0s autopkgtest [15:12:59]: starting date and time: 2025-10-18 15:12:59+0000 0s autopkgtest [15:12:59]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [15:12:59]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p6li5f2w/out --timeout-copy=6000 --setup-commands '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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/resolute/armhf 20s autopkgtest [15:13:19]: testbed dpkg architecture: armhf 22s autopkgtest [15:13:21]: testbed apt version: 3.1.6ubuntu2 26s autopkgtest [15:13:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [15:13:27]: testbed release detected to be: None 35s autopkgtest [15:13:34]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 37s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [83.3 kB] 37s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 37s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 37s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 37s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 37s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 37s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 37s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [67.3 kB] 37s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 37s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [214 kB] 37s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [2804 B] 37s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1399 kB] 37s Get:14 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [307 kB] 37s Get:15 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.1 MB] 38s Get:16 http://ftpmaster.internal/ubuntu resolute/restricted Sources [14.4 kB] 38s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1357 kB] 38s Get:18 http://ftpmaster.internal/ubuntu resolute/restricted armhf Packages [1672 B] 38s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [14.8 MB] 38s Get:20 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [182 kB] 42s Fetched 40.0 MB in 5s (7793 kB/s) 43s Reading package lists... 49s autopkgtest [15:13:48]: upgrading testbed (apt dist-upgrade and autopurge) 50s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s Calculating upgrade... 52s The following packages will be upgraded: 52s apparmor apt base-files binutils binutils-arm-linux-gnueabihf 52s binutils-common cloud-init cloud-init-base distro-info-data gcc-15-base 52s gir1.2-girepository-2.0 libapparmor1 libapt-pkg7.0 libatomic1 libbinutils 52s libctf-nobfd0 libctf0 libgcc-s1 libgirepository-1.0-1 libpython3-stdlib 52s libsframe2 libstdc++6 lto-disabled-list python3 python3-minimal sudo-rs 53s 26 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 7366 kB of archives. 53s After this operation, 14.3 kB of additional disk space will be used. 53s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf base-files armhf 14ubuntu4 [75.4 kB] 53s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libatomic1 armhf 15.2.0-5ubuntu1 [7942 B] 53s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-base armhf 15.2.0-5ubuntu1 [58.1 kB] 53s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-s1 armhf 15.2.0-5ubuntu1 [40.6 kB] 53s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++6 armhf 15.2.0-5ubuntu1 [731 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libapt-pkg7.0 armhf 3.1.8ubuntu1 [1148 kB] 54s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf apt armhf 3.1.8ubuntu1 [1404 kB] 54s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.13.7-2 [27.8 kB] 54s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.13.7-2 [23.9 kB] 54s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.13.7-2 [10.6 kB] 54s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf distro-info-data all 0.67~ubuntu1 [7004 B] 54s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libgirepository-1.0-1 armhf 1.86.0-6 [111 kB] 54s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-girepository-2.0 armhf 1.86.0-6 [25.3 kB] 54s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libapparmor1 armhf 5.0.0~alpha1-0ubuntu8.1 [52.9 kB] 54s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf sudo-rs armhf 0.2.8-1ubuntu5.1 [548 kB] 54s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf apparmor armhf 5.0.0~alpha1-0ubuntu8.1 [631 kB] 55s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libctf0 armhf 2.45-7ubuntu2 [75.7 kB] 55s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libctf-nobfd0 armhf 2.45-7ubuntu2 [79.1 kB] 55s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-arm-linux-gnueabihf armhf 2.45-7ubuntu2 [1022 kB] 55s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libbinutils armhf 2.45-7ubuntu2 [411 kB] 55s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf binutils armhf 2.45-7ubuntu2 [3240 B] 55s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-common armhf 2.45-7ubuntu2 [220 kB] 55s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libsframe2 armhf 2.45-7ubuntu2 [13.4 kB] 55s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init-base all 25.3-0ubuntu1 [625 kB] 55s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init all 25.3-0ubuntu1 [2106 B] 55s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf lto-disabled-list all 71 [12.5 kB] 56s Preconfiguring packages ... 56s Fetched 7366 kB in 3s (2721 kB/s) 56s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 56s Preparing to unpack .../base-files_14ubuntu4_armhf.deb ... 56s Unpacking base-files (14ubuntu4) over (14ubuntu3) ... 56s Setting up base-files (14ubuntu4) ... 56s Installing new version of config file /etc/issue ... 56s Installing new version of config file /etc/issue.net ... 56s Installing new version of config file /etc/lsb-release ... 57s motd-news.service is a disabled or a static unit not running, not starting it. 57s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libatomic1_15.2.0-5ubuntu1_armhf.deb ... 57s Unpacking libatomic1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 57s Preparing to unpack .../gcc-15-base_15.2.0-5ubuntu1_armhf.deb ... 57s Unpacking gcc-15-base:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up gcc-15-base:armhf (15.2.0-5ubuntu1) ... 57s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libgcc-s1_15.2.0-5ubuntu1_armhf.deb ... 57s Unpacking libgcc-s1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up libgcc-s1:armhf (15.2.0-5ubuntu1) ... 57s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libstdc++6_15.2.0-5ubuntu1_armhf.deb ... 58s Unpacking libstdc++6:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 58s Setting up libstdc++6:armhf (15.2.0-5ubuntu1) ... 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 58s Preparing to unpack .../libapt-pkg7.0_3.1.8ubuntu1_armhf.deb ... 58s Unpacking libapt-pkg7.0:armhf (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 58s Setting up libapt-pkg7.0:armhf (3.1.8ubuntu1) ... 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 58s Preparing to unpack .../apt_3.1.8ubuntu1_armhf.deb ... 58s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 58s Setting up apt (3.1.8ubuntu1) ... 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 59s Preparing to unpack .../python3-minimal_3.13.7-2_armhf.deb ... 59s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 59s Setting up python3-minimal (3.13.7-2) ... 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 59s Preparing to unpack .../00-python3_3.13.7-2_armhf.deb ... 59s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 59s Preparing to unpack .../01-libpython3-stdlib_3.13.7-2_armhf.deb ... 59s Unpacking libpython3-stdlib:armhf (3.13.7-2) over (3.13.7-1) ... 59s Preparing to unpack .../02-distro-info-data_0.67~ubuntu1_all.deb ... 59s Unpacking distro-info-data (0.67~ubuntu1) over (0.66) ... 59s Preparing to unpack .../03-libgirepository-1.0-1_1.86.0-6_armhf.deb ... 59s Unpacking libgirepository-1.0-1:armhf (1.86.0-6) over (1.84.0-1) ... 59s Preparing to unpack .../04-gir1.2-girepository-2.0_1.86.0-6_armhf.deb ... 59s Unpacking gir1.2-girepository-2.0:armhf (1.86.0-6) over (1.84.0-1) ... 60s Preparing to unpack .../05-libapparmor1_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 60s Unpacking libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 60s Preparing to unpack .../06-sudo-rs_0.2.8-1ubuntu5.1_armhf.deb ... 60s Unpacking sudo-rs (0.2.8-1ubuntu5.1) over (0.2.8-1ubuntu5) ... 60s Preparing to unpack .../07-apparmor_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 61s Unpacking apparmor (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 62s Preparing to unpack .../08-libctf0_2.45-7ubuntu2_armhf.deb ... 62s Unpacking libctf0:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 62s Preparing to unpack .../09-libctf-nobfd0_2.45-7ubuntu2_armhf.deb ... 62s Unpacking libctf-nobfd0:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 62s Preparing to unpack .../10-binutils-arm-linux-gnueabihf_2.45-7ubuntu2_armhf.deb ... 62s Unpacking binutils-arm-linux-gnueabihf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 63s Preparing to unpack .../11-libbinutils_2.45-7ubuntu2_armhf.deb ... 63s Unpacking libbinutils:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 63s Preparing to unpack .../12-binutils_2.45-7ubuntu2_armhf.deb ... 63s Unpacking binutils (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 63s Preparing to unpack .../13-binutils-common_2.45-7ubuntu2_armhf.deb ... 63s Unpacking binutils-common:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 63s Preparing to unpack .../14-libsframe2_2.45-7ubuntu2_armhf.deb ... 63s Unpacking libsframe2:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 63s Preparing to unpack .../15-cloud-init-base_25.3-0ubuntu1_all.deb ... 63s Unpacking cloud-init-base (25.3-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 64s Preparing to unpack .../16-cloud-init_25.3-0ubuntu1_all.deb ... 64s Unpacking cloud-init (25.3-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 64s Preparing to unpack .../17-lto-disabled-list_71_all.deb ... 64s Unpacking lto-disabled-list (71) over (69) ... 64s Setting up lto-disabled-list (71) ... 64s Setting up libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) ... 64s Setting up distro-info-data (0.67~ubuntu1) ... 64s Setting up libsframe2:armhf (2.45-7ubuntu2) ... 64s Setting up binutils-common:armhf (2.45-7ubuntu2) ... 64s Setting up libctf-nobfd0:armhf (2.45-7ubuntu2) ... 64s Setting up apparmor (5.0.0~alpha1-0ubuntu8.1) ... 64s Installing new version of config file /etc/apparmor.d/fusermount3 ... 64s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 64s 64s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 64s 64s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 64s 65s Reloading AppArmor profiles 65s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 65s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 65s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 65s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 65s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 65s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 65s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 65s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 65s 66s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "bwrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "babeld". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "alsamixer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "bfdd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "bgpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "dnstracer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "eigrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "fabricd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "dig". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "hostname". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "iotop-c". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "isisd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "fusermount3". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "gs". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "john". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ldpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "compressor". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "locale". /sbin/apparmor_parser: Unable to replace "lsblk". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "linux-boot-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lsusb". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "irssi". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Unable to replace "mbsync". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Unable to replace "mosquitto". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "nhrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "nslookup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "notify-send". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ospf6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "nc.openbsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "os-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "pbrd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "pathd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Unable to replace "pim6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ospfd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "pimd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ripngd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ripd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "openvpn". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "qpdf". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ssh-keyscan". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Unable to replace "staticd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "proftpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "systemd-detect-virt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "tinyproxy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "mx-extract". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "rygel". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "cmds". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "tnftp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "/usr/sbin/chronyd". /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "dumpcap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "tshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "wg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "who". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "vrrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "wg-quick". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "znc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 66s 66s Error: At least one profile failed to load 66s Setting up libatomic1:armhf (15.2.0-5ubuntu1) ... 66s Setting up libgirepository-1.0-1:armhf (1.86.0-6) ... 66s Setting up libbinutils:armhf (2.45-7ubuntu2) ... 66s Setting up sudo-rs (0.2.8-1ubuntu5.1) ... 66s Setting up libpython3-stdlib:armhf (3.13.7-2) ... 66s Setting up libctf0:armhf (2.45-7ubuntu2) ... 66s Setting up python3 (3.13.7-2) ... 66s Setting up cloud-init-base (25.3-0ubuntu1) ... 69s Setting up gir1.2-girepository-2.0:armhf (1.86.0-6) ... 69s Setting up binutils-arm-linux-gnueabihf (2.45-7ubuntu2) ... 69s Setting up cloud-init (25.3-0ubuntu1) ... 69s Setting up binutils (2.45-7ubuntu2) ... 69s Processing triggers for plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu1) ... 69s Processing triggers for procps (2:4.0.4-8ubuntu3) ... 69s Processing triggers for install-info (7.1.1-1ubuntu1) ... 69s Processing triggers for libc-bin (2.42-0ubuntu3) ... 69s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 69s Processing triggers for systemd (257.9-0ubuntu2) ... 69s Processing triggers for man-db (2.13.1-1) ... 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Solving dependencies... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s autopkgtest [15:14:17]: rebooting testbed after setup commands that affected boot 117s autopkgtest [15:14:56]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 140s autopkgtest [15:15:19]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 181s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 181s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 181s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 181s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 181s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 181s gpgv: Can't check signature: No public key 181s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 184s autopkgtest [15:16:03]: testing package apbs version 3.4.1-6build2 190s autopkgtest [15:16:09]: build not needed 197s autopkgtest [15:16:16]: test test-apbs: preparing testbed 199s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Solving dependencies... 201s The following NEW packages will be installed: 201s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax libamd3 201s libapbs-dev libapbs3t64 libarpack2t64 libblas3 libcamd3 libccolamd3 201s libcholmod5 libcolamd3 libfetk-dev libfetk1.9t64 libgfortran5 libgomp1 201s libhwloc15 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore 201s liblapack3 libmaloc-dev libmaloc1 libmpich12 libpython3.13 libspqr4 201s libsuitesparseconfig7 libsuperlu7 libumfpack6 python3-apbslib 201s sphinx-rtd-theme-common 201s 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. 201s Need to get 30.8 MB of archives. 201s After this operation, 116 MB of additional disk space will be used. 201s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-lato all 2.015-1 [2781 kB] 202s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf apbs-data all 3.4.1-6build2 [1769 kB] 202s Get:3 http://ftpmaster.internal/ubuntu resolute/universe armhf libmaloc1 armhf 1.5-2 [79.8 kB] 202s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-6build1 [133 kB] 202s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf libsuperlu7 armhf 7.0.1+dfsg1-2 [157 kB] 202s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-5ubuntu1 [129 kB] 202s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libsuitesparseconfig7 armhf 1:7.10.1+dfsg-1 [20.9 kB] 202s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf libamd3 armhf 1:7.10.1+dfsg-1 [37.7 kB] 202s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libcamd3 armhf 1:7.10.1+dfsg-1 [34.3 kB] 202s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libccolamd3 armhf 1:7.10.1+dfsg-1 [36.0 kB] 202s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libcolamd3 armhf 1:7.10.1+dfsg-1 [28.0 kB] 202s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-5ubuntu1 [334 kB] 202s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-6build1 [2091 kB] 202s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf libcholmod5 armhf 1:7.10.1+dfsg-1 [681 kB] 202s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf libumfpack6 armhf 1:7.10.1+dfsg-1 [296 kB] 202s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf libfetk1.9t64 armhf 3.4.1-6build2 [538 kB] 202s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf libapbs3t64 armhf 3.4.1-6build2 [257 kB] 202s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 202s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 202s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf libarpack2t64 armhf 3.9.1-6 [88.7 kB] 202s Get:21 http://ftpmaster.internal/ubuntu resolute/universe armhf libhwloc15 armhf 2.12.2-1 [149 kB] 202s Get:22 http://ftpmaster.internal/ubuntu resolute/universe armhf libmpich12 armhf 4.3.0+really4.2.1-1build1 [1688 kB] 202s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf libspqr4 armhf 1:7.10.1+dfsg-1 [138 kB] 202s Get:24 http://ftpmaster.internal/ubuntu resolute/universe armhf apbs armhf 3.4.1-6build2 [75.0 kB] 202s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 202s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 202s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 202s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 202s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 202s Get:30 http://ftpmaster.internal/ubuntu resolute/universe armhf apbs-doc all 3.4.1-6build2 [5850 kB] 202s Get:31 http://ftpmaster.internal/ubuntu resolute/universe armhf libapbs-dev armhf 3.4.1-6build2 [99.5 kB] 202s Get:32 http://ftpmaster.internal/ubuntu resolute/universe armhf libmaloc-dev armhf 1.5-2 [918 kB] 202s Get:33 http://ftpmaster.internal/ubuntu resolute/universe armhf libfetk-dev armhf 3.4.1-6build2 [144 kB] 202s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13 armhf 3.13.7-1 [2123 kB] 202s Get:35 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-apbslib armhf 3.4.1-6build2 [222 kB] 203s Fetched 30.8 MB in 2s (19.0 MB/s) 203s Selecting previously unselected package fonts-lato. 203s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 203s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 203s Unpacking fonts-lato (2.015-1) ... 203s Selecting previously unselected package apbs-data. 203s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 203s Unpacking apbs-data (3.4.1-6build2) ... 204s Selecting previously unselected package libmaloc1:armhf. 204s Preparing to unpack .../02-libmaloc1_1.5-2_armhf.deb ... 204s 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207s Preparing to unpack .../34-python3-apbslib_3.4.1-6build2_armhf.deb ... 207s Unpacking python3-apbslib (3.4.1-6build2) ... 207s Setting up libpython3.13:armhf (3.13.7-1) ... 207s Setting up libmaloc1:armhf (1.5-2) ... 207s Setting up fonts-lato (2.015-1) ... 207s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 207s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 207s Setting up apbs-data (3.4.1-6build2) ... 207s Setting up libgomp1:armhf (15.2.0-5ubuntu1) ... 207s Setting up libblas3:armhf (3.12.1-6build1) ... 207s 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 207s Setting up libhwloc15:armhf (2.12.2-1) ... 207s Setting up libgfortran5:armhf (15.2.0-5ubuntu1) ... 207s Setting up libmpich12:armhf (4.3.0+really4.2.1-1build1) ... 207s Setting up libsuitesparseconfig7:armhf (1:7.10.1+dfsg-1) ... 207s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 207s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 207s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 207s Setting up libmaloc-dev (1.5-2) ... 207s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 207s Setting up liblapack3:armhf (3.12.1-6build1) ... 207s 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 207s Setting up libarpack2t64:armhf (3.9.1-6) ... 207s Setting up libamd3:armhf (1:7.10.1+dfsg-1) ... 207s Setting up libcolamd3:armhf (1:7.10.1+dfsg-1) ... 207s Setting up libcamd3:armhf (1:7.10.1+dfsg-1) ... 207s Setting up libsuperlu7:armhf (7.0.1+dfsg1-2) ... 207s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 207s Setting up libccolamd3:armhf (1:7.10.1+dfsg-1) ... 207s Setting up libcholmod5:armhf (1:7.10.1+dfsg-1) ... 207s Setting up libspqr4:armhf (1:7.10.1+dfsg-1) ... 207s Setting up apbs-doc (3.4.1-6build2) ... 207s Setting up libumfpack6:armhf (1:7.10.1+dfsg-1) ... 207s Setting up libfetk1.9t64:armhf (3.4.1-6build2) ... 207s Setting up libapbs3t64:armhf (3.4.1-6build2) ... 207s Setting up libfetk-dev:armhf (3.4.1-6build2) ... 207s Setting up libapbs-dev:armhf (3.4.1-6build2) ... 207s Setting up apbs (3.4.1-6build2) ... 207s Setting up python3-apbslib (3.4.1-6build2) ... 207s Processing triggers for man-db (2.13.1-1) ... 207s Processing triggers for libc-bin (2.42-0ubuntu3) ... 228s autopkgtest [15:16:47]: test test-apbs: [----------------------- 230s TESTING WITH BINARY_NAME:apbs 230s START_DIR:/tmp/autopkgtest.UFAwfi/autopkgtest_tmp/build 230s -------------------------------------------------------------------------------- 230s Testing forces from apbs-forces.in 230s 230s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001173 seconds 230s -------------------------------------------------------------------------------- 230s -------------------------------------------------------------------------------- 230s Testing input file apbs-mol-auto.in 230s 236s CHECKING:/usr/local/sbin/apbs 236s CHECKING:/usr/local/bin/apbs 236s CHECKING:/usr/sbin/apbs 236s CHECKING:/usr/bin/apbs 236s NOTE: Using apbs binary:/usr/bin/apbs 236s Testing all sections 236s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 236s ================================================================================ 236s Running tests for born section 236s BINARY: /usr/bin/apbs 236s INPUT: apbs-mol-auto.in 236s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 236s asc_getToken: Error occurred (bailing out). 236s Vio_scanf: Format problem with input. 236s 236s 236s ---------------------------------------------------------------------- 236s APBS -- Adaptive Poisson-Boltzmann Solver 236s Version APBS 3.4.1 236s 236s Nathan A. Baker (nathan.baker@pnnl.gov) 236s Pacific Northwest National Laboratory 236s 236s Additional contributing authors listed in the code documentation. 236s 236s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 236s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 236s Northwest Division for the U.S. Department of Energy. 236s 236s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 236s Portions Copyright (c) 2002-2020, Nathan A. Baker. 236s Portions Copyright (c) 1999-2002, The Regents of the University of California. 236s Portions Copyright (c) 1995, Michael Holst. 236s All rights reserved. 236s 236s Redistribution and use in source and binary forms, with or without 236s modification, are permitted provided that the following conditions are met: 236s 236s * Redistributions of source code must retain the above copyright notice, this 236s list of conditions and the following disclaimer. 236s 236s * Redistributions in binary form must reproduce the above copyright notice, 236s this list of conditions and the following disclaimer in the documentation 236s and/or other materials provided with the distribution. 