------------------
2234s PRINT STATEMENTS
2234s 
2234s print energy 1 (methanol-solv) - 2 (methanol-ref) end
2234s   Local net energy (PE 0) = -3.757593772493E+01 kJ/mol
2234s   Global net ELEC energy = -3.757593772493E+01 kJ/mol
2234s 
2234s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end
2234s   Local net energy (PE 0) = -3.912388603848E+02 kJ/mol
2234s   Global net ELEC energy = -3.912388603848E+02 kJ/mol
2234s 
2234s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end
2234s   Local net energy (PE 0) = -3.536629226599E+02 kJ/mol
2234s   Global net ELEC energy = -3.536629226599E+02 kJ/mol
2234s ----------------------------------------
2234s CLEANING UP AND SHUTTING DOWN...
2234s Destroying force arrays.
2234s No energy arrays to destroy.
2234s Destroying multigrid structures.
2234s Destroying finite element structures.
2234s Destroying 2 molecules
2234s Final memory usage:  0.001 MB total, 61.316 MB high water
2234s 
2234s 
2234s Thanks for using APBS!
2234s 
2234s Checking for intermediate energies in input file apbs-smol.out
2234s EXPECTED COMPUTED: 7
2234s EXPECTED EXPECTED: 7
2234s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599]
2234s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02']
2234s COMPUTED RESULT 1847.86044002
2234s COMPUTED RESULT 1885.436377745
2234s COMPUTED RESULT 2734.040568569
2234s COMPUTED RESULT 3125.279428954
2234s COMPUTED RESULT -37.57593772493
2234s COMPUTED RESULT -391.2388603848
2234s COMPUTED RESULT -353.6629226599
2235s autopkgtest [15:22:51]: test test-apbs: -----------------------]
2240s test-apbs            PASS
2240s autopkgtest [15:22:56]: test test-apbs:  - - - - - - - - - - results - - - - - - - - - -
2244s autopkgtest [15:23:00]: @@@@@@@@@@@@@@@@@@@@ summary
2244s test-apbs            PASS