236s 236s * Neither the name of the developer nor the names of its contributors may be 236s used to endorse or promote products derived from this software without 236s specific prior written permission. 236s 236s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 236s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 236s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 236s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 236s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 236s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 236s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 236s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 236s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 236s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 236s ---------------------------------------------------------------------- 236s APBS uses FETK (the Finite Element ToolKit) to solve the 236s Poisson-Boltzmann equation numerically. FETK is a portable collection 236s of finite element modeling class libraries developed by the Michael Holst 236s research group and written in an object-oriented form of C. FEtk is 236s designed to solve general coupled systems of nonlinear partial differential 236s equations using adaptive finite element methods, inexact Newton methods, 236s and algebraic multilevel methods. More information about FEtk may be found 236s at . 236s ---------------------------------------------------------------------- 236s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 236s Aqua is a modified form of the Holst group PMG library 236s which has been modified by Patrice Koehl 236s for improved efficiency and 236s memory usage when solving the Poisson-Boltzmann equation. 236s ---------------------------------------------------------------------- 236s Please cite your use of APBS as: 236s 236s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 236s nanosystems: application to microtubules and the ribosome. Proc. 236s Natl. Acad. Sci. USA 98, 10037-10041 2001. 236s 236s 236s This executable compiled on Jan 3 2025 at 11:01:42 236s 236s Parsing input file apbs-mol-auto.in... 236s rank 0 size 1... 236s Parsed input file. 236s Got paths for 1 molecules 236s Reading PQR-format atom data from ion.pqr. 236s 1 atoms 236s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 236s Net charge 1.00e+00 e 236s Preparing to run 6 PBE calculations. 236s ---------------------------------------- 236s CALCULATION #1 (solvated): MULTIGRID 236s Setting up problem... 236s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 236s Debye length: 0 A 236s Current memory usage: 61.262 MB total, 61.262 MB high water 236s Using cubic spline charge discretization. 236s Grid dimensions: 65 x 65 x 65 236s Grid spacings: 0.781 x 0.781 x 0.781 236s Grid lengths: 50.000 x 50.000 x 50.000 236s Grid center: (0.000, 0.000, 0.000) 236s Multigrid levels: 5 236s Molecule ID: 1 236s Linearized traditional PBE 236s Multiple Debye-Huckel sphere boundary conditions 236s 0 ion species (0.000 M ionic strength): 236s Solute dielectric: 1.000 236s Solvent dielectric: 78.540 236s Using "molecular" surface definition; no smoothing 236s Solvent probe radius: 1.400 A 236s Temperature: 298.150 K 236s Electrostatic energies will be calculated 236s Total electrostatic energy = 9.607073836227E+02 kJ/mol 236s Calculating forces... 236s ---------------------------------------- 236s CALCULATION #2 (solvated): MULTIGRID 236s Setting up problem... 236s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 236s Debye length: 0 A 236s Current memory usage: 61.262 MB total, 122.067 MB high water 236s Using cubic spline charge discretization. 236s Grid dimensions: 65 x 65 x 65 236s Grid spacings: 0.383 x 0.383 x 0.383 236s Grid lengths: 24.495 x 24.495 x 24.495 236s Grid center: (0.000, 0.000, 0.000) 236s Multigrid levels: 5 236s Molecule ID: 1 236s Linearized traditional PBE 236s Boundary conditions from focusing 236s 0 ion species (0.000 M ionic strength): 236s Solute dielectric: 1.000 236s Solvent dielectric: 78.540 236s Using "molecular" surface definition; no smoothing 236s Solvent probe radius: 1.400 A 236s Temperature: 298.150 K 236s Electrostatic energies will be calculated 236s Total electrostatic energy = 2.200266567971E+03 kJ/mol 236s Calculating forces... 236s ---------------------------------------- 236s CALCULATION #3 (solvated): MULTIGRID 236s Setting up problem... 236s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 236s Debye length: 0 A 236s Current memory usage: 61.262 MB total, 122.067 MB high water 236s Using cubic spline charge discretization. 236s Grid dimensions: 65 x 65 x 65 236s Grid spacings: 0.188 x 0.188 x 0.188 236s Grid lengths: 12.000 x 12.000 x 12.000 236s Grid center: (0.000, 0.000, 0.000) 236s Multigrid levels: 5 236s Molecule ID: 1 236s Linearized traditional PBE 236s Boundary conditions from focusing 236s 0 ion species (0.000 M ionic strength): 236s Solute dielectric: 1.000 236s Solvent dielectric: 78.540 236s Using "molecular" surface definition; no smoothing 236s Solvent probe radius: 1.400 A 236s Temperature: 298.150 K 236s Electrostatic energies will be calculated 236s Potential to be written to potential.dx.gz 236s Total electrostatic energy = 4.732245131587E+03 kJ/mol 236s Calculating forces... 236s Writing potential to potential-PE0.dx.gz 236s ---------------------------------------- 236s CALCULATION #4 (reference): MULTIGRID 236s Setting up problem... 236s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 236s Debye length: 0 A 236s Current memory usage: 61.189 MB total, 122.067 MB high water 236s Using cubic spline charge discretization. 236s Grid dimensions: 65 x 65 x 65 236s Grid spacings: 0.781 x 0.781 x 0.781 236s Grid lengths: 50.000 x 50.000 x 50.000 236s Grid center: (0.000, 0.000, 0.000) 236s Multigrid levels: 5 236s Molecule ID: 1 236s Linearized traditional PBE 236s Multiple Debye-Huckel sphere boundary conditions 236s 0 ion species (0.000 M ionic strength): 236s Solute dielectric: 1.000 236s Solvent dielectric: 1.000 236s Using "molecular" surface definition; no smoothing 236s Solvent probe radius: 1.400 A 236s Temperature: 298.150 K 236s Electrostatic energies will be calculated 236s Total electrostatic energy = 1.190871482831E+03 kJ/mol 236s Calculating forces... 236s ---------------------------------------- 236s CALCULATION #5 (reference): MULTIGRID 236s Setting up problem... 236s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 236s Debye length: 0 A 236s Current memory usage: 61.189 MB total, 122.067 MB high water 236s Using cubic spline charge discretization. 236s Grid dimensions: 65 x 65 x 65 236s Grid spacings: 0.383 x 0.383 x 0.383 236s Grid lengths: 24.495 x 24.495 x 24.495 236s Grid center: (0.000, 0.000, 0.000) 236s Multigrid levels: 5 236s Molecule ID: 1 236s Linearized traditional PBE 236s Boundary conditions from focusing 236s 0 ion species (0.000 M ionic strength): 236s Solute dielectric: 1.000 236s Solvent dielectric: 1.000 236s Using "molecular" surface definition; no smoothing 236s Solvent probe radius: 1.400 A 236s Temperature: 298.150 K 236s Electrostatic energies will be calculated 236s Total electrostatic energy = 2.430874049735E+03 kJ/mol 236s Calculating forces... 236s [focusFillBound()]: WARNING: 236s Unusually large potential values 236s detected on the focusing boundary! 236s Convergence not guaranteed for NPBE/NRPBE calculations! 236s 236s ---------------------------------------- 236s CALCULATION #6 (reference): MULTIGRID 236s Setting up problem... 236s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 236s Debye length: 0 A 236s Current memory usage: 61.189 MB total, 122.067 MB high water 236s Using cubic spline charge discretization. 236s Grid dimensions: 65 x 65 x 65 236s Grid spacings: 0.188 x 0.188 x 0.188 236s Grid lengths: 12.000 x 12.000 x 12.000 236s Grid center: (0.000, 0.000, 0.000) 236s Multigrid levels: 5 236s Molecule ID: 1 236s Linearized traditional PBE 236s Boundary conditions from focusing 236s 0 ion species (0.000 M ionic strength): 236s Solute dielectric: 1.000 236s Solvent dielectric: 1.000 236s Using "molecular" surface definition; no smoothing 236s Solvent probe radius: 1.400 A 236s Temperature: 298.150 K 236s Electrostatic energies will be calculated 236s Total electrostatic energy = 4.962018684215E+03 kJ/mol 236s Calculating forces... 236s ---------------------------------------- 236s PRINT STATEMENTS 236s 236s print energy 1 (solvated) - 2 (reference) end 236s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 236s Global net ELEC energy = -2.297735526282E+02 kJ/mol 236s ---------------------------------------- 236s CLEANING UP AND SHUTTING DOWN... 236s Destroying force arrays. 236s No energy arrays to destroy. 236s Destroying multigrid structures. 236s Destroying finite element structures. 236s Destroying 1 molecules 236s Final memory usage: 0.001 MB total, 122.067 MB high water 236s 236s 236s Thanks for using APBS! 236s 236s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 236s *** PASSED *** 236s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 236s *** PASSED *** 236s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 236s *** PASSED *** 236s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 236s *** PASSED *** 236s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 236s *** PASSED *** 236s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 236s *** PASSED *** 236s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 236s *** PASSED *** 236s Elapsed time: 6.551354 seconds 236s -------------------------------------------------------------------------------- 236s -------------------------------------------------------------------------------- 236s Testing input file apbs-smol-auto.in 236s 241s Checking for intermediate energies in input file apbs-mol-auto.out 241s EXPECTED COMPUTED: 7 241s EXPECTED EXPECTED: 7 241s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 241s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 241s COMPUTED RESULT 960.7073836227 241s COMPUTED RESULT 2200.266567971 241s COMPUTED RESULT 4732.245131587 241s COMPUTED RESULT 1190.871482831 241s COMPUTED RESULT 2430.874049735 241s COMPUTED RESULT 4962.018684215 241s COMPUTED RESULT -229.7735526282 241s BINARY: /usr/bin/apbs 241s INPUT: apbs-smol-auto.in 241s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 241s asc_getToken: Error occurred (bailing out). 241s Vio_scanf: Format problem with input. 241s 241s 241s ---------------------------------------------------------------------- 241s APBS -- Adaptive Poisson-Boltzmann Solver 241s Version APBS 3.4.1 241s 241s Nathan A. Baker (nathan.baker@pnnl.gov) 241s Pacific Northwest National Laboratory 241s 241s Additional contributing authors listed in the code documentation. 241s 241s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 241s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 241s Northwest Division for the U.S. Department of Energy. 241s 241s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 241s Portions Copyright (c) 2002-2020, Nathan A. Baker. 241s Portions Copyright (c) 1999-2002, The Regents of the University of California. 241s Portions Copyright (c) 1995, Michael Holst. 241s All rights reserved. 241s 241s Redistribution and use in source and binary forms, with or without 241s modification, are permitted provided that the following conditions are met: 241s 241s * Redistributions of source code must retain the above copyright notice, this 241s list of conditions and the following disclaimer. 241s 241s * Redistributions in binary form must reproduce the above copyright notice, 241s this list of conditions and the following disclaimer in the documentation 241s and/or other materials provided with the distribution. 241s 241s * Neither the name of the developer nor the names of its contributors may be 241s used to endorse or promote products derived from this software without 241s specific prior written permission. 241s 241s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 241s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 241s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 241s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 241s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 241s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 241s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 241s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 241s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 241s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 241s ---------------------------------------------------------------------- 241s APBS uses FETK (the Finite Element ToolKit) to solve the 241s Poisson-Boltzmann equation numerically. FETK is a portable collection 241s of finite element modeling class libraries developed by the Michael Holst 241s research group and written in an object-oriented form of C. FEtk is 241s designed to solve general coupled systems of nonlinear partial differential 241s equations using adaptive finite element methods, inexact Newton methods, 241s and algebraic multilevel methods. More information about FEtk may be found 241s at . 241s ---------------------------------------------------------------------- 241s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 241s Aqua is a modified form of the Holst group PMG library 241s which has been modified by Patrice Koehl 241s for improved efficiency and 241s memory usage when solving the Poisson-Boltzmann equation. 241s ---------------------------------------------------------------------- 241s Please cite your use of APBS as: 241s 241s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 241s nanosystems: application to microtubules and the ribosome. Proc. 241s Natl. Acad. Sci. USA 98, 10037-10041 2001. 241s 241s 241s This executable compiled on Jan 3 2025 at 11:01:42 241s 241s Parsing input file apbs-smol-auto.in... 241s rank 0 size 1... 241s Parsed input file. 241s Got paths for 1 molecules 241s Reading PQR-format atom data from ion.pqr. 241s 1 atoms 241s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 241s Net charge 1.00e+00 e 241s Preparing to run 6 PBE calculations. 241s ---------------------------------------- 241s CALCULATION #1 (solvated): MULTIGRID 241s Setting up problem... 241s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 241s Debye length: 0 A 241s Current memory usage: 61.262 MB total, 61.262 MB high water 241s Using cubic spline charge discretization. 241s Grid dimensions: 65 x 65 x 65 241s Grid spacings: 0.781 x 0.781 x 0.781 241s Grid lengths: 50.000 x 50.000 x 50.000 241s Grid center: (0.000, 0.000, 0.000) 241s Multigrid levels: 5 241s Molecule ID: 1 241s Linearized traditional PBE 241s Multiple Debye-Huckel sphere boundary conditions 241s 0 ion species (0.000 M ionic strength): 241s Solute dielectric: 1.000 241s Solvent dielectric: 78.540 241s Using "molecular" surface definition;harmonic average smoothing 241s Solvent probe radius: 1.400 A 241s Temperature: 298.150 K 241s Electrostatic energies will be calculated 241s Total electrostatic energy = 9.532928767450E+02 kJ/mol 241s Calculating forces... 241s ---------------------------------------- 241s CALCULATION #2 (solvated): MULTIGRID 241s Setting up problem... 241s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 241s Debye length: 0 A 241s Current memory usage: 61.262 MB total, 122.067 MB high water 241s Using cubic spline charge discretization. 241s Grid dimensions: 65 x 65 x 65 241s Grid spacings: 0.383 x 0.383 x 0.383 241s Grid lengths: 24.495 x 24.495 x 24.495 241s Grid center: (0.000, 0.000, 0.000) 241s Multigrid levels: 5 241s Molecule ID: 1 241s Linearized traditional PBE 241s Boundary conditions from focusing 241s 0 ion species (0.000 M ionic strength): 241s Solute dielectric: 1.000 241s Solvent dielectric: 78.540 241s Using "molecular" surface definition;harmonic average smoothing 241s Solvent probe radius: 1.400 A 241s Temperature: 298.150 K 241s Electrostatic energies will be calculated 241s Total electrostatic energy = 2.201243880085E+03 kJ/mol 241s Calculating forces... 241s ---------------------------------------- 241s CALCULATION #3 (solvated): MULTIGRID 241s Setting up problem... 241s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 241s Debye length: 0 A 241s Current memory usage: 61.262 MB total, 122.067 MB high water 241s Using cubic spline charge discretization. 241s Grid dimensions: 65 x 65 x 65 241s Grid spacings: 0.188 x 0.188 x 0.188 241s Grid lengths: 12.000 x 12.000 x 12.000 241s Grid center: (0.000, 0.000, 0.000) 241s Multigrid levels: 5 241s Molecule ID: 1 241s Linearized traditional PBE 241s Boundary conditions from focusing 241s 0 ion species (0.000 M ionic strength): 241s Solute dielectric: 1.000 241s Solvent dielectric: 78.540 241s Using "molecular" surface definition;harmonic average smoothing 241s Solvent probe radius: 1.400 A 241s Temperature: 298.150 K 241s Electrostatic energies will be calculated 241s Total electrostatic energy = 4.733006258977E+03 kJ/mol 241s Calculating forces... 241s ---------------------------------------- 241s CALCULATION #4 (reference): MULTIGRID 241s Setting up problem... 241s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 241s Debye length: 0 A 241s Current memory usage: 61.189 MB total, 122.067 MB high water 241s Using cubic spline charge discretization. 241s Grid dimensions: 65 x 65 x 65 241s Grid spacings: 0.781 x 0.781 x 0.781 241s Grid lengths: 50.000 x 50.000 x 50.000 241s Grid center: (0.000, 0.000, 0.000) 241s Multigrid levels: 5 241s Molecule ID: 1 241s Linearized traditional PBE 241s Multiple Debye-Huckel sphere boundary conditions 241s 0 ion species (0.000 M ionic strength): 241s Solute dielectric: 1.000 241s Solvent dielectric: 1.000 241s Using "molecular" surface definition;harmonic average smoothing 241s Solvent probe radius: 1.400 A 241s Temperature: 298.150 K 241s Electrostatic energies will be calculated 241s Total electrostatic energy = 1.190871482831E+03 kJ/mol 241s Calculating forces... 241s ---------------------------------------- 241s CALCULATION #5 (reference): MULTIGRID 241s Setting up problem... 241s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 241s Debye length: 0 A 241s Current memory usage: 61.189 MB total, 122.067 MB high water 241s Using cubic spline charge discretization. 241s Grid dimensions: 65 x 65 x 65 241s Grid spacings: 0.383 x 0.383 x 0.383 241s Grid lengths: 24.495 x 24.495 x 24.495 241s Grid center: (0.000, 0.000, 0.000) 241s Multigrid levels: 5 241s Molecule ID: 1 241s Linearized traditional PBE 241s Boundary conditions from focusing 241s 0 ion species (0.000 M ionic strength): 241s Solute dielectric: 1.000 241s Solvent dielectric: 1.000 241s Using "molecular" surface definition;harmonic average smoothing 241s Solvent probe radius: 1.400 A 241s Temperature: 298.150 K 241s Electrostatic energies will be calculated 241s Total electrostatic energy = 2.430874049735E+03 kJ/mol 241s Calculating forces... 241s [focusFillBound()]: WARNING: 241s Unusually large potential values 241s detected on the focusing boundary! 241s Convergence not guaranteed for NPBE/NRPBE calculations! 241s 241s ---------------------------------------- 241s CALCULATION #6 (reference): MULTIGRID 241s Setting up problem... 241s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 241s Debye length: 0 A 241s Current memory usage: 61.189 MB total, 122.067 MB high water 241s Using cubic spline charge discretization. 241s Grid dimensions: 65 x 65 x 65 241s Grid spacings: 0.188 x 0.188 x 0.188 241s Grid lengths: 12.000 x 12.000 x 12.000 241s Grid center: (0.000, 0.000, 0.000) 241s Multigrid levels: 5 241s Molecule ID: 1 241s Linearized traditional PBE 241s Boundary conditions from focusing 241s 0 ion species (0.000 M ionic strength): 241s Solute dielectric: 1.000 241s Solvent dielectric: 1.000 241s Using "molecular" surface definition;harmonic average smoothing 241s Solvent probe radius: 1.400 A 241s Temperature: 298.150 K 241s Electrostatic energies will be calculated 241s Total electrostatic energy = 4.962018684215E+03 kJ/mol 241s Calculating forces... 241s ---------------------------------------- 241s PRINT STATEMENTS 241s 241s print energy 1 (solvated) - 2 (reference) end 241s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 241s Global net ELEC energy = -2.290124252387E+02 kJ/mol 241s ---------------------------------------- 241s CLEANING UP AND SHUTTING DOWN... 241s Destroying force arrays. 241s No energy arrays to destroy. 241s Destroying multigrid structures. 241s Destroying finite element structures. 241s Destroying 1 molecules 241s Final memory usage: 0.001 MB total, 122.067 MB high water 241s 241s 241s Thanks for using APBS! 241s 241s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 241s *** PASSED *** 241s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 241s *** PASSED *** 241s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 241s *** PASSED *** 241s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 241s *** PASSED *** 241s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 241s *** PASSED *** 241s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 241s *** PASSED *** 241s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 241s *** PASSED *** 241s Elapsed time: 4.988224 seconds 241s -------------------------------------------------------------------------------- 241s -------------------------------------------------------------------------------- 241s Testing input file apbs-mol-parallel.in 241s 241s Splitting the input file into 4 separate files using the inputgen utility 241s 248s Checking for intermediate energies in input file apbs-smol-auto.out 248s EXPECTED COMPUTED: 7 248s EXPECTED EXPECTED: 7 248s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 248s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 248s COMPUTED RESULT 953.292876745 248s COMPUTED RESULT 2201.243880085 248s COMPUTED RESULT 4733.006258977 248s COMPUTED RESULT 1190.871482831 248s COMPUTED RESULT 2430.874049735 248s COMPUTED RESULT 4962.018684215 248s COMPUTED RESULT -229.0124252387 248s BINARY: /usr/bin/apbs 248s INPUT: apbs-mol-parallel-PE0.in 248s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 248s 248s ---------------------------------------------------------------------- 248s APBS -- Adaptive Poisson-Boltzmann Solver 248s Version APBS 3.4.1 248s 248s Nathan A. Baker (nathan.baker@pnnl.gov) 248s Pacific Northwest National Laboratory 248s 248s Additional contributing authors listed in the code documentation. 248s 248s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 248s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 248s Northwest Division for the U.S. Department of Energy. 248s 248s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 248s Portions Copyright (c) 2002-2020, Nathan A. Baker. 248s Portions Copyright (c) 1999-2002, The Regents of the University of California. 248s Portions Copyright (c) 1995, Michael Holst. 248s All rights reserved. 248s 248s Redistribution and use in source and binary forms, with or without 248s modification, are permitted provided that the following conditions are met: 248s 248s * Redistributions of source code must retain the above copyright notice, this 248s list of conditions and the following disclaimer. 248s 248s * Redistributions in binary form must reproduce the above copyright notice, 248s this list of conditions and the following disclaimer in the documentation 248s and/or other materials provided with the distribution. 248s 248s * Neither the name of the developer nor the names of its contributors may be 248s used to endorse or promote products derived from this software without 248s specific prior written permission. 248s 248s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 248s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 248s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 248s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 248s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 248s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 248s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 248s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 248s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 248s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 248s ---------------------------------------------------------------------- 248s APBS uses FETK (the Finite Element ToolKit) to solve the 248s Poisson-Boltzmann equation numerically. FETK is a portable collection 248s of finite element modeling class libraries developed by the Michael Holst 248s research group and written in an object-oriented form of C. FEtk is 248s designed to solve general coupled systems of nonlinear partial differential 248s equations using adaptive finite element methods, inexact Newton methods, 248s and algebraic multilevel methods. More information about FEtk may be found 248s at . 248s ---------------------------------------------------------------------- 248s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 248s Aqua is a modified form of the Holst group PMG library 248s which has been modified by Patrice Koehl 248s for improved efficiency and 248s memory usage when solving the Poisson-Boltzmann equation. 248s ---------------------------------------------------------------------- 248s Please cite your use of APBS as: 248s 248s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 248s nanosystems: application to microtubules and the ribosome. Proc. 248s Natl. Acad. Sci. USA 98, 10037-10041 2001. 248s 248s 248s This executable compiled on Jan 3 2025 at 11:01:42 248s 248s Parsing input file apbs-mol-parallel-PE0.in... 248s rank 0 size 1... 248s Parsed input file. 248s Got paths for 1 molecules 248s Reading PQR-format atom data from ion.pqr. 248s 1 atoms 248s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 248s Net charge 1.00e+00 e 248s Preparing to run 6 PBE calculations. 248s ---------------------------------------- 248s CALCULATION #1 (solvated): MULTIGRID 248s Setting up problem... 248s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 248s Debye length: 0 A 248s Current memory usage: 61.262 MB total, 61.262 MB high water 248s Using cubic spline charge discretization. 248s Partition overlap fraction = 0.1 248s Processor array = 2 x 2 x 1 248s Grid dimensions: 65 x 65 x 65 248s Grid spacings: 0.781 x 0.781 x 0.781 248s Grid lengths: 50.000 x 50.000 x 50.000 248s Grid center: (0.000, 0.000, 0.000) 248s Multigrid levels: 5 248s Molecule ID: 1 248s Linearized traditional PBE 248s Multiple Debye-Huckel sphere boundary conditions 248s 0 ion species (0.000 M ionic strength): 248s Solute dielectric: 1.000 248s Solvent dielectric: 78.540 248s Using "molecular" surface definition; no smoothing 248s Solvent probe radius: 1.400 A 248s Temperature: 298.150 K 248s Electrostatic energies will be calculated 248s Total electrostatic energy = 2.401768459022E+02 kJ/mol 248s Calculating forces... 248s ---------------------------------------- 248s CALCULATION #2 (solvated): MULTIGRID 248s Setting up problem... 248s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 248s Debye length: 0 A 248s Current memory usage: 61.262 MB total, 122.067 MB high water 248s Using cubic spline charge discretization. 248s Partition overlap fraction = 0.1 248s Processor array = 2 x 2 x 1 248s Grid dimensions: 65 x 65 x 65 248s Grid spacings: 0.296 x 0.296 x 0.383 248s Grid lengths: 18.944 x 18.944 x 24.495 248s Grid center: (-2.411, -2.411, 0.000) 248s Multigrid levels: 5 248s Molecule ID: 1 248s Linearized traditional PBE 248s Boundary conditions from focusing 248s 0 ion species (0.000 M ionic strength): 248s Solute dielectric: 1.000 248s Solvent dielectric: 78.540 248s Using "molecular" surface definition; no smoothing 248s Solvent probe radius: 1.400 A 248s Temperature: 298.150 K 248s Electrostatic energies will be calculated 248s Total electrostatic energy = 8.142935592471E+02 kJ/mol 248s Calculating forces... 248s [focusFillBound()]: WARNING: 248s Unusually large potential values 248s detected on the focusing boundary! 248s Convergence not guaranteed for NPBE/NRPBE calculations! 248s 248s ---------------------------------------- 248s CALCULATION #3 (solvated): MULTIGRID 248s Setting up problem... 248s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 248s Debye length: 0 A 248s Current memory usage: 61.262 MB total, 122.067 MB high water 248s Using cubic spline charge discretization. 248s Partition overlap fraction = 0.1 248s Processor array = 2 x 2 x 1 248s Grid dimensions: 65 x 65 x 65 248s Grid spacings: 0.112 x 0.112 x 0.188 248s Grid lengths: 7.178 x 7.178 x 12.000 248s Grid center: (-2.411, -2.411, 0.000) 248s Multigrid levels: 5 248s Molecule ID: 1 248s Linearized traditional PBE 248s Boundary conditions from focusing 248s 0 ion species (0.000 M ionic strength): 248s Solute dielectric: 1.000 248s Solvent dielectric: 78.540 248s Using "molecular" surface definition; no smoothing 248s Solvent probe radius: 1.400 A 248s Temperature: 298.150 K 248s Electrostatic energies will be calculated 248s Total electrostatic energy = 1.485255308186E+03 kJ/mol 248s Calculating forces... 248s ---------------------------------------- 248s CALCULATION #4 (reference): MULTIGRID 248s Setting up problem... 248s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 248s Debye length: 0 A 248s Current memory usage: 61.189 MB total, 122.067 MB high water 248s Using cubic spline charge discretization. 248s Partition overlap fraction = 0.1 248s PrProcessor 0 results: 248s 2.401768459022e+02 248s 8.142935592471e+02 248s 1.485255308186e+03 248s 2.977178707009e+02 248s 8.799304557588e+02 248s 1.542873949131e+03 248s -5.761864094552e+01 248s 248s ocessor array = 2 x 2 x 1 248s Grid dimensions: 65 x 65 x 65 248s Grid spacings: 0.781 x 0.781 x 0.781 248s Grid lengths: 50.000 x 50.000 x 50.000 248s Grid center: (0.000, 0.000, 0.000) 248s Multigrid levels: 5 248s Molecule ID: 1 248s Linearized traditional PBE 248s Multiple Debye-Huckel sphere boundary conditions 248s 0 ion species (0.000 M ionic strength): 248s Solute dielectric: 1.000 248s Solvent dielectric: 1.000 248s Using "molecular" surface definition; no smoothing 248s Solvent probe radius: 1.400 A 248s Temperature: 298.150 K 248s Electrostatic energies will be calculated 248s Total electrostatic energy = 2.977178707009E+02 kJ/mol 248s Calculating forces... 248s ---------------------------------------- 248s CALCULATION #5 (reference): MULTIGRID 248s Setting up problem... 248s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 248s Debye length: 0 A 248s Current memory usage: 61.189 MB total, 122.067 MB high water 248s Using cubic spline charge discretization. 248s Partition overlap fraction = 0.1 248s Processor array = 2 x 2 x 1 248s Grid dimensions: 65 x 65 x 65 248s Grid spacings: 0.296 x 0.296 x 0.383 248s Grid lengths: 18.944 x 18.944 x 24.495 248s Grid center: (-2.411, -2.411, 0.000) 248s Multigrid levels: 5 248s Molecule ID: 1 248s Linearized traditional PBE 248s Boundary conditions from focusing 248s 0 ion species (0.000 M ionic strength): 248s Solute dielectric: 1.000 248s Solvent dielectric: 1.000 248s Using "molecular" surface definition; no smoothing 248s Solvent probe radius: 1.400 A 248s Temperature: 298.150 K 248s Electrostatic energies will be calculated 248s Total electrostatic energy = 8.799304557588E+02 kJ/mol 248s Calculating forces... 248s [focusFillBound()]: WARNING: 248s Unusually large potential values 248s detected on the focusing boundary! 248s Convergence not guaranteed for NPBE/NRPBE calculations! 248s 248s ---------------------------------------- 248s CALCULATION #6 (reference): MULTIGRID 248s Setting up problem... 248s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 248s Debye length: 0 A 248s Current memory usage: 61.189 MB total, 122.067 MB high water 248s Using cubic spline charge discretization. 248s Partition overlap fraction = 0.1 248s Processor array = 2 x 2 x 1 248s Grid dimensions: 65 x 65 x 65 248s Grid spacings: 0.112 x 0.112 x 0.188 248s Grid lengths: 7.178 x 7.178 x 12.000 248s Grid center: (-2.411, -2.411, 0.000) 248s Multigrid levels: 5 248s Molecule ID: 1 248s Linearized traditional PBE 248s Boundary conditions from focusing 248s 0 ion species (0.000 M ionic strength): 248s Solute dielectric: 1.000 248s Solvent dielectric: 1.000 248s Using "molecular" surface definition; no smoothing 248s Solvent probe radius: 1.400 A 248s Temperature: 298.150 K 248s Electrostatic energies will be calculated 248s Total electrostatic energy = 1.542873949131E+03 kJ/mol 248s Calculating forces... 248s ---------------------------------------- 248s PRINT STATEMENTS 248s 248s print energy 1 (solvated) - 2 (reference) end 248s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 248s Global net ELEC energy = -5.761864094552E+01 kJ/mol 248s ---------------------------------------- 248s CLEANING UP AND SHUTTING DOWN... 248s Destroying force arrays. 248s No energy arrays to destroy. 248s Destroying multigrid structures. 248s Destroying finite element structures. 248s Destroying 1 molecules 248s Final memory usage: 0.001 MB total, 122.067 MB high water 248s 248s 248s Thanks for using APBS! 248s 255s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 255s BINARY: /usr/bin/apbs 255s INPUT: apbs-mol-parallel-PE1.in 255s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 255s asc_getToken: Error occurred (bailing out). 255s Vio_scanf: Format problem with input. 255s 255s 255s ---------------------------------------------------------------------- 255s APBS -- Adaptive Poisson-Boltzmann Solver 255s Version APBS 3.4.1 255s 255s Nathan A. Baker (nathan.baker@pnnl.gov) 255s Pacific Northwest National Laboratory 255s 255s Additional contributing authors listed in the code documentation. 255s 255s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 255s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 255s Northwest Division for the U.S. Department of Energy. 255s 255s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 255s Portions Copyright (c) 2002-2020, Nathan A. Baker. 255s Portions Copyright (c) 1999-2002, The Regents of the University of California. 255s Portions Copyright (c) 1995, Michael Holst. 255s All rights reserved. 255s 255s Redistribution and use in source and binary forms, with or without 255s modification, are permitted provided that the following conditions are met: 255s 255s * Redistributions of source code must retain the above copyright notice, this 255s list of conditions and the following disclaimer. 255s 255s * Redistributions in binary form must reproduce the above copyright notice, 255s this list of conditions and the following disclaimer in the documentation 255s and/or other materials provided with the distribution. 255s 255s * Neither the name of the developer nor the names of its contributors may be 255s used to endorse or promote products derived from this software without 255s specific prior written permission. 255s 255s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 255s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 255s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 255s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 255s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 255s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 255s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 255s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 255s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 255s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 255s ---------------------------------------------------------------------- 255s APBS uses FETK (the Finite Element ToolKit) to solve the 255s Poisson-Boltzmann equation numerically. FETK is a portable collection 255s of finite element modeling class libraries developed by the Michael Holst 255s research group and written in an object-oriented form of C. FEtk is 255s designed to solve general coupled systems of nonlinear partial differential 255s equations using adaptive finite element methods, inexact Newton methods, 255s and algebraic multilevel methods. More information about FEtk may be found 255s at . 255s ---------------------------------------------------------------------- 255s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 255s Aqua is a modified form of the Holst group PMG library 255s which has been modified by Patrice Koehl 255s for improved efficiency and 255s memory usage when solving the Poisson-Boltzmann equation. 255s ---------------------------------------------------------------------- 255s Please cite your use of APBS as: 255s 255s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 255s nanosystems: application to microtubules and the ribosome. Proc. 255s Natl. Acad. Sci. USA 98, 10037-10041 2001. 255s 255s 255s This executable compiled on Jan 3 2025 at 11:01:42 255s 255s Parsing input file apbs-mol-parallel-PE1.in... 255s rank 0 size 1... 255s Parsed input file. 255s Got paths for 1 molecules 255s Reading PQR-format atom data from ion.pqr. 255s 1 atoms 255s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 255s Net charge 1.00e+00 e 255s Preparing to run 6 PBE calculations. 255s ---------------------------------------- 255s CALCULATION #1 (solvated): MULTIGRID 255s Setting up problem... 255s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 255s Debye length: 0 A 255s Current memory usage: 61.262 MB total, 61.262 MB high water 255s Using cubic spline charge discretization. 255s Partition overlap fraction = 0.1 255s Processor array = 2 x 2 x 1 255s Grid dimensions: 65 x 65 x 65 255s Grid spacings: 0.781 x 0.781 x 0.781 255s Grid lengths: 50.000 x 50.000 x 50.000 255s Grid center: (0.000, 0.000, 0.000) 255s Multigrid levels: 5 255s Molecule ID: 1 255s Linearized traditional PBE 255s Multiple Debye-Huckel sphere boundary conditions 255s 0 ion species (0.000 M ionic strength): 255s Solute dielectric: 1.000 255s Solvent dielectric: 78.540 255s Using "molecular" surface definition; no smoothing 255s Solvent probe radius: 1.400 A 255s Temperature: 298.150 K 255s Electrostatic energies will be calculated 255s Total electrostatic energy = 2.401768459022E+02 kJ/mol 255s Calculating forces... 255s ---------------------------------------- 255s CALCULATION #2 (solvated): MULTIGRID 255s Setting up problem... 255s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 255s Debye length: 0 A 255s Current memory usage: 61.262 MB total, 122.067 MB high water 255s Using cubic spline charge discretization. 255s Partition overlap fraction = 0.1 255s Processor array = 2 x 2 x 1 255s Grid dimensions: 65 x 65 x 65 255s Grid spacings: 0.296 x 0.296 x 0.383 255s Grid lengths: 18.944 x 18.944 x 24.495 255s Grid center: (2.411, -2.411, 0.000) 255s Multigrid levels: 5 255s Molecule ID: 1 255s Linearized traditional PBE 255s Boundary conditions from focusing 255s 0 ion species (0.000 M ionic strength): 255s Solute dielectric: 1.000 255s Solvent dielectric: 78.540 255s Using "molecular" surface definition; no smoothing 255s Solvent probe radius: 1.400 A 255s Temperature: 298.150 K 255s Electrostatic energies will be calculated 255s Total electrostatic energy = 8.142778312125E+02 kJ/mol 255s Calculating forces... 255s [focusFillBound()]: WARNING: 255s Unusually large potential values 255s detected on the focusing boundary! 255s Convergence not guaranteed for NPBE/NRPBE calculations! 255s 255s ---------------------------------------- 255s CALCULATION #3 (solvated): MULTIGRID 255s Setting up problem... 255s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 255s Debye length: 0 A 255s Current memory usage: 61.262 MB total, 122.067 MB high water 255s Using cubic spline charge discretization. 255s Partition overlap fraction = 0.1 255s Processor array = 2 x 2 x 1 255s Grid dimensions: 65 x 65 x 65 255s Grid spacings: 0.112 x 0.112 x 0.188 255s Grid lengths: 7.178 x 7.178 x 12.000 255s Grid center: (2.411, -2.411, 0.000) 255s Multigrid levels: 5 255s Molecule ID: 1 255s Linearized traditional PBE 255s Boundary conditions from focusing 255s 0 ion species (0.000 M ionic strength): 255s Solute dielectric: 1.000 255s Solvent dielectric: 78.540 255s Using "molecular" surface definition; no smoothing 255s Solvent probe radius: 1.400 A 255s Temperature: 298.150 K 255s Electrostatic energies will be calculated 255s Total electrostatic energy = 1.485246667424E+03 kJ/mol 255s Calculating forces... 255s ---------------------------------------- 255s CALCULATION #4 (reference): MULTIGRID 255s Setting up problem... 255s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 255s Debye length: 0 A 255s Current memory usage: 61.189 MB total, 122.067 MB high water 255s Using cubic spline charge discretization. 255s Partition overlap fraction = 0.1 255s Processor array = 2 x 2 x 1 255s Grid dimensions: 65 x 65 x 65 255s Grid spacings: 0.781 x 0.781 x 0.781 255s Grid lengths: 50.000 x 50.000 x 50.000 255s Grid center: (0.000, 0.000, 0.000) 255s Multigrid levels: 5 255s Molecule ID: 1 255s Linearized traditional PBE 255s Multiple Debye-Huckel sphere boundary conditions 255s 0 ion species (0.000 M ionic strength): 255s Solute dielectric: 1.000 255s Solvent dielectric: 1.000 255s Using "molecular" surface definition; no smoothing 255s Solvent probe radius: 1.400 A 255s Temperature: 298.150 K 255s Electrostatic energies will be calculated 255s Total electrostatic energy = 2.977178707009E+02 kJ/mol 255s Calculating forces... 255s ---------------------------------------- 255s CALCULATION #5 (reference): MULTIGRID 255s Setting up problem... 255s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 255s Debye length: 0 A 255s Current memory usage: 61.189 MB total, 122.067 MB high water 255s Using cubic spline charge discretization. 255s Partition overlap fraction = 0.1 255s Processor array = 2 x 2 x 1 255s Grid dimensions: 65 x 65 x 65 255s Grid spacings: 0.296 x 0.296 x 0.383 255s Grid lengths: 18.944 x 18.944 x 24.495 255s Grid center: (2.411, -2.411, 0.000) 255s Multigrid levels: 5 255s Molecule ID: 1 255s Linearized traditional PBE 255s Boundary conditions from focusing 255s 0 ion species (0.000 M ionic strength): 255s Solute dielectric: 1.000 255s Solvent dielectric: 1.000 255s Using "molecular" surface definition; no smoothing 255s Solvent probe radius: 1.400 A 255s Temperature: 298.150 K 255s Electrostatic energies will be calculated 255s Total electrostatic energy = 8.799304557588E+02 kJ/mol 255s Calculating forces... 255s [focusFillBound()]: WARNING: 255s Unusually large potential values 255s detected on the focusing boundary! 255s Convergence not guaranteed for NPBE/NRPBE calculations! 255s 255s ---------------------------------------- 255s CALCULATION #6 (reference): MULTIGRID 255s Setting up problem... 255s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 255s Debye length: 0 A 255s Current memory usage: 61.189 MB total, 122.067 MB high water 255s Using cubic spline charge discretization. 255s Partition overlap fraction = 0.1 255s Processor array = 2 x 2 x 1 255s Grid dimensions: 65 x 65 x 65 255s Grid spacings: 0.112 x 0.112 x 0.188 255s Grid lengths: 7.178 x 7.178 x 12.000 255s Grid center: (2.411, -2.411, 0.000) 255s Multigrid levels: 5 255s Molecule ID: 1 255s Linearized traditional PBE 255s Boundary conditions from focusing 255s 0 ion species (0.000 M ionic strength): 255s Solute dielectric: 1.000 255s Solvent dielectric: 1.000 255s Using "molecular" surface definition; no smoothing 255s Solvent probe radius: 1.400 A 255s Temperature: 298.150 K 255s Electrostatic energies will be calculated 255s Total electrostatic energy = 1.542873949131E+03 kJ/mol 255s Calculating forces... 255s ---------------------------------------- 255s PRINT STATEMENTS 255s 255s print energy 1 (solvated) - 2 (reference) end 255s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 255s Global net ELEC energy = -5.762728170718E+01 kJ/mol 255s ---------------------------------------- 255s CLEANING UP AND SHUTTING DOWN... 255s Destroying force arrays. 255s No energy arrays to destroy. 255s Destroying multigrid structures. 255s Destroying finite element structures. 255s Destroying 1 molecules 255s Final memory usage: 0.001 MB total, 122.067 MB high water 255s 255s 255s Thanks for using APBS! 255s 255s Processor 1 results: 255s 2.401768459022e+02 255s 8.142778312125e+02 255s 1.485246667424e+03 255s 2.977178707009e+02 255s 8.799304557588e+02 255s 1.542873949131e+03 255s -5.762728170718e+01 255s 263s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 263s BINARY: /usr/bin/apbs 263s INPUT: apbs-mol-parallel-PE2.in 263s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 263s asc_getToken: Error occurred (bailing out). 263s Vio_scanf: Format problem with input. 263s 263s 263s ---------------------------------------------------------------------- 263s APBS -- Adaptive Poisson-Boltzmann Solver 263s Version APBS 3.4.1 263s 263s Nathan A. Baker (nathan.baker@pnnl.gov) 263s Pacific Northwest National Laboratory 263s 263s Additional contributing authors listed in the code documentation. 263s 263s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 263s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 263s Northwest Division for the U.S. Department of Energy. 263s 263s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 263s Portions Copyright (c) 2002-2020, Nathan A. Baker. 263s Portions Copyright (c) 1999-2002, The Regents of the University of California. 263s Portions Copyright (c) 1995, Michael Holst. 263s All rights reserved. 263s 263s Redistribution and use in source and binary forms, with or without 263s modification, are permitted provided that the following conditions are met: 263s 263s * Redistributions of source code must retain the above copyright notice, this 263s list of conditions and the following disclaimer. 263s 263s * Redistributions in binary form must reproduce the above copyright notice, 263s this list of conditions and the following disclaimer in the documentation 263s and/or other materials provided with the distribution. 263s 263s * Neither the name of the developer nor the names of its contributors may be 263s used to endorse or promote products derived from this software without 263s specific prior written permission. 263s 263s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 263s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 263s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 263s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 263s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 263s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 263s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 263s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 263s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 263s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 263s ---------------------------------------------------------------------- 263s APBS uses FETK (the Finite Element ToolKit) to solve the 263s Poisson-Boltzmann equation numerically. FETK is a portable collection 263s of finite element modeling class libraries developed by the Michael Holst 263s research group and written in an object-oriented form of C. FEtk is 263s designed to solve general coupled systems of nonlinear partial differential 263s equations using adaptive finite element methods, inexact Newton methods, 263s and algebraic multilevel methods. More information about FEtk may be found 263s at . 263s ---------------------------------------------------------------------- 263s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 263s Aqua is a modified form of the Holst group PMG library 263s which has been modified by Patrice Koehl 263s for improved efficiency and 263s memory usage when solving the Poisson-Boltzmann equation. 263s ---------------------------------------------------------------------- 263s Please cite your use of APBS as: 263s 263s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 263s nanosystems: application to microtubules and the ribosome. Proc. 263s Natl. Acad. Sci. USA 98, 10037-10041 2001. 263s 263s 263s This executable compiled on Jan 3 2025 at 11:01:42 263s 263s Parsing input file apbs-mol-parallel-PE2.in... 263s rank 0 size 1... 263s Parsed input file. 263s Got paths for 1 molecules 263s Reading PQR-format atom data from ion.pqr. 263s 1 atoms 263s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 263s Net charge 1.00e+00 e 263s Preparing to run 6 PBE calculations. 263s ---------------------------------------- 263s CALCULATION #1 (solvated): MULTIGRID 263s Setting up problem... 263s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 263s Debye length: 0 A 263s Current memory usage: 61.262 MB total, 61.262 MB high water 263s Using cubic spline charge discretization. 263s Partition overlap fraction = 0.1 263s Processor array = 2 x 2 x 1 263s Grid dimensions: 65 x 65 x 65 263s Grid spacings: 0.781 x 0.781 x 0.781 263s Grid lengths: 50.000 x 50.000 x 50.000 263s Grid center: (0.000, 0.000, 0.000) 263s Multigrid levels: 5 263s Molecule ID: 1 263s Linearized traditional PBE 263s Multiple Debye-Huckel sphere boundary conditions 263s 0 ion species (0.000 M ionic strength): 263s Solute dielectric: 1.000 263s Solvent dielectric: 78.540 263s Using "molecular" surface definition; no smoothing 263s Solvent probe radius: 1.400 A 263s Temperature: 298.150 K 263s Electrostatic energies will be calculated 263s Total electrostatic energy = 2.401768459091E+02 kJ/mol 263s Calculating forces... 263s ---------------------------------------- 263s CALCULATION #2 (solvated): MULTIGRID 263s Setting up problem... 263s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 263s Debye length: 0 A 263s Current memory usage: 61.262 MB total, 122.067 MB high water 263s Using cubic spline charge discretization. 263s Partition overlap fraction = 0.1 263s Processor array = 2 x 2 x 1 263s Grid dimensions: 65 x 65 x 65 263s Grid spacings: 0.296 x 0.296 x 0.383 263s Grid lengths: 18.944 x 18.944 x 24.495 263s Grid center: (-2.411, 2.411, 0.000) 263s Multigrid levels: 5 263s Molecule ID: 1 263s Linearized traditional PBE 263s Boundary conditions from focusing 263s 0 ion species (0.000 M ionic strength): 263s Solute dielectric: 1.000 263s Solvent dielectric: 78.540 263s Using "molecular" surface definition; no smoothing 263s Solvent probe radius: 1.400 A 263s Temperature: 298.150 K 263s Electrostatic energies will be calculated 263s Total electrostatic energy = 8.142935605696E+02 kJ/mol 263s Calculating forces... 263s [focusFillBound()]: WARNING: 263s Unusually large potential values 263s detected on the focusing boundary! 263s Convergence not guaranteed for NPBE/NRPBE calculations! 263s 263s ---------------------------------------- 263s CALCULATION #3 (solvated): MULTIGRID 263s Setting up problem... 263s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 263s Debye length: 0 A 263s Current memory usage: 61.262 MB total, 122.067 MB high water 263s Using cubic spline charge discretization. 263s Partition overlap fraction = 0.1 263s Processor array = 2 x 2 x 1 263s Grid dimensions: 65 x 65 x 65 263s Grid spacings: 0.112 x 0.112 x 0.188 263s Grid lengths: 7.178 x 7.178 x 12.000 263s Grid center: (-2.411, 2.411, 0.000) 263s Multigrid levels: 5 263s Molecule ID: 1 263s Linearized traditional PBE 263s Boundary conditions from focusing 263s 0 ion species (0.000 M ionic strength): 263s Solute dielectric: 1.000 263s Solvent dielectric: 78.540 263s Using "molecular" surface definition; no smoothing 263s Solvent probe radius: 1.400 A 263s Temperature: 298.150 K 263s Electrostatic energies will be calculated 263s Total electrostatic energy = 1.485255306569E+03 kJ/mol 263s Calculating forces... 263s ---------------------------------------- 263s CALCULATION #4 (reference): MULTIGRID 263s Setting up problem... 263s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 263s Debye length: 0 A 263s Current memory usage: 61.189 MB total, 122.067 MB high water 263s Using cubic spline charge discretization. 263s Partition overlap fraction = 0.1 263s Processor array = 2 x 2 x 1 263s Grid dimensions: 65 x 65 x 65 263s Grid spacings: 0.781 x 0.781 x 0.781 263s Grid lengths: 50.000 x 50.000 x 50.000 263s Grid center: (0.000, 0.000, 0.000) 263s Multigrid levels: 5 263s Molecule ID: 1 263s Linearized traditional PBE 263s Multiple Debye-Huckel sphere boundary conditions 263s 0 ion species (0.000 M ionic strength): 263s Solute dielectric: 1.000 263s Solvent dielectric: 1.000 263s Using "molecular" surface definition; no smoothing 263s Solvent probe radius: 1.400 A 263s Temperature: 298.150 K 263s Electrostatic energies will be calculated 263s Total electrostatic energy = 2.977178707146E+02 kJ/mol 263s Calculating forces... 263s ---------------------------------------- 263s CALCULATION #5 (reference): MULTIGRID 263s Setting up problem... 263s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 263s Debye length: 0 A 263s Current memory usage: 61.189 MB total, 122.067 MB high water 263s Using cubic spline charge discretization. 263s Partition overlap fraction = 0.1 263s Processor array = 2 x 2 x 1 263s Grid dimensions: 65 x 65 x 65 263s Grid spacings: 0.296 x 0.296 x 0.383 263s Grid lengths: 18.944 x 18.944 x 24.495 263s Grid center: (-2.411, 2.411, 0.000) 263s Multigrid levels: 5 263s Molecule ID: 1 263s Linearized traditional PBE 263s Boundary conditions from focusing 263s 0 ion species (0.000 M ionic strength): 263s Solute dielectric: 1.000 263s Solvent dielectric: 1.000 263s Using "molecular" surface definition; no smoothing 263s Solvent probe radius: 1.400 A 263s Temperature: 298.150 K 263s Electrostatic energies will be calculated 263s Total electrostatic energy = 8.799304557596E+02 kJ/mol 263s Calculating forces... 263s [focusFillBound()]: WARNING: 263s Unusually large potential values 263s detected on the focusing boundary! 263s Convergence not guaranteed for NPBE/NRPBE calculations! 263s 263s ---------------------------------------- 263s CALCULATION #6 (reference): MULTIGRID 263s Setting up problem... 263s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 263s Debye length: 0 A 263s Current memory usage: 61.189 MB total, 122.067 MB high water 263s Using cubic spline charge discretization. 263s Partition overlap fraction = 0.1 263s Processor array = 2 x 2 x 1 263s Grid dimensions: 65 x 65 x 65 263s Grid spacings: 0.112 x 0.112 x 0.188 263s Grid lengths: 7.178 x 7.178 x 12.000 263s Grid center: (-2.411, 2.411, 0.000) 263s Multigrid levels: 5 263s Molecule ID: 1 263s Linearized traditional PBE 263s Boundary conditions from focusing 263s 0 ion species (0.000 M ionic strength): 263s Solute dielectric: 1.000 263s Solvent dielectric: 1.000 263s Using "molecular" surface definition; no smoothing 263s Solvent probe radius: 1.400 A 263s Temperature: 298.150 K 263s Electrostatic energies will be calculated 263s Total electrostatic energy = 1.542873949141E+03 kJ/mol 263s Calculating forces... 263s ---------------------------------------- 263s PRINT STATEMENTS 263s 263s print energy 1 (solvated) - 2 (reference) end 263s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 263s Global net ELEC energy = -5.761864257239E+01 kJ/mol 263s ---------------------------------------- 263s CLEANING UP AND SHUTTING DOWN... 263s Destroying force arrays. 263s No energy arrays to destroy. 263s Destroying multigrid structures. 263s Destroying finite element structures. 263s Destroying 1 molecules 263s Final memory usage: 0.001 MB total, 122.067 MB high water 263s 263s 263s Thanks for using APBS! 263s 263s Processor 2 results: 263s 2.401768459091e+02 263s 8.142935605696e+02 263s 1.485255306569e+03 263s 2.977178707146e+02 263s 8.799304557596e+02 263s 1.542873949141e+03 263s -5.761864257239e+01 263s 271s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 271s BINARY: /usr/bin/apbs 271s INPUT: apbs-mol-parallel-PE3.in 271s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 271s asc_getToken: Error occurred (bailing out). 271s Vio_scanf: Format problem with input. 271s 271s 271s ---------------------------------------------------------------------- 271s APBS -- Adaptive Poisson-Boltzmann Solver 271s Version APBS 3.4.1 271s 271s Nathan A. Baker (nathan.baker@pnnl.gov) 271s Pacific Northwest National Laboratory 271s 271s Additional contributing authors listed in the code documentation. 271s 271s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 271s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 271s Northwest Division for the U.S. Department of Energy. 271s 271s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 271s Portions Copyright (c) 2002-2020, Nathan A. Baker. 271s Portions Copyright (c) 1999-2002, The Regents of the University of California. 271s Portions Copyright (c) 1995, Michael Holst. 271s All rights reserved. 271s 271s Redistribution and use in source and binary forms, with or without 271s modification, are permitted provided that the following conditions are met: 271s 271s * Redistributions of source code must retain the above copyright notice, this 271s list of conditions and the following disclaimer. 271s 271s * Redistributions in binary form must reproduce the above copyright notice, 271s this list of conditions and the following disclaimer in the documentation 271s and/or other materials provided with the distribution. 271s 271s * Neither the name of the developer nor the names of its contributors may be 271s used to endorse or promote products derived from this software without 271s specific prior written permission. 271s 271s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 271s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 271s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 271s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 271s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 271s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 271s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 271s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 271s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 271s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 271s ---------------------------------------------------------------------- 271s APBS uses FETK (the Finite Element ToolKit) to solve the 271s Poisson-Boltzmann equation numerically. FETK is a portable collection 271s of finite element modeling class libraries developed by the Michael Holst 271s research group and written in an object-oriented form of C. FEtk is 271s designed to solve general coupled systems of nonlinear partial differential 271s equations using adaptive finite element methods, inexact Newton methods, 271s and algebraic multilevel methods. More information about FEtk may be found 271s at . 271s ---------------------------------------------------------------------- 271s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 271s Aqua is a modified form of the Holst group PMG library 271s which has been modified by Patrice Koehl 271s for improved efficiency and 271s memory usage when solving the Poisson-Boltzmann equation. 271s ---------------------------------------------------------------------- 271s Please cite your use of APBS as: 271s 271s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 271s nanosystems: application to microtubules and the ribosome. Proc. 271s Natl. Acad. Sci. USA 98, 10037-10041 2001. 271s 271s 271s This executable compiled on Jan 3 2025 at 11:01:42 271s 271s Parsing input file apbs-mol-parallel-PE3.in... 271s rank 0 size 1... 271s Parsed input file. 271s Got paths for 1 molecules 271s Reading PQR-format atom data from ion.pqr. 271s 1 atoms 271s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 271s Net charge 1.00e+00 e 271s Preparing to ruProcessor 3 results: 271s 2.401768459091e+02 271s 8.142778325440e+02 271s 1.485246665692e+03 271s 2.977178707146e+02 271s 8.799304557596e+02 271s 1.542873949141e+03 271s -5.762728344954e+01 271s 271s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 271s *** PASSED *** 271s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 271s *** PASSED *** 271s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 271s *** PASSED *** 271s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 271s *** PASSED *** 271s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 271s *** PASSED *** 271s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 271s *** PASSED *** 271s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 271s *** PASSED *** 271s Elapsed time: 29.330202 seconds 271s -------------------------------------------------------------------------------- 271s -------------------------------------------------------------------------------- 271s Testing input file apbs-smol-parallel.in 271s 271s Splitting the input file into 4 separate files using the inputgen utility 271s 271s n 6 PBE calculations. 271s ---------------------------------------- 271s CALCULATION #1 (solvated): MULTIGRID 271s Setting up problem... 271s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 271s Debye length: 0 A 271s Current memory usage: 61.262 MB total, 61.262 MB high water 271s Using cubic spline charge discretization. 271s Partition overlap fraction = 0.1 271s Processor array = 2 x 2 x 1 271s Grid dimensions: 65 x 65 x 65 271s Grid spacings: 0.781 x 0.781 x 0.781 271s Grid lengths: 50.000 x 50.000 x 50.000 271s Grid center: (0.000, 0.000, 0.000) 271s Multigrid levels: 5 271s Molecule ID: 1 271s Linearized traditional PBE 271s Multiple Debye-Huckel sphere boundary conditions 271s 0 ion species (0.000 M ionic strength): 271s Solute dielectric: 1.000 271s Solvent dielectric: 78.540 271s Using "molecular" surface definition; no smoothing 271s Solvent probe radius: 1.400 A 271s Temperature: 298.150 K 271s Electrostatic energies will be calculated 271s Total electrostatic energy = 2.401768459091E+02 kJ/mol 271s Calculating forces... 271s ---------------------------------------- 271s CALCULATION #2 (solvated): MULTIGRID 271s Setting up problem... 271s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 271s Debye length: 0 A 271s Current memory usage: 61.262 MB total, 122.067 MB high water 271s Using cubic spline charge discretization. 271s Partition overlap fraction = 0.1 271s Processor array = 2 x 2 x 1 271s Grid dimensions: 65 x 65 x 65 271s Grid spacings: 0.296 x 0.296 x 0.383 271s Grid lengths: 18.944 x 18.944 x 24.495 271s Grid center: (2.411, 2.411, 0.000) 271s Multigrid levels: 5 271s Molecule ID: 1 271s Linearized traditional PBE 271s Boundary conditions from focusing 271s 0 ion species (0.000 M ionic strength): 271s Solute dielectric: 1.000 271s Solvent dielectric: 78.540 271s Using "molecular" surface definition; no smoothing 271s Solvent probe radius: 1.400 A 271s Temperature: 298.150 K 271s Electrostatic energies will be calculated 271s Total electrostatic energy = 8.142778325440E+02 kJ/mol 271s Calculating forces... 271s [focusFillBound()]: WARNING: 271s Unusually large potential values 271s detected on the focusing boundary! 271s Convergence not guaranteed for NPBE/NRPBE calculations! 271s 271s ---------------------------------------- 271s CALCULATION #3 (solvated): MULTIGRID 271s Setting up problem... 271s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 271s Debye length: 0 A 271s Current memory usage: 61.262 MB total, 122.067 MB high water 271s Using cubic spline charge discretization. 271s Partition overlap fraction = 0.1 271s Processor array = 2 x 2 x 1 271s Grid dimensions: 65 x 65 x 65 271s Grid spacings: 0.112 x 0.112 x 0.188 271s Grid lengths: 7.178 x 7.178 x 12.000 271s Grid center: (2.411, 2.411, 0.000) 271s Multigrid levels: 5 271s Molecule ID: 1 271s Linearized traditional PBE 271s Boundary conditions from focusing 271s 0 ion species (0.000 M ionic strength): 271s Solute dielectric: 1.000 271s Solvent dielectric: 78.540 271s Using "molecular" surface definition; no smoothing 271s Solvent probe radius: 1.400 A 271s Temperature: 298.150 K 271s Electrostatic energies will be calculated 271s Total electrostatic energy = 1.485246665692E+03 kJ/mol 271s Calculating forces... 271s ---------------------------------------- 271s CALCULATION #4 (reference): MULTIGRID 271s Setting up problem... 271s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 271s Debye length: 0 A 271s Current memory usage: 61.189 MB total, 122.067 MB high water 271s Using cubic spline charge discretization. 271s Partition overlap fraction = 0.1 271s Processor array = 2 x 2 x 1 271s Grid dimensions: 65 x 65 x 65 271s Grid spacings: 0.781 x 0.781 x 0.781 271s Grid lengths: 50.000 x 50.000 x 50.000 271s Grid center: (0.000, 0.000, 0.000) 271s Multigrid levels: 5 271s Molecule ID: 1 271s Linearized traditional PBE 271s Multiple Debye-Huckel sphere boundary conditions 271s 0 ion species (0.000 M ionic strength): 271s Solute dielectric: 1.000 271s Solvent dielectric: 1.000 271s Using "molecular" surface definition; no smoothing 271s Solvent probe radius: 1.400 A 271s Temperature: 298.150 K 271s Electrostatic energies will be calculated 271s Total electrostatic energy = 2.977178707146E+02 kJ/mol 271s Calculating forces... 271s ---------------------------------------- 271s CALCULATION #5 (reference): MULTIGRID 271s Setting up problem... 271s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 271s Debye length: 0 A 271s Current memory usage: 61.189 MB total, 122.067 MB high water 271s Using cubic spline charge discretization. 271s Partition overlap fraction = 0.1 271s Processor array = 2 x 2 x 1 271s Grid dimensions: 65 x 65 x 65 271s Grid spacings: 0.296 x 0.296 x 0.383 271s Grid lengths: 18.944 x 18.944 x 24.495 271s Grid center: (2.411, 2.411, 0.000) 271s Multigrid levels: 5 271s Molecule ID: 1 271s Linearized traditional PBE 271s Boundary conditions from focusing 271s 0 ion species (0.000 M ionic strength): 271s Solute dielectric: 1.000 271s Solvent dielectric: 1.000 271s Using "molecular" surface definition; no smoothing 271s Solvent probe radius: 1.400 A 271s Temperature: 298.150 K 271s Electrostatic energies will be calculated 271s Total electrostatic energy = 8.799304557596E+02 kJ/mol 271s Calculating forces... 271s [focusFillBound()]: WARNING: 271s Unusually large potential values 271s detected on the focusing boundary! 271s Convergence not guaranteed for NPBE/NRPBE calculations! 271s 271s ---------------------------------------- 271s CALCULATION #6 (reference): MULTIGRID 271s Setting up problem... 271s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 271s Debye length: 0 A 271s Current memory usage: 61.189 MB total, 122.067 MB high water 271s Using cubic spline charge discretization. 271s Partition overlap fraction = 0.1 271s Processor array = 2 x 2 x 1 271s Grid dimensions: 65 x 65 x 65 271s Grid spacings: 0.112 x 0.112 x 0.188 271s Grid lengths: 7.178 x 7.178 x 12.000 271s Grid center: (2.411, 2.411, 0.000) 271s Multigrid levels: 5 271s Molecule ID: 1 271s Linearized traditional PBE 271s Boundary conditions from focusing 271s 0 ion species (0.000 M ionic strength): 271s Solute dielectric: 1.000 271s Solvent dielectric: 1.000 271s Using "molecular" surface definition; no smoothing 271s Solvent probe radius: 1.400 A 271s Temperature: 298.150 K 271s Electrostatic energies will be calculated 271s Total electrostatic energy = 1.542873949141E+03 kJ/mol 271s Calculating forces... 271s ---------------------------------------- 271s PRINT STATEMENTS 271s 271s print energy 1 (solvated) - 2 (reference) end 271s Local net energy (PE 0) = -5.762728344954E+01 kJ/mol 271s Global net ELEC energy = -5.762728344954E+01 kJ/mol 271s ---------------------------------------- 271s CLEANING UP AND SHUTTING DOWN... 271s Destroying force arrays. 271s No energy arrays to destroy. 271s Destroying multigrid structures. 271s Destroying finite element structures. 271s Destroying 1 molecules 271s Final memory usage: 0.001 MB total, 122.067 MB high water 271s 271s 271s Thanks for using APBS! 271s 278s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 278s EXPECTED COMPUTED: 7 278s EXPECTED EXPECTED: 7 278s COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] 278s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 278s COMPUTED RESULT 960.7073836226 278s COMPUTED RESULT 3257.1427835731997 278s COMPUTED RESULT 5941.0039478710005 278s COMPUTED RESULT 1190.8714828309999 278s COMPUTED RESULT 3519.7218230368003 278s COMPUTED RESULT 6171.495796544 278s COMPUTED RESULT -230.49184867463003 278s BINARY: /usr/bin/apbs 278s INPUT: apbs-smol-parallel-PE0.in 278s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 278s asc_getToken: Error occurred (bailing out). 278s Vio_scanf: Format problem with input. 278s 278s 278s ---------------------------------------------------------------------- 278s APBS -- Adaptive Poisson-Boltzmann Solver 278s Version APBS 3.4.1 278s 278s Nathan A. Baker (nathan.baker@pnnl.gov) 278s Pacific Northwest National Laboratory 278s 278s Additional contributing authors listed in the code documentation. 278s 278s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 278s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 278s Northwest Division for the U.S. Department of Energy. 278s 278s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 278s Portions Copyright (c) 2002-2020, Nathan A. Baker. 278s Portions Copyright (c) 1999-2002, The Regents of the University of California. 278s Portions Copyright (c) 1995, Michael Holst. 278s All rights reserved. 278s 278s Redistribution and use in source and binary forms, with or without 278s modification, are permitted provided that the following conditions are met: 278s 278s * Redistributions of source code must retain the above copyright notice, this 278s list of conditions and the following disclaimer. 278s 278s * Redistributions in binary form must reproduce the above copyright notice, 278s this list of conditions and the following disclaimer in the documentation 278s and/or other materials provided with the distribution. 278s 278s * Neither the name of the developer nor the names of its contributors may be 278s used to endorse or promote products derived from this software without 278s specific prior written permission. 278s 278s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 278s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 278s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 278s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 278s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 278s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 278s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 278s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 278s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 278s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 278s ---------------------------------------------------------------------- 278s APBS uses FETK (the Finite Element ToolKit) to solve the 278s Poisson-Boltzmann equation numerically. FETK is a portable collection 278s of finite element modeling class libraries developed by the Michael Holst 278s research group and written in an object-oriented form of C. FEtk is 278s designed to solve general coupled systems of nonlinear partial differential 278s equations using adaptive finite element methods, inexact Newton methods, 278s and algebraic multilevel methods. More information about FEtk may be found 278s at . 278s ---------------------------------------------------------------------- 278s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 278s Aqua is a modified form of the Holst group PMG library 278s which has been modified by Patrice Koehl 278s for improved efficiency and 278s memory usage when solving the Poisson-Boltzmann equation. 278s ---------------------------------------------------------------------- 278s Please cite your use of APBS as: 278s 278s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 278s nanosystems: application to microtubules and the ribosome. Proc. 278s Natl. Acad. Sci. USA 98, 10037-10041 2001. 278s 278s 278s This executable compiled on Jan 3 2025 at 11:01:42 278s 278s Parsing input file apbs-smol-parallel-PE0.in... 278s rank 0 size 1... 278s Parsed input file. 278s Got paths for 1 molecules 278s Reading PQR-format atom data from ion.pqr. 278s 1 atoms 278s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 278s Net charge 1.00e+00 e 278s Preparing to run 6 PBE calculations. 278s ---------------------------------------- 278s CALCULATION #1 (solvated): MULTIGRID 278s Setting up problem... 278s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 278s Debye length: 0 A 278s Current memory usage: 61.262 MB total, 61.262 MB high water 278s Using cubic spline charge discretization. 278s Partition overlap fraction = 0.1 278s Processor array = 2 x 2 x 1 278s Grid dimensions: 65 x 65 x 65 278s Grid spacings: 0.781 x 0.781 x 0.781 278s Grid lengths: 50.000 x 50.000 x 50.000 278s Grid center: (0.000, 0.000, 0.000) 278s Multigrid levels: 5 278s Molecule ID: 1 278s Linearized traditional PBE 278s Multiple Debye-Huckel sphere boundary conditions 278s 0 ion species (0.000 M ionic strength): 278s Solute dielectric: 1.000 278s Solvent dielectric: 78.540 278s Using "molecular" surface definition;harmonic average smoothing 278s Solvent probe radius: 1.400 A 278s Temperature: 298.150 K 278s Electrostatic energies will be calculated 278s Total electrostatic energy = 2.383232191816E+02 kJ/mol 278s Calculating forces... 278s ---------------------------------------- 278s CALCULATION #2 (solvated): MULTIGRID 278s Setting up problem... 278s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 278s Debye length: 0 A 278s Current memory usage: 61.262 MB total, 122.067 MB high water 278s Using cubic spline charge discretization. 278s Partition overlap fraction = 0.1 278s Processor array = 2 x 2 x 1 278s Grid dimensions: 65 x 65 x 65 278s Grid spacings: 0.296 x 0.296 x 0.383 278s Grid lengths: 18.944 x 18.944 x 24.495 278s Grid center: (-2.411, -2.411, 0.000) 278s Multigrid levels: 5 278s Molecule ID: 1 278s Linearized traditional PBE 278s Boundary conditions from focusing 278s 0 ion species (0.000 M ionic strength): 278s Solute dielectric: 1.000 278s Solvent dielectric: 78.540 278s Using "molecular" surface definition;harmonic average smoothing 278s Solvent probe radius: 1.400 A 278s Temperature: 298.150 K 278s Electrostatic energies will be calculated 278s Total electrostatic energy = 8.145369591602E+02 kJ/mol 278s Calculating forces... 278s [focusFillBound()]: WARNING: 278s Unusually large potential values 278s detected on the focusing boundary! 278s Convergence not guaranteed for NPBE/NRPBE calculations! 278s 278s ---------------------------------------- 278s CALCULATION #3 (solvated): MULTIGRID 278s Setting up problem... 278s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 278s Debye length: 0 A 278s Current memory usage: 61.262 MB total, 122.067 MB high water 278s Using cubic spline charge discretization. 278s Partition overlap fraction = 0.1 278s Processor array = 2 x 2 x 1 278s Grid dimensions: 65 x 65 x 65 278s Grid spacings: 0.112 x 0.112 x 0.188 278s Grid lengths: 7.178 x 7.178 x 12.000 278s Grid center: (-2.411, -2.411, 0.000) 278s Multigrid levels: 5 278s Molecule ID: 1 278s Linearized traditional PBE 278s Boundary conditions from focusing 278s 0 ion species (0.000 M ionic strength): 278s Solute dielectric: 1.000 278s Solvent dielectric: 78.540 278s Using "molecular" surface definition;harmonic average smoothing 278s Solvent probe radius: 1.400 A 278s Temperature: 298.150 K 278s Electrostatic energies will be calculated 278s Total electrostatic energy = 1.485524998001E+03 kJ/mol 278s Calculating forces... 278s ---------------------------------------- 278s CALCULATION #4 (reference): MULTIGRID 278s Setting up problem... 278s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 278s Debye length: 0 A 278s Current memory usage: 61.189 MB total, 122.067 MB high water 278s Using cubic spline charge discretization. 278s Partition overlap fraction = 0.1 278s Processor array = 2 x 2 x 1 278s Grid dimensions: 65 x 65 x 65 278s Grid spacings: 0.781 x 0.781 x 0.781 278s Grid lengths: 50.000 x 50.000 x 50.000 278s Grid center: (0.000, 0.000, 0.000) 278s Multigrid levels: 5 278s Molecule ID: 1 278s Linearized traditional PBE 278s Multiple Debye-Huckel sphere boundary conditions 278s 0 ion species (0.000 M ionic strength): 278s Solute dielectric: 1.000 278s Solvent dielectric: 1.000 278s Using "molecular" surface definition;harmonic average smoothing 278s Solvent probe radius: 1.400 A 278s Temperature: 298.150 K 278s Electrostatic energies will be calculated 278s Total electrostatic energy = 2.977178707009E+02 kJ/mol 278s Calculating forces... 278s ---------------------------------------- 278s CALCULATION #5 (reference): MULTIGRID 278s Setting up problem... 278s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 278s Debye length: 0 A 278s Current memory usage: 61.189 MB total, 122.067 MB high water 278s Using cubic spline charge discretization. 278s Partition overlap fraction = 0.1 278s Processor array = 2 x 2 x 1 278s Grid dimensions: 65 x 65 x 65 278s Grid spacings: 0.296 x 0.296 x 0.383 278s Grid lengths: 18.944 x 18.944 x 24.495 278s Grid center: (-2.411, -2.411, 0.000) 278s Multigrid levels: 5 278s Molecule ID: 1 278s Linearized traditional PBE 278s Boundary conditions from focusing 278s 0 ion species (0.000 M ionic strength): 278s Solute dielectric: 1.000 278s Solvent dielectric: 1.000 278s Using "molecular" surface definition;harmonic average smoothing 278s Solvent probe radius: 1.400 A 278s Temperature: 298.150 K 278s Electrostatic energies will be calculated 278s Total electrostatic energy = 8.799304557588E+02 kJ/mol 278s Calculating forces... 278s [focusFillBound()]: WARNING: 278s Unusually large potential values 278s detected on the focusing boundary! 278s Convergence not guaranteed for NPBE/NRPBE calculations! 278s 278s ---------------------------------------- 278s CALCULATION #6 (reference): MULTIGRID 278s Setting up problem... 278s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 278s Debye length: 0 A 278s Current memory usage: 61.189 MB total, 122.067 MB high water 278s Using cubic spline charge discretization. 278s Partition overlap fraction = 0.1 278s Processor array = 2 x 2 x 1 278s Grid dimensions: 65 x 65 x 65 278s Grid spacings: 0.112 x 0.112 x 0.188 278s Grid lengths: 7.178 x 7.178 x 12.000 278s Grid center: (-2.411, -2.411, 0.000) 278s Multigrid levels: 5 278s Molecule ID: 1 278s Linearized traditional PBE 278s Boundary conditions from focusing 278s 0 ion species (0.000 M ionic strength): 278s Solute dielectric: 1.000 278s Solvent dielectric: 1.000 278s Using "molecular" surface definition;harmonic average smoothing 278s Solvent probe radius: 1.400 A 278s Temperature: 298.150 K 278s Electrostatic energies will be calculated 278s Total electrostatic energy = 1.542873949131E+03 kJ/mol 278s Calculating forces... 278s ---------------------------------------- 278s PRINT STATEMENTS 278s 278s print energy 1 (solvated) - 2 (reference) end 278s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 278s Global net ELEC energy = -5.734895113069E+01 kJ/mol 278s ---------------------------------------- 278s CLEANING UP AND SHUTTING DOWN... 278s Destroying force arrays. 278s No energy arrays to destroy. 278s Destroying multigrid structures. 278s Destroying finite element structures. 278s Destroying 1 molecules 278s Final memory usage: 0.001 MB total, 122.067 MB high water 278s 278s 278s Thanks for using APBS! 278s 278s Processor 0 results: 278s 2.383232191816e+02 278s 8.145369591602e+02 278s 1.485524998001e+03 278s 2.977178707009e+02 278s 8.799304557588e+02 278s 1.542873949131e+03 278s -5.734895113069e+01 278s 286s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 286s BINARY: /usr/bin/apbs 286s INPUT: apbs-smol-parallel-PE1.in 286s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 286s asc_getToken: Error occurred (bailing out). 286s Vio_scanf: Format problem with input. 286s 286s 286s ---------------------------------------------------------------------- 286s APBS -- Adaptive Poisson-Boltzmann Solver 286s Version APBS 3.4.1 286s 286s Nathan A. Baker (nathan.baker@pnnl.gov) 286s Pacific Northwest National Laboratory 286s 286s Additional contributing authors listed in the code documentation. 286s 286s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 286s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 286s Northwest Division for the U.S. Department of Energy. 286s 286s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 286s Portions Copyright (c) 2002-2020, Nathan A. Baker. 286s Portions Copyright (c) 1999-2002, The Regents of the University of California. 286s Portions Copyright (c) 1995, Michael Holst. 286s All rights reserved. 286s 286s Redistribution and use in source and binary forms, with or without 286s modification, are permitted provided that the following conditions are met: 286s 286s * Redistributions of source code must retain the above copyright notice, this 286s list of conditions and the following disclaimer. 286s 286s * Redistributions in binary form must reproduce the above copyright notice, 286s this list of conditions and the following disclaimer in the documentation 286s and/or other materials provided with the distribution. 286s 286s * Neither the name of the developer nor the names of its contributors may be 286s used to endorse or promote products derived from this software without 286s specific prior written permission. 286s 286s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 286s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 286s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 286s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 286s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 286s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 286s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 286s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 286s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 286s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 286s ---------------------------------------------------------------------- 286s APBS uses FETK (the Finite Element ToolKit) to solve the 286s Poisson-Boltzmann equation numerically. FETK is a portable collection 286s of finite element modeling class libraries developed by the Michael Holst 286s research group and written in an object-oriented form of C. FEtk is 286s designed to solve general coupled systems of nonlinear partial differential 286s equations using adaptive finite element methods, inexact Newton methods, 286s and algebraic multilevel methods. More information about FEtk may be found 286s at . 286s ---------------------------------------------------------------------- 286s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 286s Aqua is a modified form of the Holst group PMG library 286s which has been modified by Patrice Koehl 286s for improved efficiency and 286s memory usage when solving the Poisson-Boltzmann equation. 286s ---------------------------------------------------------------------- 286s Please cite your use of APBS as: 286s 286s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 286s nanosystems: application to microtubules and the ribosome. Proc. 286s Natl. Acad. Sci. USA 98, 10037-10041 2001. 286s 286s 286s This executable compiled on Jan 3 2025 at 11:01:42 286s 286s Parsing input file apbs-smol-parallel-PE1.in... 286s rank 0 size 1... 286s Parsed input file. 286s Got paths for 1 molecules 286s Reading PQR-format atom data from ion.pqr. 286s 1 atoms 286s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 286s Net charge 1.00e+00 e 286s Preparing to run 6 PBE calculations. 286s ---------------------------------------- 286s CALCULATION #1 (solvated): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.262 MB total, 61.262 MB high water 286s Using cubic spline charge discretization. 286s Partition overlap fraction = 0.1 286s Processor array = 2 x 2 x 1 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.781 x 0.781 x 0.781 286s Grid lengths: 50.000 x 50.000 x 50.000 286s Grid center: (0.000, 0.000, 0.000) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 0 ion species (0.000 M ionic strength): 286s Solute dielectric: 1.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 1.400 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 2.383232191816E+02 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #2 (solvated): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.262 MB total, 122.067 MB high water 286s Using cubic spline charge discretization. 286s Partition overlap fraction = 0.1 286s Processor array = 2 x 2 x 1 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.296 x 0.296 x 0.383 286s Grid lengths: 18.944 x 18.944 x 24.495 286s Grid center: (2.411, -2.411, 0.000) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 0 ion species (0.000 M ionic strength): 286s Solute dielectric: 1.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 1.400 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 8.145419898332E+02 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #3 (solvated): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.262 MB total, 122.067 MB high water 286s Using cubic spline charge discretization. 286s Partition overlap fraction = 0.1 286s Processor array = 2 x 2 x 1 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.112 x 0.112 x 0.188 286s Grid lengths: 7.178 x 7.178 x 12.000 286s Grid center: (2.411, -2.411, 0.000) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 0 ion species (0.000 M ionic strength): 286s Solute dielectric: 1.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 1.400 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.485529328612E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #4 (reference): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.189 MB total, 122.067 MB high water 286s Using cubic spline charge discretization. 286s Partition overlap fraction = 0.1 286s Processor array = 2 x 2 x 1 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.781 x 0.781 x 0.781 286s Grid lengths: 50.000 x 50.000 x 50.000 286s Grid center: (0.000, 0.000, 0.000) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 0 ion species (0.000 M ionic strength): 286s Solute dielectric: 1.000 286s Solvent dielectric: 1.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 1.400 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 2.977178707009E+02 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #5 (reference): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.189 MB total, 122.067 MB high water 286s Using cubic spline charge discretization. 286s Partition overlap fraction = 0.1 286s Processor array = 2 x 2 x 1 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.296 x 0.296 x 0.383 286s Grid lengths: 18.944 x 18.944 x 24.495 286s Grid center: (2.411, -2.411, 0.000) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 0 ion species (0.000 M ionic strength): 286s Solute dielectric: 1.000 286s Solvent dielectric: 1.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 1.400 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 8.799304557588E+02 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #6 (reference): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.189 MB total, 122.067 MB high water 286s Using cubic spline charge discretization. 286s Partition overlap fraction = 0.1 286s Processor array = 2 x 2 x 1 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.112 x 0.112 x 0.188 286s Grid lengths: 7.178 x 7.178 x 12.000 286s Grid center: (2.411, -2.411, 0.000) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 0 ion species (0.000 M ionic strength): 286s Solute dielectric: 1.000 286s Solvent dielectric: 1.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 1.400 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.542873949131E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s PRINT STATEMENTS 286s 286s print energy 1 (solvated) - 2 (reference) end 286s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 286s Global net ELEC energy = -5.734462051928E+01 kJ/mol 286s ---------------------------------------- 286s CLEANING UP AND SHUTTING DOWN... 286s Destroying force arrays. 286s No energy arrays to destroy. 286s Destroying multigrid structures. 286s Destroying finite element structures. 286s Destroying 1 molecules 286s Final memory usage: 0.001 MB total, 122.067 MB high water 286s 286s 286s Thanks for using APBS! 286s 286s Processor 1 results: 286s 2.383232191816e+02 286s 8.145419898332e+02 286s 1.485529328612e+03 286s 2.977178707009e+02 286s 8.799304557588e+02 286s 1.542873949131e+03 286s -5.734462051928e+01 286s 293s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 293s BINARY: /usr/bin/apbs 293s INPUT: apbs-smol-parallel-PE2.in 293s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 293s asc_getToken: Error occurred (bailing out). 293s Vio_scanf: Format problem with input. 293s 293s 293s ---------------------------------------------------------------------- 293s APBS -- Adaptive Poisson-Boltzmann Solver 293s Version APBS 3.4.1 293s 293s Nathan A. Baker (nathan.baker@pnnl.gov) 293s Pacific Northwest National Laboratory 293s 293s Additional contributing authors listed in the code documentation. 293s 293s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 293s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 293s Northwest Division for the U.S. Department of Energy. 293s 293s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 293s Portions Copyright (c) 2002-2020, Nathan A. Baker. 293s Portions Copyright (c) 1999-2002, The Regents of the University of California. 293s Portions Copyright (c) 1995, Michael Holst. 293s All rights reserved. 293s 293s Redistribution and use in source and binary forms, with or without 293s modification, are permitted provided that the following conditions are met: 293s 293s * Redistributions of source code must retain the above copyright notice, this 293s list of conditions and the following disclaimer. 293s 293s * Redistributions in binary form must reproduce the above copyright notice, 293s this list of conditions and the following disclaimer in the documentation 293s and/or other materials provided with the distribution. 293s 293s * Neither the name of the developer nor the names of its contributors may be 293s used to endorse or promote products derived from this software without 293s specific prior written permission. 293s 293s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 293s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 293s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 293s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 293s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 293s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 293s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 293s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 293s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 293s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 293s ---------------------------------------------------------------------- 293s APBS uses FETK (the Finite Element ToolKit) to solve the 293s Poisson-Boltzmann equation numerically. FETK is a portable collection 293s of finite element modeling class libraries developed by the Michael Holst 293s research group and written in an object-oriented form of C. FEtk is 293s designed to solve general coupled systems of nonlinear partial differential 293s equations using adaptive finite element methods, inexact Newton methods, 293s and algebraic multilevel methods. More information about FEtk may be found 293s at . 293s ---------------------------------------------------------------------- 293s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 293s Aqua is a modified form of the Holst group PMG library 293s which has been modified by Patrice Koehl 293s for improved efficiency and 293s memory usage when solving the Poisson-Boltzmann equation. 293s ---------------------------------------------------------------------- 293s Please cite your use of APBS as: 293s 293s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 293s nanosystems: application to microtubules and the ribosome. Proc. 293s Natl. Acad. Sci. USA 98, 10037-10041 2001. 293s 293s 293s This executable compiled on Jan 3 2025 at 11:01:42 293s 293s Parsing input file apbs-smol-parallel-PE2.in... 293s rank 0 size 1... 293s Parsed input file. 293s Got paths for 1 molecules 293s Reading PQR-format atom data from ion.pqr. 293s 1 atoms 293s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 293s Net charge 1.00e+00 e 293s Preparing to run 6 PBE calculations. 293s ---------------------------------------- 293s CALCULATION #1 (solvated): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 61.262 MB total, 61.262 MB high water 293s Using cubic spline charge discretization. 293s Partition overlap fraction = 0.1 293s Processor array = 2 x 2 x 1 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.781 x 0.781 x 0.781 293s Grid lengths: 50.000 x 50.000 x 50.000 293s Grid center: (0.000, 0.000, 0.000) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 0 ion species (0.000 M ionic strength): 293s Solute dielectric: 1.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 1.400 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 2.383232191909E+02 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #2 (solvated): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 61.262 MB total, 122.067 MB high water 293s Using cubic spline charge discretization. 293s Partition overlap fraction = 0.1 293s Processor array = 2 x 2 x 1 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.296 x 0.296 x 0.383 293s Grid lengths: 18.944 x 18.944 x 24.495 293s Grid center: (-2.411, 2.411, 0.000) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 0 ion species (0.000 M ionic strength): 293s Solute dielectric: 1.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 1.400 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 8.145369593489E+02 kJ/mol 293s Calculating forces... 293s [focusFillBound()]: WARNING: 293s Unusually large potential values 293s detected on the focusing boundary! 293s Convergence not guaranteed for NPBE/NRPBE calculations! 293s 293s ---------------------------------------- 293s CALCULATION #3 (solvated): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 61.262 MB total, 122.067 MB high water 293s Using cubic spline charge discretization. 293s Partition overlap fraction = 0.1 293s Processor array = 2 x 2 x 1 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.112 x 0.112 x 0.188 293s Grid lengths: 7.178 x 7.178 x 12.000 293s Grid center: (-2.411, 2.411, 0.000) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 0 ion species (0.000 M ionic strength): 293s Solute dielectric: 1.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 1.400 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.485524997676E+03 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #4 (reference): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 61.189 MB total, 122.067 MB high water 293s Using cubic spline charge discretization. 293s Partition overlap fraction = 0.1 293s Processor array = 2 x 2 x 1 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.781 x 0.781 x 0.781 293s Grid lengths: 50.000 x 50.000 x 50.000 293s Grid center: (0.000, 0.000, 0.000) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 0 ion species (0.000 M ionic strength): 293s Solute dielectric: 1.000 293s Solvent dielectric: 1.000 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 1.400 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 2.977178707146E+02 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #5 (reference): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 61.189 MB total, 122.067 MB high water 293s Using cubic spline charge discretization. 293s Partition overlap fraction = 0.1 293s Processor array = 2 x 2 x 1 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.296 x 0.296 x 0.383 293s Grid lengths: 18.944 x 18.944 x 24.495 293s Grid center: (-2.411, 2.411, 0.000) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 0 ion species (0.000 M ionic strength): 293s Solute dielectric: 1.000 293s Solvent dielectric: 1.000 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 1.400 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 8.799304557596E+02 kJ/mol 293s Calculating forces... 293s [focusFillBound()]: WARNING: 293s Unusually large potential values 293s detected on the focusing boundary! 293s Convergence not guaranteed for NPBE/NRPBE calculations! 293s 293s ---------------------------------------- 293s CALCULATION #6 (reference): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 61.189 MB total, 122.067 MB high water 293s Using cubic spline charge discretization. 293s Partition overlap fraction = 0.1 293s Processor array = 2 x 2 x 1 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.112 x 0.112 x 0.188 293s Grid lengths: 7.178 x 7.178 x 12.000 293s Grid center: (-2.411, 2.411, 0.000) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 0 ion species (0.000 M ionic strength): 293s Solute dielectric: 1.000 293s Solvent dielectric: 1.000 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 1.400 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.542873949141E+03 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s PRINT STATEMENTS 293s 293s print energy 1 (solvated) - 2 (reference) end 293s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 293s Global net ELEC energy = -5.734895146550E+01 kJ/mol 293s ---------------------------------------- 293s CLEANING UP AND SHUTTING DOWN... 293s Destroying force arrays. 293s No energy arrays to destroy. 293s Destroying multigrid structures. 293s Destroying finite element structures. 293s Destroying 1 molecules 293s Final memory usage: 0.001 MB total, 122.067 MB high water 293s 293s 293s Thanks for using APBS! 293s 293s Processor 2 results: 293s 2.383232191909e+02 293s 8.145369593489e+02 293s 1.485524997676e+03 293s 2.977178707146e+02 293s 8.799304557596e+02 293s 1.542873949141e+03 293s -5.734895146550e+01 293s 301s Processor 3 results: 301s 2.383232191909e+02 301s 8.145419900310e+02 301s 1.485529328301e+03 301s 2.977178707146e+02 301s 8.799304557596e+02 301s 1.542873949141e+03 301s -5.734462084052e+01 301s 301s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 301s *** PASSED *** 301s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 301s *** PASSED *** 301s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 301s *** PASSED *** 301s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 301s *** PASSED *** 301s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 301s *** PASSED *** 301s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 301s *** PASSED *** 301s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 301s *** PASSED *** 301s Elapsed time: 30.83955 seconds 301s -------------------------------------------------------------------------------- 301s Total elapsed time: 71.710503 seconds 301s Test results have been logged 301s -------------------------------------------------------------------------------- 301s -------------------------------------------------------------------------------- 301s Testing input file apbs-mol-auto.in 301s 301s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 301s BINARY: /usr/bin/apbs 301s INPUT: apbs-smol-parallel-PE3.in 301s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 301s asc_getToken: Error occurred (bailing out). 301s Vio_scanf: Format problem with input. 301s 301s 301s ---------------------------------------------------------------------- 301s APBS -- Adaptive Poisson-Boltzmann Solver 301s Version APBS 3.4.1 301s 301s Nathan A. Baker (nathan.baker@pnnl.gov) 301s Pacific Northwest National Laboratory 301s 301s Additional contributing authors listed in the code documentation. 301s 301s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 301s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 301s Northwest Division for the U.S. Department of Energy. 301s 301s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 301s Portions Copyright (c) 2002-2020, Nathan A. Baker. 301s Portions Copyright (c) 1999-2002, The Regents of the University of California. 301s Portions Copyright (c) 1995, Michael Holst. 301s All rights reserved. 301s 301s Redistribution and use in source and binary forms, with or without 301s modification, are permitted provided that the following conditions are met: 301s 301s * Redistributions of source code must retain the above copyright notice, this 301s list of conditions and the following disclaimer. 301s 301s * Redistributions in binary form must reproduce the above copyright notice, 301s this list of conditions and the following disclaimer in the documentation 301s and/or other materials provided with the distribution. 301s 301s * Neither the name of the developer nor the names of its contributors may be 301s used to endorse or promote products derived from this software without 301s specific prior written permission. 301s 301s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 301s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 301s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 301s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 301s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 301s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 301s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 301s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 301s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 301s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 301s ---------------------------------------------------------------------- 301s APBS uses FETK (the Finite Element ToolKit) to solve the 301s Poisson-Boltzmann equation numerically. FETK is a portable collection 301s of finite element modeling class libraries developed by the Michael Holst 301s research group and written in an object-oriented form of C. FEtk is 301s designed to solve general coupled systems of nonlinear partial differential 301s equations using adaptive finite element methods, inexact Newton methods, 301s and algebraic multilevel methods. More information about FEtk may be found 301s at . 301s ---------------------------------------------------------------------- 301s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 301s Aqua is a modified form of the Holst group PMG library 301s which has been modified by Patrice Koehl 301s for improved efficiency and 301s memory usage when solving the Poisson-Boltzmann equation. 301s ---------------------------------------------------------------------- 301s Please cite your use of APBS as: 301s 301s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 301s nanosystems: application to microtubules and the ribosome. Proc. 301s Natl. Acad. Sci. USA 98, 10037-10041 2001. 301s 301s 301s This executable compiled on Jan 3 2025 at 11:01:42 301s 301s Parsing input file apbs-smol-parallel-PE3.in... 301s rank 0 size 1... 301s Parsed input file. 301s Got paths for 1 molecules 301s Reading PQR-format atom data from ion.pqr. 301s 1 atoms 301s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 301s Net charge 1.00e+00 e 301s Preparing to run 6 PBE calculations. 301s ---------------------------------------- 301s CALCULATION #1 (solvated): MULTIGRID 301s Setting up problem... 301s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 301s Debye length: 0 A 301s Current memory usage: 61.262 MB total, 61.262 MB high water 301s Using cubic spline charge discretization. 301s Partition overlap fraction = 0.1 301s Processor array = 2 x 2 x 1 301s Grid dimensions: 65 x 65 x 65 301s Grid spacings: 0.781 x 0.781 x 0.781 301s Grid lengths: 50.000 x 50.000 x 50.000 301s Grid center: (0.000, 0.000, 0.000) 301s Multigrid levels: 5 301s Molecule ID: 1 301s Linearized traditional PBE 301s Multiple Debye-Huckel sphere boundary conditions 301s 0 ion species (0.000 M ionic strength): 301s Solute dielectric: 1.000 301s Solvent dielectric: 78.540 301s Using "molecular" surface definition;harmonic average smoothing 301s Solvent probe radius: 1.400 A 301s Temperature: 298.150 K 301s Electrostatic energies will be calculated 301s Total electrostatic energy = 2.383232191909E+02 kJ/mol 301s Calculating forces... 301s ---------------------------------------- 301s CALCULATION #2 (solvated): MULTIGRID 301s Setting up problem... 301s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 301s Debye length: 0 A 301s Current memory usage: 61.262 MB total, 122.067 MB high water 301s Using cubic spline charge discretization. 301s Partition overlap fraction = 0.1 301s Processor array = 2 x 2 x 1 301s Grid dimensions: 65 x 65 x 65 301s Grid spacings: 0.296 x 0.296 x 0.383 301s Grid lengths: 18.944 x 18.944 x 24.495 301s Grid center: (2.411, 2.411, 0.000) 301s Multigrid levels: 5 301s Molecule ID: 1 301s Linearized traditional PBE 301s Boundary conditions from focusing 301s 0 ion species (0.000 M ionic strength): 301s Solute dielectric: 1.000 301s Solvent dielectric: 78.540 301s Using "molecular" surface definition;harmonic average smoothing 301s Solvent probe radius: 1.400 A 301s Temperature: 298.150 K 301s Electrostatic energies will be calculated 301s Total electrostatic energy = 8.145419900310E+02 kJ/mol 301s Calculating forces... 301s [focusFillBound()]: WARNING: 301s Unusually large potential values 301s detected on the focusing boundary! 301s Convergence not guaranteed for NPBE/NRPBE calculations! 301s 301s ---------------------------------------- 301s CALCULATION #3 (solvated): MULTIGRID 301s Setting up problem... 301s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 301s Debye length: 0 A 301s Current memory usage: 61.262 MB total, 122.067 MB high water 301s Using cubic spline charge discretization. 301s Partition overlap fraction = 0.1 301s Processor array = 2 x 2 x 1 301s Grid dimensions: 65 x 65 x 65 301s Grid spacings: 0.112 x 0.112 x 0.188 301s Grid lengths: 7.178 x 7.178 x 12.000 301s Grid center: (2.411, 2.411, 0.000) 301s Multigrid levels: 5 301s Molecule ID: 1 301s Linearized traditional PBE 301s Boundary conditions from focusing 301s 0 ion species (0.000 M ionic strength): 301s Solute dielectric: 1.000 301s Solvent dielectric: 78.540 301s Using "molecular" surface definition;harmonic average smoothing 301s Solvent probe radius: 1.400 A 301s Temperature: 298.150 K 301s Electrostatic energies will be calculated 301s Total electrostatic energy = 1.485529328301E+03 kJ/mol 301s Calculating forces... 301s ---------------------------------------- 301s CALCULATION #4 (reference): MULTIGRID 301s Setting up problem... 301s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 301s Debye length: 0 A 301s Current memory usage: 61.189 MB total, 122.067 MB high water 301s Using cubic spline charge discretization. 301s Partition overlap fraction = 0.1 301s Processor array = 2 x 2 x 1 301s Grid dimensions: 65 x 65 x 65 301s Grid spacings: 0.781 x 0.781 x 0.781 301s Grid lengths: 50.000 x 50.000 x 50.000 301s Grid center: (0.000, 0.000, 0.000) 301s Multigrid levels: 5 301s Molecule ID: 1 301s Linearized traditional PBE 301s Multiple Debye-Huckel sphere boundary conditions 301s 0 ion species (0.000 M ionic strength): 301s Solute dielectric: 1.000 301s Solvent dielectric: 1.000 301s Using "molecular" surface definition;harmonic average smoothing 301s Solvent probe radius: 1.400 A 301s Temperature: 298.150 K 301s Electrostatic energies will be calculated 301s Total electrostatic energy = 2.977178707146E+02 kJ/mol 301s Calculating forces... 301s ---------------------------------------- 301s CALCULATION #5 (reference): MULTIGRID 301s Setting up problem... 301s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 301s Debye length: 0 A 301s Current memory usage: 61.189 MB total, 122.067 MB high water 301s Using cubic spline charge discretization. 301s Partition overlap fraction = 0.1 301s Processor array = 2 x 2 x 1 301s Grid dimensions: 65 x 65 x 65 301s Grid spacings: 0.296 x 0.296 x 0.383 301s Grid lengths: 18.944 x 18.944 x 24.495 301s Grid center: (2.411, 2.411, 0.000) 301s Multigrid levels: 5 301s Molecule ID: 1 301s Linearized traditional PBE 301s Boundary conditions from focusing 301s 0 ion species (0.000 M ionic strength): 301s Solute dielectric: 1.000 301s Solvent dielectric: 1.000 301s Using "molecular" surface definition;harmonic average smoothing 301s Solvent probe radius: 1.400 A 301s Temperature: 298.150 K 301s Electrostatic energies will be calculated 301s Total electrostatic energy = 8.799304557596E+02 kJ/mol 301s Calculating forces... 301s [focusFillBound()]: WARNING: 301s Unusually large potential values 301s detected on the focusing boundary! 301s Convergence not guaranteed for NPBE/NRPBE calculations! 301s 301s ---------------------------------------- 301s CALCULATION #6 (reference): MULTIGRID 301s Setting up problem... 301s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 301s Debye length: 0 A 301s Current memory usage: 61.189 MB total, 122.067 MB high water 301s Using cubic spline charge discretization. 301s Partition overlap fraction = 0.1 301s Processor array = 2 x 2 x 1 301s Grid dimensions: 65 x 65 x 65 301s Grid spacings: 0.112 x 0.112 x 0.188 301s Grid lengths: 7.178 x 7.178 x 12.000 301s Grid center: (2.411, 2.411, 0.000) 301s Multigrid levels: 5 301s Molecule ID: 1 301s Linearized traditional PBE 301s Boundary conditions from focusing 301s 0 ion species (0.000 M ionic strength): 301s Solute dielectric: 1.000 301s Solvent dielectric: 1.000 301s Using "molecular" surface definition;harmonic average smoothing 301s Solvent probe radius: 1.400 A 301s Temperature: 298.150 K 301s Electrostatic energies will be calculated 301s Total electrostatic energy = 1.542873949141E+03 kJ/mol 301s Calculating forces... 301s ---------------------------------------- 301s PRINT STATEMENTS 301s 301s print energy 1 (solvated) - 2 (reference) end 301s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 301s Global net ELEC energy = -5.734462084052E+01 kJ/mol 301s ---------------------------------------- 301s CLEANING UP AND SHUTTING DOWN... 301s Destroying force arrays. 301s No energy arrays to destroy. 301s Destroying multigrid structures. 301s Destroying finite element structures. 301s Destroying 1 molecules 301s Final memory usage: 0.001 MB total, 122.067 MB high water 301s 301s 301s Thanks for using APBS! 301s 483s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 483s *** PASSED *** 483s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 483s *** PASSED *** 483s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 483s *** PASSED *** 483s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 483s *** PASSED *** 483s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 483s *** PASSED *** 483s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 483s *** PASSED *** 483s Testing computed result against expected result (1.048683058628e+02, 1.048683060915e+02) 483s *** PASSED *** 483s Elapsed time: 181.981212 seconds 483s -------------------------------------------------------------------------------- 483s -------------------------------------------------------------------------------- 483s Testing input file apbs-smol-auto.in 483s 483s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 483s EXPECTED COMPUTED: 7 483s EXPECTED EXPECTED: 7 483s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 483s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 483s COMPUTED RESULT 953.292876745 483s COMPUTED RESULT 3258.1578983732998 483s COMPUTED RESULT 5942.108652589999 483s COMPUTED RESULT 1190.8714828309999 483s COMPUTED RESULT 3519.7218230368003 483s COMPUTED RESULT 6171.495796544 483s COMPUTED RESULT -229.38714395599 483s Running tests for actin-dimer-auto section 483s BINARY: /usr/bin/apbs 483s INPUT: apbs-mol-auto.in 483s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 483s asc_getToken: Error occurred (bailing out). 483s Vio_scanf: Format problem with input. 483s 483s 483s ---------------------------------------------------------------------- 483s APBS -- Adaptive Poisson-Boltzmann Solver 483s Version APBS 3.4.1 483s 483s Nathan A. Baker (nathan.baker@pnnl.gov) 483s Pacific Northwest National Laboratory 483s 483s Additional contributing authors listed in the code documentation. 483s 483s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 483s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 483s Northwest Division for the U.S. Department of Energy. 483s 483s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 483s Portions Copyright (c) 2002-2020, Nathan A. Baker. 483s Portions Copyright (c) 1999-2002, The Regents of the University of California. 483s Portions Copyright (c) 1995, Michael Holst. 483s All rights reserved. 483s 483s Redistribution and use in source and binary forms, with or without 483s modification, are permitted provided that the following conditions are met: 483s 483s * Redistributions of source code must retain the above copyright notice, this 483s list of conditions and the following disclaimer. 483s 483s * Redistributions in binary form must reproduce the above copyright notice, 483s this list of conditions and the following disclaimer in the documentation 483s and/or other materials provided with the distribution. 483s 483s * Neither the name of the developer nor the names of its contributors may be 483s used to endorse or promote products derived from this software without 483s specific prior written permission. 483s 483s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 483s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 483s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 483s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 483s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 483s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 483s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 483s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 483s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 483s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 483s ---------------------------------------------------------------------- 483s APBS uses FETK (the Finite Element ToolKit) to solve the 483s Poisson-Boltzmann equation numerically. FETK is a portable collection 483s of finite element modeling class libraries developed by the Michael Holst 483s research group and written in an object-oriented form of C. FEtk is 483s designed to solve general coupled systems of nonlinear partial differential 483s equations using adaptive finite element methods, inexact Newton methods, 483s and algebraic multilevel methods. More information about FEtk may be found 483s at . 483s ---------------------------------------------------------------------- 483s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 483s Aqua is a modified form of the Holst group PMG library 483s which has been modified by Patrice Koehl 483s for improved efficiency and 483s memory usage when solving the Poisson-Boltzmann equation. 483s ---------------------------------------------------------------------- 483s Please cite your use of APBS as: 483s 483s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 483s nanosystems: application to microtubules and the ribosome. Proc. 483s Natl. Acad. Sci. USA 98, 10037-10041 2001. 483s 483s 483s This executable compiled on Jan 3 2025 at 11:01:42 483s 483s Parsing input file apbs-mol-auto.in... 483s rank 0 size 1... 483s Parsed input file. 483s Got paths for 3 molecules 483s Reading PQR-format atom data from mol1.pqr. 483s asc_getToken: Error occurred (bailing out). 483s Vio_scanf: Format problem with input. 483s 5877 atoms 483s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 483s Net charge -1.20e+01 e 483s Reading PQR-format atom data from mol2.pqr. 483s asc_getToken: Error occurred (bailing out). 483s Vio_scanf: Format problem with input. 483s 5877 atoms 483s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 483s Net charge -1.20e+01 e 483s Reading PQR-format atom data from complex.pqr. 483s 11754 atoms 483s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 483s Net charge -2.40e+01 e 483s Preparing to run 6 PBE calculations. 483s ---------------------------------------- 483s CALCULATION #1 (mol1): MULTIGRID 483s Setting up problem... 483s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 483s Debye length: 13.5959 A 483s Current memory usage: 1004.896 MB total, 1004.896 MB high water 483s Using linear spline charge discretization. 483s Grid dimensions: 161 x 161 x 161 483s Grid spacings: 0.975 x 0.756 x 1.012 483s Grid lengths: 156.000 x 121.000 x 162.000 483s Grid center: (2.518, -2.465, 16.742) 483s Multigrid levels: 4 483s Molecule ID: 1 483s Nonlinear traditional PBE 483s Single Debye-Huckel sphere boundary conditions 483s 2 ion species (0.050 M ionic strength): 483s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 483s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 483s Solute dielectric: 2.000 483s Solvent dielectric: 78.400 483s Using "molecular" surface definition; no smoothing 483s Solvent probe radius: 1.400 A 483s Temperature: 298.150 K 483s Electrostatic energies will be calculated 483s Total electrostatic energy = 1.527617850342E+05 kJ/mol 483s Calculating forces... 483s ---------------------------------------- 483s CALCULATION #2 (mol1): MULTIGRID 483s Setting up problem... 483s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 483s Debye length: 13.5959 A 483s Current memory usage: 1004.896 MB total, 1995.284 MB high water 483s Using linear spline charge discretization. 483s Grid dimensions: 161 x 161 x 161 483s Grid spacings: 0.700 x 0.569 x 0.725 483s Grid lengths: 112.000 x 91.000 x 116.000 483s Grid center: (2.518, -2.465, 16.742) 483s Multigrid levels: 4 483s Molecule ID: 1 483s Nonlinear traditional PBE 483s Boundary conditions from focusing 483s 2 ion species (0.050 M ionic strength): 483s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 483s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 483s Solute dielectric: 2.000 483s Solvent dielectric: 78.400 483s Using "molecular" surface definition; no smoothing 483s Solvent probe radius: 1.400 A 483s Temperature: 298.150 K 483s Electrostatic energies will be calculated 483s Total electrostatic energy = 2.919510754196E+05 kJ/mol 483s Calculating forces... 483s ---------------------------------------- 483s CALCULATION #3 (mol2): MULTIGRID 483s Setting up problem... 483s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 483s Debye length: 13.5959 A 483s Current memory usage: 1005.881 MB total, 1995.284 MB high water 483s Using linear spline charge discretization. 483s Grid dimensions: 161 x 161 x 161 483s Grid spacings: 0.975 x 0.756 x 1.012 483s Grid lengths: 156.000 x 121.000 x 162.000 483s Grid center: (2.518, -2.465, 16.742) 483s Multigrid levels: 4 483s Molecule ID: 2 483s Nonlinear traditional PBE 483s Single Debye-Huckel sphere boundary conditions 483s 2 ion species (0.050 M ionic strength): 483s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 483s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 483s Solute dielectric: 2.000 483s Solvent dielectric: 78.400 483s Using "molecular" surface definition; no smoothing 483s Solvent probe radius: 1.400 A 483s Temperature: 298.150 K 483s Electrostatic energies will be calculated 483s Total electrostatic energy = 1.527671844880E+05 kJ/mol 483s Calculating forces... 483s ---------------------------------------- 483s CALCULATION #4 (mol2): MULTIGRID 483s Setting up problem... 483s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 483s Debye length: 13.5959 A 483s Current memory usage: 1005.881 MB total, 1997.252 MB high water 483s Using linear spline charge discretization. 483s Grid dimensions: 161 x 161 x 161 483s Grid spacings: 0.700 x 0.569 x 0.725 483s Grid lengths: 112.000 x 91.000 x 116.000 483s Grid center: (2.518, -2.465, 16.742) 483s Multigrid levels: 4 483s Molecule ID: 2 483s Nonlinear traditional PBE 483s Boundary conditions from focusing 483s 2 ion species (0.050 M ionic strength): 483s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 483s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 483s Solute dielectric: 2.000 483s Solvent dielectric: 78.400 483s Using "molecular" surface definition; no smoothing 483s Solvent probe radius: 1.400 A 483s Temperature: 298.150 K 483s Electrostatic energies will be calculated 483s Total electrostatic energy = 2.915468859278E+05 kJ/mol 483s Calculating forces... 483s ---------------------------------------- 483s CALCULATION #5 (complex): MULTIGRID 483s Setting up problem... 483s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 483s Debye length: 13.5959 A 483s Current memory usage: 1018.381 MB total, 1997.252 MB high water 483s Using linear spline charge discretization. 483s Grid dimensions: 161 x 161 x 161 483s Grid spacings: 0.975 x 0.756 x 1.012 483s Grid lengths: 156.000 x 121.000 x 162.000 483s Grid center: (2.518, -2.465, 16.742) 483s Multigrid levels: 4 483s Molecule ID: 3 483s Nonlinear traditional PBE 483s Single Debye-Huckel sphere boundary conditions 483s 2 ion species (0.050 M ionic strength): 483s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 483s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 483s Solute dielectric: 2.000 483s Solvent dielectric: 78.400 483s Using "molecular" surface definition; no smoothing 483s Solvent probe radius: 1.400 A 483s Temperature: 298.150 K 483s Electrostatic energies will be calculated 483s Total electrostatic energy = 3.056317807611E+05 kJ/mol 483s Calculating forces... 483s ---------------------------------------- 483s CALCULATION #6 (complex): MULTIGRID 483s Setting up problem... 483s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 483s Debye length: 13.5959 A 483s Current memory usage: 1018.381 MB total, 2013.407 MB high water 483s Using linear spline charge discretization. 483s Grid dimensions: 161 x 161 x 161 483s Grid spacings: 0.700 x 0.569 x 0.725 483s Grid lengths: 112.000 x 91.000 x 116.000 483s Grid center: (2.518, -2.465, 16.742) 483s Multigrid levels: 4 483s Molecule ID: 3 483s Nonlinear traditional PBE 483s Boundary conditions from focusing 483s 2 ion species (0.050 M ionic strength): 483s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 483s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 483s Solute dielectric: 2.000 483s Solvent dielectric: 78.400 483s Using "molecular" surface definition; no smoothing 483s Solvent probe radius: 1.400 A 483s Temperature: 298.150 K 483s Electrostatic energies will be calculated 483s Total electrostatic energy = 5.836028296532E+05 kJ/mol 483s Calculating forces... 483s ---------------------------------------- 483s PRINT STATEMENTS 483s 483s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 483s Local net energy (PE 0) = 1.048683058628E+02 kJ/mol 483s Global net ELEC energy = 1.048683058628E+02 kJ/mol 483s ---------------------------------------- 483s CLEANING UP AND SHUTTING DOWN... 483s Destroying force arrays. 483s No energy arrays to destroy. 483s Destroying multigrid structures. 483s Destroying finite element structures. 483s Destroying 3 molecules 483s Final memory usage: 0.001 MB total, 2013.407 MB high water 483s 483s 483s Thanks for using APBS! 483s 607s Checking for intermediate energies in input file apbs-mol-auto.out 607s EXPECTED COMPUTED: 7 607s EXPECTED EXPECTED: 7 607s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058628] 607s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 607s COMPUTED RESULT 152761.7850342 607s COMPUTED RESULT 291951.0754196 607s COMPUTED RESULT 152767.184488 607s COMPUTED RESULT 291546.8859278 607s COMPUTED RESULT 305631.7807611 607s COMPUTED RESULT 583602.8296532 607s COMPUTED RESULT 104.8683058628 607s BINARY: /usr/bin/apbs 607s INPUT: apbs-smol-auto.in 607s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 607s asc_getToken: Error occurred (bailing out). 607s Vio_scanf: Format problem with input. 607s 607s 607s ---------------------------------------------------------------------- 607s APBS -- Adaptive Poisson-Boltzmann Solver 607s Version APBS 3.4.1 607s 607s Nathan A. Baker (nathan.baker@pnnl.gov) 607s Pacific Northwest National Laboratory 607s 607s Additional contributing authors listed in the code documentation. 607s 607s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 607s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 607s Northwest Division for the U.S. Department of Energy. 607s 607s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 607s Portions Copyright (c) 2002-2020, Nathan A. Baker. 607s Portions Copyright (c) 1999-2002, The Regents of the University of California. 607s Portions Copyright (c) 1995, Michael Holst. 607s All rights reserved. 607s 607s Redistribution and use in source and binary forms, with or without 607s modification, are permitted provided that the following conditions are met: 607s 607s * Redistributions of source code must retain the above copyright notice, this 607s list of conditions and the following disclaimer. 607s 607s * Redistributions in binary form must reproduce the above copyright notice, 607s this list of conditions and the following disclaimer in the documentation 607s and/or other materials provided with the distribution. 607s 607s * Neither the name of the developer nor the names of its contributors may be 607s used to endorse or promote products derived from this software without 607s specific prior written permission. 607s 607s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 607s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 607s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 607s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 607s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 607s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 607s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 607s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 607s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 607s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 607s ---------------------------------------------------------------------- 607s APBS uses FETK (the Finite Element ToolKit) to solve the 607s Poisson-Boltzmann equation numerically. FETK is a portable collection 607s of finite element modeling class libraries developed by the Michael Holst 607s research group and written in an object-oriented form of C. FEtk is 607s designed to solve general coupled systems of nonlinear partial differential 607s equations using adaptive finite element methods, inexact Newton methods, 607s and algebraic multilevel methods. More information about FEtk may be found 607s at . 607s ---------------------------------------------------------------------- 607s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 607s Aqua is a modified form of the Holst group PMG library 607s which has been modified by Patrice Koehl 607s for improved efficiency and 607s memory usage when solving the Poisson-Boltzmann equation. 607s ---------------------------------------------------------------------- 607s Please cite your use of APBS as: 607s 607s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 607s nanosystems: application to microtubules and the ribosome. Proc. 607s Natl. Acad. Sci. USA 98, 10037-10041 2001. 607s 607s 607s This executable compiled on Jan 3 2025 at 11:01:42 607s 607s Parsing input file apbs-smol-auto.in... 607s rank 0 size 1... 607s Parsed input file. 607s Got paths for 3 molecules 607s Reading PQR-format atom data from mol1.pqr. 607s asc_getToken: Error occurred (bailing out). 607s Vio_scanf: Format problem with input. 607s 5877 atoms 607s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 607s Net charge -1.20e+01 e 607s Reading PQR-format atom data from mol2.pqr. 607s asc_getToken: Error occurred (bailing out). 607s Vio_scanf: Format problem with input. 607s 5877 atoms 607s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 607s Net charge -1.20e+01 e 607s Reading PQR-format atom data from complex.pqr. 607s 11754 atoms 607s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 607s Net charge -2.40e+01 e 607s Preparing to run 6 PBE calculations. 607s ---------------------------------------- 607s CALCULATION #1 (mol1): MULTIGRID 607s Setting up problem... 607s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 607s Debye length: 13.5959 A 607s Current memory usage: 1004.896 MB total, 1004.896 MB high water 607s Using linear spline charge discretization. 607s Grid dimensions: 161 x 161 x 161 607s Grid spacings: 0.975 x 0.756 x 1.012 607s Grid lengths: 156.000 x 121.000 x 162.000 607s Grid center: (2.518, -2.465, 16.742) 607s Multigrid levels: 4 607s Molecule ID: 1 607s Nonlinear traditional PBE 607s Single Debye-Huckel sphere boundary conditions 607s 2 ion species (0.050 M ionic strength): 607s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 607s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 607s Solute dielectric: 2.000 607s Solvent dielectric: 78.400 607s Using "molecular" surface definition;harmonic average smoothing 607s Solvent probe radius: 1.400 A 607s Temperature: 298.150 K 607s Electrostatic energies will be calculated 607s Total electrostatic energy = 1.528632421825E+05 kJ/mol 607s Calculating forces... 607s ---------------------------------------- 607s CALCULATION #2 (mol1): MULTIGRID 607s Setting up problem... 607s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 607s Debye length: 13.5959 A 607s Current memory usage: 1004.896 MB total, 1995.284 MB high water 607s Using linear spline charge discretization. 607s Grid dimensions: 161 x 161 x 161 607s Grid spacings: 0.700 x 0.569 x 0.725 607s Grid lengths: 112.000 x 91.000 x 116.000 607s Grid center: (2.518, -2.465, 16.742) 607s Multigrid levels: 4 607s Molecule ID: 1 607s Nonlinear traditional PBE 607s Boundary conditions from focusing 607s 2 ion species (0.050 M ionic strength): 607s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 607s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 607s Solute dielectric: 2.000 607s Solvent dielectric: 78.400 607s Using "molecular" surface definition;harmonic average smoothing 607s Solvent probe radius: 1.400 A 607s Temperature: 298.150 K 607s Electrostatic energies will be calculated 607s Total electrostatic energy = 2.920618662320E+05 kJ/mol 607s Calculating forces... 607s ---------------------------------------- 607s CALCULATION #3 (mol2): MULTIGRID 607s Setting up problem... 607s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 607s Debye length: 13.5959 A 607s Current memory usage: 1005.881 MB total, 1995.284 MB high water 607s Using linear spline charge discretization. 607s Grid dimensions: 161 x 161 x 161 607s Grid spacings: 0.975 x 0.756 x 1.012 607s Grid lengths: 156.000 x 121.000 x 162.000 607s Grid center: (2.518, -2.465, 16.742) 607s Multigrid levels: 4 607s Molecule ID: 2 607s Nonlinear traditional PBE 607s Single Debye-Huckel sphere boundary conditions 607s 2 ion species (0.050 M ionic strength): 607s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 607s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 607s Solute dielectric: 2.000 607s Solvent dielectric: 78.400 607s Using "molecular" surface definition;harmonic average smoothing 607s Solvent probe radius: 1.400 A 607s Temperature: 298.150 K 607s Electrostatic energies will be calculated 607s Total electrostatic energy = 1.529297900572E+05 kJ/mol 607s Calculating forces... 607s ---------------------------------------- 607s CALCULATION #4 (mol2): MULTIGRID 607s Setting up problem... 607s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 607s Debye length: 13.5959 A 607s Current memory usage: 1005.881 MB total, 1997.252 MB high water 607s Using linear spline charge discretization. 607s Grid dimensions: 161 x 161 x 161 607s Grid spacings: 0.700 x 0.569 x 0.725 607s Grid lengths: 112.000 x 91.000 x 116.000 607s Grid center: (2.518, -2.465, 16.742) 607s Multigrid levels: 4 607s Molecule ID: 2 607s Nonlinear traditional PBE 607s Boundary conditions from focusing 607s 2 ion species (0.050 M ionic strength): 607s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 607s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 607s Solute dielectric: 2.000 607s Solvent dielectric: 78.400 607s Using "molecular" surface definition;harmonic average smoothing 607s Solvent probe radius: 1.400 A 607s Temperature: 298.150 K 607s Electrostatic energies will be calculated 607s Total electrostatic energy = 2.916592202835E+05 kJ/mol 607s Calculating forces... 607s ---------------------------------------- 607s CALCULATION #5 (complex): MULTIGRID 607s Setting up problem... 607s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 607s Debye length: 13.5959 A 607s Current memory usage: 1018.381 MB total, 1997.252 MB high water 607s Using linear spline charge discretization. 607s Grid dimensions: 161 x 161 x 161 607s Grid spacings: 0.975 x 0.756 x 1.012 607s Grid lengths: 156.000 x 121.000 x 162.000 607s Grid center: (2.518, -2.465, 16.742) 607s Multigrid levels: 4 607s Molecule ID: 3 607s Nonlinear traditional PBE 607s Single Debye-Huckel sphere boundary conditions 607s 2 ion species (0.050 M ionic strength): 607s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 607s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 607s Solute dielectric: 2.000 607s Solvent dielectric: 78.400 607s Using "molecular" surface definition;harmonic average smoothing 607s Solvent probe radius: 1.400 A 607s Temperature: 298.150 K 607s Electrostatic energies will be calculated 607s Total electrostatic energy = 3.059244262535E+05 kJ/mol 607s Calculating forces... 607s ---------------------------------------- 607s CALCULATION #6 (complex): MULTIGRID 607s Setting up problem... 607s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 607s Debye length: 13.5959 A 607s Current memory usage: 1018.381 MB total, 2013.407 MB high water 607s Using linear spline charge discretization. 607s Grid dimensions: 161 x 161 x 161 607s Grid spacings: 0.700 x 0.569 x 0.725 607s Grid lengths: 112.000 x 91.000 x 116.000 607s Grid center: (2.518, -2.465, 16.742) 607s Multigrid levels: 4 607s Molecule ID: 3 607s Nonlinear traditional PBE 607s Boundary conditions from focusing 607s 2 ion species (0.050 M ionic strength): 607s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 607s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 607s Solute dielectric: 2.000 607s Solvent dielectric: 78.400 607s Using "molecular" surface definition;harmonic average smoothing 607s Solvent probe radius: 1.400 A 607s Temperature: 298.150 K 607s Electrostatic energies will be calculated 607s Total electrostatic energy = 5.838306706232E+05 kJ/mol 607s Calculating forces... 607s ---------------------------------------- 607s PRINT STATEMENTS 607s 607s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 607s Local net energy (PE 0) = 1.095841077691E+02 kJ/mol 607s Global net ELEC energy = 1.095841077691E+02 kJ/mol 607s ---------------------------------------- 607s CLEANING UP AND SHUTTING DOWN... 607s Destroying force arrays. 607s No energy arrays to destroy. 607s Destroying multigrid structures. 607s Destroying finite element structures. 607s Destroying 3 molecules 607s Final memory usage: 0.001 MB total, 2013.407 MB high water 607s 607s 607s Thanks for using APBS! 607s 607s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 607s *** PASSED *** 607s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 607s *** PASSED *** 607s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 607s *** PASSED *** 607s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 607s *** PASSED *** 607s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 607s *** PASSED *** 607s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 607s *** PASSED *** 607s Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) 607s *** PASSED *** 607s Elapsed time: 123.536769 seconds 607s -------------------------------------------------------------------------------- 607s Total elapsed time: 305.517981 seconds 607s Test results have been logged 607s -------------------------------------------------------------------------------- 607s -------------------------------------------------------------------------------- 607s Testing input file alkanes.in 607s 620s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 620s *** PASSED *** 620s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 620s *** PASSED *** 620s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 620s *** PASSED *** 620s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 620s *** PASSED *** 620s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 620s *** PASSED *** 620s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 620s *** PASSED *** 620s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 620s *** PASSED *** 620s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 620s *** PASSED *** 620s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 620s *** PASSED *** 620s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 620s *** PASSED *** 620s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 620s *** PASSED *** 620s Elapsed time: 12.758338 seconds 620s -------------------------------------------------------------------------------- 620s Total elapsed time: 12.758338 seconds 620s Test results have been logged 620s -------------------------------------------------------------------------------- 620s -------------------------------------------------------------------------------- 620s Testing input file 1d7h-dmso-mol.in 620s 620s Checking for intermediate energies in input file apbs-smol-auto.out 620s EXPECTED COMPUTED: 7 620s EXPECTED EXPECTED: 7 620s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] 620s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 620s COMPUTED RESULT 152863.2421825 620s COMPUTED RESULT 292061.866232 620s COMPUTED RESULT 152929.7900572 620s COMPUTED RESULT 291659.2202835 620s COMPUTED RESULT 305924.4262535 620s COMPUTED RESULT 583830.6706232 620s COMPUTED RESULT 109.5841077691 620s Running tests for alkanes section 620s BINARY: /usr/bin/apbs 620s INPUT: alkanes.in 620s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 620s 620s ---------------------------------------------------------------------- 620s APBS -- Adaptive Poisson-Boltzmann Solver 620s Version APBS 3.4.1 620s 620s Nathan A. Baker (nathan.baker@pnnl.gov) 620s Pacific Northwest National Laboratory 620s 620s Additional contributing authors listed in the code documentation. 620s 620s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 620s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 620s Northwest Division for the U.S. Department of Energy. 620s 620s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 620s Portions Copyright (c) 2002-2020, Nathan A. Baker. 620s Portions Copyright (c) 1999-2002, The Regents of the University of California. 620s Portions Copyright (c) 1995, Michael Holst. 620s All rights reserved. 620s 620s Redistribution and use in source and binary forms, with or without 620s modification, are permitted provided that the following conditions are met: 620s 620s * Redistributions of source code must retain the above copyright notice, this 620s list of conditions and the following disclaimer. 620s 620s * Redistributions in binary form must reproduce the above copyright notice, 620s this list of conditions and the following disclaimer in the documentation 620s and/or other materials provided with the distribution. 620s 620s * Neither the name of the developer nor the names of its contributors may be 620s used to endorse or promote products derived from this software without 620s specific prior written permission. 620s 620s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 620s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 620s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 620s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 620s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 620s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 620s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 620s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 620s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 620s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 620s ---------------------------------------------------------------------- 620s APBS uses FETK (the Finite Element ToolKit) to solve the 620s Poisson-Boltzmann equation numerically. FETK is a portable collection 620s of finite element modeling class libraries developed by the Michael Holst 620s research group and written in an object-oriented form of C. FEtk is 620s designed to solve general coupled systems of nonlinear partial differential 620s equations using adaptive finite element methods, inexact Newton methods, 620s and algebraic multilevel methods. More information about FEtk may be found 620s at . 620s ---------------------------------------------------------------------- 620s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 620s Aqua is a modified form of the Holst group PMG library 620s which has been modified by Patrice Koehl 620s for improved efficiency and 620s memory usage when solving the Poisson-Boltzmann equation. 620s ---------------------------------------------------------------------- 620s Please cite your use of APBS as: 620s 620s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 620s nanosystems: application to microtubules and the ribosome. Proc. 620s Natl. Acad. Sci. USA 98, 10037-10041 2001. 620s 620s 620s This executable compiled on Jan 3 2025 at 11:01:42 620s 620s Parsing input file alkanes.in... 620s rank 0 size 1... 620s Parsed input file. 620s Reading parameter data from parm.dat. 620s Got paths for 11 molecules 620s Reading PDB-format atom data from 2-methylbutane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 17 atoms 620s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 620s Net charge 4.33e+00 e 620s Reading PDB-format atom data from butane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 14 atoms 620s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 620s Net charge 3.51e+00 e 620s Reading PDB-format atom data from cyclohexane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 18 atoms 620s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 620s Net charge 4.93e+00 e 620s Reading PDB-format atom data from cyclopentane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 13 atoms 620s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 620s Net charge 3.88e+00 e 620s Reading PDB-format atom data from ethane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 8 atoms 620s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 620s Net charge 1.87e+00 e 620s Reading PDB-format atom data from hexane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 20 atoms 620s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 620s Net charge 5.16e+00 e 620s Reading PDB-format atom data from isobutane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 14 atoms 620s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 620s Net charge 3.51e+00 e 620s Reading PDB-format atom data from methane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 5 atoms 620s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 620s Net charge 1.05e+00 e 620s Reading PDB-format atom data from neopentane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 17 atoms 620s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 620s Net charge 4.33e+00 e 620s Reading PDB-format atom data from pentane.pdb. 620s asc_getToken: Error occurred (bailing out). 620s Vio_scanf: Format problem with input. 620s 17 atoms 620s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 620s Net charge 4.33e+00 e 620s Reading PDB-format atom data from propane.pdb. 620s 11 atoms 620s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 620s Net charge 2.69e+00 e 620s Preparing to run 11 PBE calculations. 620s ---------------------------------------- 620s CALCULATION #1 (solvated-2-methylbutane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 3.815624614267E+00 620s SASA for atom 1: 0.000000000000E+00 620s SASA for atom 2: 6.122920124655E-01 620s SASA for atom 3: 3.957497153740E+00 620s SASA for atom 4: 4.308445014544E+00 620s SASA for atom 5: 1.843264951960E+01 620s SASA for atom 6: 1.837011296483E+01 620s SASA for atom 7: 1.666599184724E+01 620s SASA for atom 8: 1.480031796315E+01 620s SASA for atom 9: 1.603020354037E+01 620s SASA for atom 10: 1.473778140838E+01 620s SASA for atom 11: 1.611879699297E+01 620s SASA for atom 12: 1.810954398660E+01 620s SASA for atom 13: 1.420100931324E+01 620s SASA for atom 14: 1.437298483886E+01 620s SASA for atom 15: 1.814081226399E+01 620s SASA for atom 16: 2.152820898091E+01 620s 620s Total solvent accessible surface area: 214.202 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 3.243280922127E-02 620s Surface tension*area energy for atom 1: 0.000000000000E+00 620s Surface tension*area energy for atom 2: 5.204482105957E-03 620s Surface tension*area energy for atom 3: 3.363872580679E-02 620s Surface tension*area energy for atom 4: 3.662178262362E-02 620s Surface tension*area energy for atom 5: 1.566775209166E-01 620s Surface tension*area energy for atom 6: 1.561459602010E-01 620s Surface tension*area energy for atom 7: 1.416609307015E-01 620s Surface tension*area energy for atom 8: 1.258027026868E-01 620s Surface tension*area energy for atom 9: 1.362567300932E-01 620s Surface tension*area energy for atom 10: 1.252711419712E-01 620s Surface tension*area energy for atom 11: 1.370097744402E-01 620s Surface tension*area energy for atom 12: 1.539311238861E-01 620s Surface tension*area energy for atom 13: 1.207085791625E-01 620s Surface tension*area energy for atom 14: 1.221703711303E-01 620s Surface tension*area energy for atom 15: 1.541969042439E-01 620s Surface tension*area energy for atom 16: 1.829897763377E-01 620s 620s Total surface tension energy: 1.82072 kJ/mol 620s 620s Total solvent accessible volume: 253.665 A^3 620s 620s Total pressure*volume energy: 60.7274 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.271287875274E+00 620s WCA energy for atom 1: -5.600872869478E+00 620s WCA energy for atom 2: -5.773775123943E+00 620s WCA energy for atom 3: -6.072801488986E+00 620s WCA energy for atom 4: -6.378470721845E+00 620s WCA energy for atom 5: -1.573474558351E+00 620s WCA energy for atom 6: -1.582338715648E+00 620s WCA energy for atom 7: -1.504044838266E+00 620s WCA energy for atom 8: -1.351002262819E+00 620s WCA energy for atom 9: -1.437367175239E+00 620s WCA energy for atom 10: -1.384626257493E+00 620s WCA energy for atom 11: -1.468867560891E+00 620s WCA energy for atom 12: -1.557005662832E+00 620s WCA energy for atom 13: -1.473759654043E+00 620s WCA energy for atom 14: -1.502261431335E+00 620s WCA energy for atom 15: -1.550940901474E+00 620s WCA energy for atom 16: -1.667828659696E+00 620s 620s Total WCA energy: -48.1507 kJ/mol 620s 620s Total non-polar energy = 1.439739455792E+01 kJ/mol 620s ---------------------------------------- 620s CALCULATION #2 (solvated-butane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 4.405515699447E+00 620s SASA for atom 1: 8.213673337951E-01 620s SASA for atom 2: 8.064333822716E-01 620s SASA for atom 3: 4.375647796400E+00 620s SASA for atom 4: 1.855251124959E+01 620s SASA for atom 5: 2.147609518526E+01 620s SASA for atom 6: 1.852645435176E+01 620s SASA for atom 7: 1.660345529247E+01 620s SASA for atom 8: 1.658782115377E+01 620s SASA for atom 9: 1.658260977421E+01 620s SASA for atom 10: 1.658260977421E+01 620s SASA for atom 11: 2.145003828744E+01 620s SASA for atom 12: 1.852124297220E+01 620s SASA for atom 13: 1.856293400871E+01 620s 620s Total solvent accessible surface area: 193.855 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 3.744688344530E-02 620s Surface tension*area energy for atom 1: 6.981622337259E-03 620s Surface tension*area energy for atom 2: 6.854683749309E-03 620s Surface tension*area energy for atom 3: 3.719300626940E-02 620s Surface tension*area energy for atom 4: 1.576963456215E-01 620s Surface tension*area energy for atom 5: 1.825468090747E-01 620s Surface tension*area energy for atom 6: 1.574748619900E-01 620s Surface tension*area energy for atom 7: 1.411293699860E-01 620s Surface tension*area energy for atom 8: 1.409964798071E-01 620s Surface tension*area energy for atom 9: 1.409521830808E-01 620s Surface tension*area energy for atom 10: 1.409521830808E-01 620s Surface tension*area energy for atom 11: 1.823253254433E-01 620s Surface tension*area energy for atom 12: 1.574305652637E-01 620s Surface tension*area energy for atom 13: 1.577849390741E-01 620s 620s Total surface tension energy: 1.64777 kJ/mol 620s 620s Total solvent accessible volume: 217.863 A^3 620s 620s Total pressure*volume energy: 52.1564 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.728858147814E+00 620s WCA energy for atom 1: -6.204037472587E+00 620s WCA energy for atom 2: -6.202937735018E+00 620s WCA energy for atom 3: -6.728762249931E+00 620s WCA energy for atom 4: -1.623549989062E+00 620s WCA energy for atom 5: -1.709092300778E+00 620s WCA energy for atom 6: -1.625196457114E+00 620s WCA energy for atom 7: -1.484289341167E+00 620s WCA energy for atom 8: -1.485410538626E+00 620s WCA energy for atom 9: -1.485593139015E+00 620s WCA energy for atom 10: -1.484878734279E+00 620s WCA energy for atom 11: -1.708585062695E+00 620s WCA energy for atom 12: -1.625094916482E+00 620s WCA energy for atom 13: -1.624416805392E+00 620s 620s Total WCA energy: -41.7207 kJ/mol 620s 620s Total non-polar energy = 1.208346456826E+01 kJ/mol 620s ---------------------------------------- 620s CALCULATION #3 (solvated-cyclohexane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 7.840324549863E-01 620s SASA for atom 1: 8.064333822716E-01 620s SASA for atom 2: 8.288343095569E-01 620s SASA for atom 3: 7.840324549863E-01 620s SASA for atom 4: 7.989664065098E-01 620s SASA for atom 5: 8.363012853187E-01 620s SASA for atom 6: 2.001169752764E+01 620s SASA for atom 7: 1.616048802948E+01 620s SASA for atom 8: 2.001169752764E+01 620s SASA for atom 9: 1.619175630687E+01 620s SASA for atom 10: 1.616048802948E+01 620s SASA for atom 11: 1.993352683418E+01 620s SASA for atom 12: 2.001169752764E+01 620s SASA for atom 13: 1.618133354774E+01 620s SASA for atom 14: 1.617091078861E+01 620s SASA for atom 15: 2.001690890721E+01 620s SASA for atom 16: 1.993873821374E+01 620s SASA for atom 17: 1.617091078861E+01 620s 620s Total solvent accessible surface area: 221.799 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 6.664275867383E-03 620s Surface tension*area energy for atom 1: 6.854683749309E-03 620s Surface tension*area energy for atom 2: 7.045091631234E-03 620s Surface tension*area energy for atom 3: 6.664275867383E-03 620s Surface tension*area energy for atom 4: 6.791214455333E-03 620s Surface tension*area energy for atom 5: 7.108560925209E-03 620s Surface tension*area energy for atom 6: 1.700994289850E-01 620s Surface tension*area energy for atom 7: 1.373641482506E-01 620s Surface tension*area energy for atom 8: 1.700994289850E-01 620s Surface tension*area energy for atom 9: 1.376299286084E-01 620s Surface tension*area energy for atom 10: 1.373641482506E-01 620s Surface tension*area energy for atom 11: 1.694349780905E-01 620s Surface tension*area energy for atom 12: 1.700994289850E-01 620s Surface tension*area energy for atom 13: 1.375413351558E-01 620s Surface tension*area energy for atom 14: 1.374527417032E-01 620s Surface tension*area energy for atom 15: 1.701437257113E-01 620s Surface tension*area energy for atom 16: 1.694792748168E-01 620s Surface tension*area energy for atom 17: 1.374527417032E-01 620s 620s Total surface tension energy: 1.88529 kJ/mol 620s 620s Total solvent accessible volume: 267.435 A^3 620s 620s Total pressure*volume energy: 64.0239 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -5.793234697241E+00 620s WCA energy for atom 1: -5.784370526583E+00 620s WCA energy for atom 2: -5.791799130412E+00 620s WCA energy for atom 3: -5.788504399087E+00 620s WCA energy for atom 4: -5.797319672490E+00 620s WCA energy for atom 5: -5.787358035342E+00 620s WCA energy for atom 6: -1.523887929614E+00 620s WCA energy for atom 7: -1.413678912317E+00 620s WCA energy for atom 8: -1.521751604392E+00 620s WCA energy for atom 9: -1.414741802525E+00 620s WCA energy for atom 10: -1.413367854344E+00 620s WCA energy for atom 11: -1.523407238081E+00 620s WCA energy for atom 12: -1.523000623583E+00 620s WCA energy for atom 13: -1.413922068538E+00 620s WCA energy for atom 14: -1.416316744211E+00 620s WCA energy for atom 15: -1.524577474659E+00 620s WCA energy for atom 16: -1.523300410052E+00 620s WCA energy for atom 17: -1.414522566061E+00 620s 620s Total WCA energy: -52.3691 kJ/mol 620s 620s Total non-polar energy = 1.354016672221E+01 kJ/mol 620s ---------------------------------------- 620s CALCULATION #4 (solvated-cyclopentane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 9.490526193215E+00 620s SASA for atom 1: 9.512927120500E+00 620s SASA for atom 2: 2.299828534626E+00 620s SASA for atom 3: 1.919012770776E+00 620s SASA for atom 4: 2.307295510388E+00 620s SASA for atom 5: 2.325838699632E+01 620s SASA for atom 6: 2.325838699632E+01 620s SASA for atom 7: 2.045987617019E+01 620s SASA for atom 8: 2.067875411190E+01 620s SASA for atom 9: 2.028790064456E+01 620s SASA for atom 10: 1.897463299431E+01 620s SASA for atom 11: 2.048593306801E+01 620s SASA for atom 12: 2.070481100972E+01 620s 620s Total solvent accessible surface area: 193.638 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 8.066947264233E-02 620s Surface tension*area energy for atom 1: 8.085988052425E-02 620s Surface tension*area energy for atom 2: 1.954854254432E-02 620s Surface tension*area energy for atom 3: 1.631160855160E-02 620s Surface tension*area energy for atom 4: 1.961201183830E-02 620s Surface tension*area energy for atom 5: 1.976962894687E-01 620s Surface tension*area energy for atom 6: 1.976962894687E-01 620s Surface tension*area energy for atom 7: 1.739089474466E-01 620s Surface tension*area energy for atom 8: 1.757694099511E-01 620s Surface tension*area energy for atom 9: 1.724471554788E-01 620s Surface tension*area energy for atom 10: 1.612843804516E-01 620s Surface tension*area energy for atom 11: 1.741304310781E-01 620s Surface tension*area energy for atom 12: 1.759908935826E-01 620s 620s Total surface tension energy: 1.64593 kJ/mol 620s 620s Total solvent accessible volume: 217.998 A^3 620s 620s Total pressure*volume energy: 52.1887 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.343496616804E+00 620s WCA energy for atom 1: -6.327869601807E+00 620s WCA energy for atom 2: -6.334858040579E+00 620s WCA energy for atom 3: -6.296075406417E+00 620s WCA energy for atom 4: -6.345600816761E+00 620s WCA energy for atom 5: -1.663697465126E+00 620s WCA energy for atom 6: -1.662444032853E+00 620s WCA energy for atom 7: -1.572325104493E+00 620s WCA energy for atom 8: -1.604626551065E+00 620s WCA energy for atom 9: -1.586431484963E+00 620s WCA energy for atom 10: -1.554291291374E+00 620s WCA energy for atom 11: -1.574315220751E+00 620s WCA energy for atom 12: -1.604941679892E+00 620s 620s Total WCA energy: -44.471 kJ/mol 620s 620s Total non-polar energy = 9.363673200142E+00 kJ/mol 620s ---------------------------------------- 620s CALCULATION #5 (solvated-ethane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 5.995981536705E+00 620s SASA for atom 1: 5.966113633657E+00 620s SASA for atom 2: 2.121552620704E+01 620s SASA for atom 3: 2.124158310486E+01 620s SASA for atom 4: 2.125200586399E+01 620s SASA for atom 5: 2.123116034573E+01 620s SASA for atom 6: 2.125200586399E+01 620s SASA for atom 7: 2.127285138225E+01 620s 620s Total solvent accessible surface area: 139.427 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 5.096584306199E-02 620s Surface tension*area energy for atom 1: 5.071196588609E-02 620s Surface tension*area energy for atom 2: 1.803319727598E-01 620s Surface tension*area energy for atom 3: 1.805534563913E-01 620s Surface tension*area energy for atom 4: 1.806420498439E-01 620s Surface tension*area energy for atom 5: 1.804648629387E-01 620s Surface tension*area energy for atom 6: 1.806420498439E-01 620s Surface tension*area energy for atom 7: 1.808192367491E-01 620s 620s Total surface tension energy: 1.18513 kJ/mol 620s 620s Total solvent accessible volume: 140.346 A^3 620s 620s Total pressure*volume energy: 33.5988 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -7.360066353115E+00 620s WCA energy for atom 1: -7.355483516201E+00 620s WCA energy for atom 2: -1.776106201066E+00 620s WCA energy for atom 3: -1.773973940651E+00 620s WCA energy for atom 4: -1.775401936843E+00 620s WCA energy for atom 5: -1.773464835521E+00 620s WCA energy for atom 6: -1.774382856097E+00 620s WCA energy for atom 7: -1.772366599434E+00 620s 620s Total WCA energy: -25.3612 kJ/mol 620s 620s Total non-polar energy = 9.422717598546E+00 kJ/mol 620s ---------------------------------------- 620s CALCULATION #6 (solvated-hexane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 4.405515699447E+00 620s SASA for atom 1: 8.213673337951E-01 620s SASA for atom 2: 3.285469335181E-01 620s SASA for atom 3: 2.986790304710E-01 620s SASA for atom 4: 1.855251124959E+01 620s SASA for atom 5: 2.147609518526E+01 620s SASA for atom 6: 1.852645435176E+01 620s SASA for atom 7: 1.655655287639E+01 620s SASA for atom 8: 1.655134149682E+01 620s SASA for atom 9: 1.360170066332E+01 620s SASA for atom 10: 1.357043238593E+01 620s SASA for atom 11: 1.381536722546E+01 620s SASA for atom 12: 1.384142412329E+01 620s SASA for atom 13: 7.765654792245E-01 620s SASA for atom 14: 1.684839013200E+01 620s SASA for atom 15: 1.682233323417E+01 620s SASA for atom 16: 4.166572475070E+00 620s SASA for atom 17: 2.179398933870E+01 620s SASA for atom 18: 1.877660057086E+01 620s SASA for atom 19: 1.876096643216E+01 620s 620s Total solvent accessible surface area: 250.291 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 3.744688344530E-02 620s Surface tension*area energy for atom 1: 6.981622337259E-03 620s Surface tension*area energy for atom 2: 2.792648934903E-03 620s Surface tension*area energy for atom 3: 2.538771759003E-03 620s Surface tension*area energy for atom 4: 1.576963456215E-01 620s Surface tension*area energy for atom 5: 1.825468090747E-01 620s Surface tension*area energy for atom 6: 1.574748619900E-01 620s Surface tension*area energy for atom 7: 1.407306994493E-01 620s Surface tension*area energy for atom 8: 1.406864027230E-01 620s Surface tension*area energy for atom 9: 1.156144556382E-01 620s Surface tension*area energy for atom 10: 1.153486752804E-01 620s Surface tension*area energy for atom 11: 1.174306214164E-01 620s Surface tension*area energy for atom 12: 1.176521050479E-01 620s Surface tension*area energy for atom 13: 6.600806573408E-03 620s Surface tension*area energy for atom 14: 1.432113161220E-01 620s Surface tension*area energy for atom 15: 1.429898324905E-01 620s Surface tension*area energy for atom 16: 3.541586603809E-02 620s Surface tension*area energy for atom 17: 1.852489093789E-01 620s Surface tension*area energy for atom 18: 1.596011048523E-01 620s Surface tension*area energy for atom 19: 1.594682146734E-01 620s 620s Total surface tension energy: 2.12748 kJ/mol 620s 620s Total solvent accessible volume: 298.053 A^3 620s 620s Total pressure*volume energy: 71.3539 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.635406071935E+00 620s WCA energy for atom 1: -5.957247427848E+00 620s WCA energy for atom 2: -5.524801144538E+00 620s WCA energy for atom 3: -5.522294168859E+00 620s WCA energy for atom 4: -1.605314409440E+00 620s WCA energy for atom 5: -1.701051761776E+00 620s WCA energy for atom 6: -1.606669162773E+00 620s WCA energy for atom 7: -1.442505934938E+00 620s WCA energy for atom 8: -1.443059002759E+00 620s WCA energy for atom 9: -1.328947132810E+00 620s WCA energy for atom 10: -1.328906972440E+00 620s WCA energy for atom 11: -1.331566344214E+00 620s WCA energy for atom 12: -1.328041776815E+00 620s WCA energy for atom 13: -5.937562025661E+00 620s WCA energy for atom 14: -1.442277774427E+00 620s WCA energy for atom 15: -1.442777091510E+00 620s WCA energy for atom 16: -6.602262542378E+00 620s WCA energy for atom 17: -1.698172146664E+00 620s WCA energy for atom 18: -1.600970858835E+00 620s WCA energy for atom 19: -1.600841970217E+00 620s 620s Total WCA energy: -57.0807 kJ/mol 620s 620s Total non-polar energy = 1.640068943201E+01 kJ/mol 620s ---------------------------------------- 620s CALCULATION #7 (solvated-isobutane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 3.464676753463E+00 620s SASA for atom 1: 1.984493338158E+01 620s SASA for atom 2: 1.778643845361E+01 620s SASA for atom 3: 1.671289426332E+01 620s SASA for atom 4: 0.000000000000E+00 620s SASA for atom 5: 3.531879535319E+00 620s SASA for atom 6: 1.673895116114E+01 620s SASA for atom 7: 1.793756846098E+01 620s SASA for atom 8: 1.973549441072E+01 620s SASA for atom 9: 1.710895911022E+01 620s SASA for atom 10: 4.599657069253E+00 620s SASA for atom 11: 1.937069784121E+01 620s SASA for atom 12: 1.654613011726E+01 620s SASA for atom 13: 1.936548646165E+01 620s 620s Total solvent accessible surface area: 192.744 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 2.944975240444E-02 620s Surface tension*area energy for atom 1: 1.686819337434E-01 620s Surface tension*area energy for atom 2: 1.511847268556E-01 620s Surface tension*area energy for atom 3: 1.420596012382E-01 620s Surface tension*area energy for atom 4: 0.000000000000E+00 620s Surface tension*area energy for atom 5: 3.002097605021E-02 620s Surface tension*area energy for atom 6: 1.422810848697E-01 620s Surface tension*area energy for atom 7: 1.524693319183E-01 620s Surface tension*area energy for atom 8: 1.677517024912E-01 620s Surface tension*area energy for atom 9: 1.454261524369E-01 620s Surface tension*area energy for atom 10: 3.909708508865E-02 620s Surface tension*area energy for atom 11: 1.646509316503E-01 620s Surface tension*area energy for atom 12: 1.406421059967E-01 620s Surface tension*area energy for atom 13: 1.646066349240E-01 620s 620s Total surface tension energy: 1.63832 kJ/mol 620s 620s Total solvent accessible volume: 218.943 A^3 620s 620s Total pressure*volume energy: 52.415 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.381016335247E+00 620s WCA energy for atom 1: -1.612317964554E+00 620s WCA energy for atom 2: -1.588013719598E+00 620s WCA energy for atom 3: -1.532162371190E+00 620s WCA energy for atom 4: -5.987950445279E+00 620s WCA energy for atom 5: -6.393089030861E+00 620s WCA energy for atom 6: -1.533454887042E+00 620s WCA energy for atom 7: -1.587650918485E+00 620s WCA energy for atom 8: -1.614083521570E+00 620s WCA energy for atom 9: -1.442402031577E+00 620s WCA energy for atom 10: -6.408813541353E+00 620s WCA energy for atom 11: -1.605830214390E+00 620s WCA energy for atom 12: -1.529385873788E+00 620s WCA energy for atom 13: -1.605662490385E+00 620s 620s Total WCA energy: -40.8218 kJ/mol 620s 620s Total non-polar energy = 1.323144287435E+01 kJ/mol 620s ---------------------------------------- 620s CALCULATION #8 (solvated-methane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 1.231304303117E+01 620s SASA for atom 1: 2.323233009850E+01 620s SASA for atom 2: 2.345641941977E+01 620s SASA for atom 3: 2.377431357320E+01 620s SASA for atom 4: 2.264344420771E+01 620s 620s Total solvent accessible surface area: 105.42 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 1.046608657649E-01 620s Surface tension*area energy for atom 1: 1.974748058372E-01 620s Surface tension*area energy for atom 2: 1.993795650680E-01 620s Surface tension*area energy for atom 3: 2.020816653722E-01 620s Surface tension*area energy for atom 4: 1.924692757655E-01 620s 620s Total surface tension energy: 0.896066 kJ/mol 620s 620s Total solvent accessible volume: 95.985 A^3 620s 620s Total pressure*volume energy: 22.9788 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -8.133807570805E+00 620s WCA energy for atom 1: -1.962181541765E+00 620s WCA energy for atom 2: -1.964078319162E+00 620s WCA energy for atom 3: -1.963015006647E+00 620s WCA energy for atom 4: -1.957425549100E+00 620s 620s Total WCA energy: -15.9805 kJ/mol 620s 620s Total non-polar energy = 7.894367190329E+00 kJ/mol 620s ---------------------------------------- 620s CALCULATION #9 (solvated-neopentane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 2.441701074100E+00 620s SASA for atom 1: 1.663993494942E+01 620s SASA for atom 2: 1.715586152630E+01 620s SASA for atom 3: 1.645753666466E+01 620s SASA for atom 4: 0.000000000000E+00 620s SASA for atom 5: 2.389432243768E+00 620s SASA for atom 6: 1.638457735076E+01 620s SASA for atom 7: 1.667641460637E+01 620s SASA for atom 8: 1.721839808108E+01 620s SASA for atom 9: 2.419300146815E+00 620s SASA for atom 10: 1.640021148945E+01 620s SASA for atom 11: 1.666599184724E+01 620s SASA for atom 12: 1.719234118325E+01 620s SASA for atom 13: 2.449168049862E+00 620s SASA for atom 14: 1.723403221977E+01 620s SASA for atom 15: 1.639500010989E+01 620s SASA for atom 16: 1.663472356985E+01 620s 620s Total solvent accessible surface area: 210.755 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 2.075445912985E-02 620s Surface tension*area energy for atom 1: 1.414394470700E-01 620s Surface tension*area energy for atom 2: 1.458248229736E-01 620s Surface tension*area energy for atom 3: 1.398890616496E-01 620s Surface tension*area energy for atom 4: 0.000000000000E+00 620s Surface tension*area energy for atom 5: 2.031017407203E-02 620s Surface tension*area energy for atom 6: 1.392689074814E-01 620s Surface tension*area energy for atom 7: 1.417495241541E-01 620s Surface tension*area energy for atom 8: 1.463563836891E-01 620s Surface tension*area energy for atom 9: 2.056405124793E-02 620s Surface tension*area energy for atom 10: 1.394017976603E-01 620s Surface tension*area energy for atom 11: 1.416609307015E-01 620s Surface tension*area energy for atom 12: 1.461349000577E-01 620s Surface tension*area energy for atom 13: 2.081792842383E-02 620s Surface tension*area energy for atom 14: 1.464892738680E-01 620s Surface tension*area energy for atom 15: 1.393575009340E-01 620s Surface tension*area energy for atom 16: 1.413951503437E-01 620s 620s Total surface tension energy: 1.79141 kJ/mol 620s 620s Total solvent accessible volume: 251.127 A^3 620s 620s Total pressure*volume energy: 60.1198 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.011082520236E+00 620s WCA energy for atom 1: -1.497367782613E+00 620s WCA energy for atom 2: -1.498546483218E+00 620s WCA energy for atom 3: -1.492562171495E+00 620s WCA energy for atom 4: -5.447325863939E+00 620s WCA energy for atom 5: -6.004516149175E+00 620s WCA energy for atom 6: -1.492776531092E+00 620s WCA energy for atom 7: -1.496078170066E+00 620s WCA energy for atom 8: -1.501529655270E+00 620s WCA energy for atom 9: -5.996267554365E+00 620s WCA energy for atom 10: -1.492194267752E+00 620s WCA energy for atom 11: -1.496027211216E+00 620s WCA energy for atom 12: -1.500561393960E+00 620s WCA energy for atom 13: -6.000218612907E+00 620s WCA energy for atom 14: -1.500859921426E+00 620s WCA energy for atom 15: -1.492908499790E+00 620s WCA energy for atom 16: -1.494057174414E+00 620s 620s Total WCA energy: -47.4149 kJ/mol 620s 620s Total non-polar energy = 1.449633815052E+01 kJ/mol 620s ---------------------------------------- 620s CALCULATION #10 (solvated-pentane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 4.405515699447E+00 620s SASA for atom 1: 8.213673337951E-01 620s SASA for atom 2: 3.285469335181E-01 620s SASA for atom 3: 7.466975761774E-01 620s SASA for atom 4: 1.855251124959E+01 620s SASA for atom 5: 2.147609518526E+01 620s SASA for atom 6: 1.852645435176E+01 620s SASA for atom 7: 1.655655287639E+01 620s SASA for atom 8: 1.655134149682E+01 620s SASA for atom 9: 1.360170066332E+01 620s SASA for atom 10: 1.357043238593E+01 620s SASA for atom 11: 1.685881289113E+01 620s SASA for atom 12: 1.687444702982E+01 620s SASA for atom 13: 4.196440378117E+00 620s SASA for atom 14: 1.881308022781E+01 620s SASA for atom 15: 1.882350298694E+01 620s SASA for atom 16: 2.182004623652E+01 620s 620s Total solvent accessible surface area: 222.524 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 3.744688344530E-02 620s Surface tension*area energy for atom 1: 6.981622337259E-03 620s Surface tension*area energy for atom 2: 2.792648934903E-03 620s Surface tension*area energy for atom 3: 6.346929397508E-03 620s Surface tension*area energy for atom 4: 1.576963456215E-01 620s Surface tension*area energy for atom 5: 1.825468090747E-01 620s Surface tension*area energy for atom 6: 1.574748619900E-01 620s Surface tension*area energy for atom 7: 1.407306994493E-01 620s Surface tension*area energy for atom 8: 1.406864027230E-01 620s Surface tension*area energy for atom 9: 1.156144556382E-01 620s Surface tension*area energy for atom 10: 1.153486752804E-01 620s Surface tension*area energy for atom 11: 1.432999095746E-01 620s Surface tension*area energy for atom 12: 1.434327997535E-01 620s Surface tension*area energy for atom 13: 3.566974321399E-02 620s Surface tension*area energy for atom 14: 1.599111819364E-01 620s Surface tension*area energy for atom 15: 1.599997753890E-01 620s Surface tension*area energy for atom 16: 1.854703930104E-01 620s 620s Total surface tension energy: 1.89145 kJ/mol 620s 620s Total solvent accessible volume: 258.93 A^3 620s 620s Total pressure*volume energy: 61.9878 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.655804319869E+00 620s WCA energy for atom 1: -6.027315962813E+00 620s WCA energy for atom 2: -5.696430965386E+00 620s WCA energy for atom 3: -6.016749084714E+00 620s WCA energy for atom 4: -1.608595384643E+00 620s WCA energy for atom 5: -1.703300955380E+00 620s WCA energy for atom 6: -1.609931495887E+00 620s WCA energy for atom 7: -1.457107525189E+00 620s WCA energy for atom 8: -1.457741620594E+00 620s WCA energy for atom 9: -1.354235498709E+00 620s WCA energy for atom 10: -1.354106470090E+00 620s WCA energy for atom 11: -1.456736412636E+00 620s WCA energy for atom 12: -1.455995435596E+00 620s WCA energy for atom 13: -6.633650611186E+00 620s WCA energy for atom 14: -1.605996088477E+00 620s WCA energy for atom 15: -1.606549890103E+00 620s WCA energy for atom 16: -1.700042300035E+00 620s 620s Total WCA energy: -49.4003 kJ/mol 620s 620s Total non-polar energy = 1.447900211546E+01 kJ/mol 620s ---------------------------------------- 620s CALCULATION #11 (solvated-propane): APOLAR 620s 620s Solvent Accessible Surface Area (SASA) for each atom: 620s SASA for atom 0: 3.173464698754E+00 620s SASA for atom 1: 1.931858404557E+01 620s SASA for atom 2: 2.014198201675E+01 620s SASA for atom 3: 2.149694070352E+01 620s SASA for atom 4: 1.904078819252E+00 620s SASA for atom 5: 2.067354273233E+01 620s SASA for atom 6: 1.937590922077E+01 620s SASA for atom 7: 3.098794941136E+00 620s SASA for atom 8: 1.942802301642E+01 620s SASA for atom 9: 1.973028303116E+01 620s SASA for atom 10: 2.204934693736E+01 620s 620s Total solvent accessible surface area: 170.391 A^2 620s 620s Surface tension*area energies (gamma * SASA) for each atom: 620s Surface tension*area energy for atom 0: 2.697444993941E-02 620s Surface tension*area energy for atom 1: 1.642079643873E-01 620s Surface tension*area energy for atom 2: 1.712068471424E-01 620s Surface tension*area energy for atom 3: 1.827239959799E-01 620s Surface tension*area energy for atom 4: 1.618466996365E-02 620s Surface tension*area energy for atom 5: 1.757251132248E-01 620s Surface tension*area energy for atom 6: 1.646952283766E-01 620s Surface tension*area energy for atom 7: 2.633975699966E-02 620s Surface tension*area energy for atom 8: 1.651381956396E-01 620s Surface tension*area energy for atom 9: 1.677074057649E-01 620s Surface tension*area energy for atom 10: 1.874194489675E-01 620s 620s Total surface tension energy: 1.44832 kJ/mol 620s 620s Total solvent accessible volume: 183.573 A^3 620s 620s Total pressure*volume energy: 43.9474 kJ/mol 620s 620s WCA dispersion Energies for each atom: 620s WCA energy for atom 0: -6.818670105515E+00 620s WCA energy for atom 1: -1.641297645338E+00 620s WCA energy for atom 2: -1.649584120441E+00 620s WCA energy for atom 3: -1.711408141255E+00 620s WCA energy for atom 4: -6.624720142882E+00 620s WCA energy for atom 5: -1.610117050515E+00 620s WCA energy for atom 6: -1.596858009746E+00 620s WCA energy for atom 7: -6.816460624835E+00 620s WCA energy for atom 8: -1.642782751806E+00 620s WCA energy for atom 9: -1.645779566650E+00 620s WCA energy for atom 10: -1.714436154542E+00 620s 620s Total WCA energy: -33.4721 kJ/mol 620s 620s Total non-polar energy = 1.192358496286E+01 kJ/mol 620s ---------------------------------------- 620s PRINT STATEMENTS 620s 620s print APOL energy 1 (solvated-2-methylbutane) end 620s Global net APOL energy = 1.439739455792E+01 kJ/mol 620s 620s print APOL energy 2 (solvated-butane) end 620s Global net APOL energy = 1.208346456826E+01 kJ/mol 620s 620s print APOL energy 3 (solvated-cyclohexane) end 620s Global net APOL energy = 1.354016672221E+01 kJ/mol 620s 620s print APOL energy 4 (solvated-cyclopentane) end 620s Global net APOL energy = 9.363673200142E+00 kJ/mol 620s 620s print APOL energy 5 (solvated-ethane) end 620s Global net APOL energy = 9.422717598546E+00 kJ/mol 620s 620s print APOL energy 6 (solvated-hexane) end 620s Global net APOL energy = 1.640068943201E+01 kJ/mol 620s 620s print APOL energy 7 (solvated-isobutane) end 620s Global net APOL energy = 1.323144287435E+01 kJ/mol 620s 620s print APOL energy 8 (solvated-methane) end 620s Global net APOL energy = 7.894367190329E+00 kJ/mol 620s 620s print APOL energy 9 (solvated-neopentane) end 620s Global net APOL energy = 1.449633815052E+01 kJ/mol 620s 620s print APOL energy 10 (solvated-pentane) end 620s Global net APOL energy = 1.447900211546E+01 kJ/mol 620s 620s print APOL energy 11 (solvated-propane) end 620s Global net APOL energy = 1.192358496286E+01 kJ/mol 620s ---------------------------------------- 620s CLEANING UP AND SHUTTING DOWN... 620s Destroying force arrays. 620s No energy arrays to destroy. 620s Destroying multigrid structures. 620s Destroying finite element structures. 620s Destroying 11 molecules 620s Final memory usage: 0.001 MB total, 2.204 MB high water 620s 620s 620s Thanks for using APBS! 620s 640s Checking for intermediate energies in input file alkanes.out 640s EXPECTED COMPUTED: 11 640s EXPECTED EXPECTED: 11 640s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 640s 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'] 640s COMPUTED RESULT 14.39739455792 640s COMPUTED RESULT 12.08346456826 640s COMPUTED RESULT 13.54016672221 640s COMPUTED RESULT 9.363673200142 640s COMPUTED RESULT 9.422717598546 640s COMPUTED RESULT 16.40068943201 640s COMPUTED RESULT 13.23144287435 640s COMPUTED RESULT 7.894367190329 640s COMPUTED RESULT 14.49633815052 640s COMPUTED RESULT 14.47900211546 640s COMPUTED RESULT 11.92358496286 640s Running tests for FKBP section 640s BINARY: /usr/bin/apbs 640s INPUT: 1d7h-dmso-mol.in 640s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 640s asc_getToken: Error occurred (bailing out). 640s Vio_scanf: Format problem with input. 640s 640s 640s ---------------------------------------------------------------------- 640s APBS -- Adaptive Poisson-Boltzmann Solver 640s Version APBS 3.4.1 640s 640s Nathan A. Baker (nathan.baker@pnnl.gov) 640s Pacific Northwest National Laboratory 640s 640s Additional contributing authors listed in the code documentation. 640s 640s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 640s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 640s Northwest Division for the U.S. Department of Energy. 640s 640s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 640s Portions Copyright (c) 2002-2020, Nathan A. Baker. 640s Portions Copyright (c) 1999-2002, The Regents of the University of California. 640s Portions Copyright (c) 1995, Michael Holst. 640s All rights reserved. 640s 640s Redistribution and use in source and binary forms, with or without 640s modification, are permitted provided that the following conditions are met: 640s 640s * Redistributions of source code must retain the above copyright notice, this 640s list of conditions and the following disclaimer. 640s 640s * Redistributions in binary form must reproduce the above copyright notice, 640s this list of conditions and the following disclaimer in the documentation 640s and/or other materials provided with the distribution. 640s 640s * Neither the name of the developer nor the names of its contributors may be 640s used to endorse or promote products derived from this software without 640s specific prior written permission. 640s 640s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 640s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 640s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 640s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 640s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 640s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 640s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 640s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 640s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 640s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 640s ---------------------------------------------------------------------- 640s APBS uses FETK (the Finite Element ToolKit) to solve the 640s Poisson-Boltzmann equation numerically. FETK is a portable collection 640s of finite element modeling class libraries developed by the Michael Holst 640s research group and written in an object-oriented form of C. FEtk is 640s designed to solve general coupled systems of nonlinear partial differential 640s equations using adaptive finite element methods, inexact Newton methods, 640s and algebraic multilevel methods. More information about FEtk may be found 640s at . 640s ---------------------------------------------------------------------- 640s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 640s Aqua is a modified form of the Holst group PMG library 640s which has been modified by Patrice Koehl 640s for improved efficiency and 640s memory usage when solving the Poisson-Boltzmann equation. 640s ---------------------------------------------------------------------- 640s Please cite your use of APBS as: 640s 640s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 640s nanosystems: application to microtubules and the ribosome. Proc. 640s Natl. Acad. Sci. USA 98, 10037-10041 2001. 640s 640s 640s This executable compiled on Jan 3 2025 at 11:01:42 640s 640s Parsing input file 1d7h-dmso-mol.in... 640s rank 0 size 1... 640s Parsed input file. 640s Got paths for 3 molecules 640s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 640s asc_getToken: Error occurred (bailing out). 640s Vio_scanf: Format problem with input. 640s 1673 atoms 640s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 640s Net charge 9.91e-01 e 640s Reading PQR-format atom data from dmso-min.pqr. 640s asc_getToken: Error occurred (bailing out). 640s Vio_scanf: Format problem with input. 640s 10 atoms 640s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 640s Net charge 2.78e-17 e 640s Reading PQR-format atom data from 1d7h-min.pqr. 640s 1663 atoms 640s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 640s Net charge 9.91e-01 e 640s Preparing to run 12 PBE calculations. 640s ---------------------------------------- 640s CALCULATION #1 (complex-solv-coarse): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 30.4176 A 640s Current memory usage: 102.625 MB total, 102.625 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 1.500 x 1.500 x 1.500 640s Grid lengths: 96.000 x 96.000 x 96.000 640s Grid center: (25.875, 18.349, 19.112) 640s Multigrid levels: 5 640s Molecule ID: 1 640s Linearized traditional PBE 640s Multiple Debye-Huckel sphere boundary conditions 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 78.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 1.060899690259E+04 kJ/mol 640s Calculating forces... 640s [focusFillBound()]: WARNING: 640s Unusually large potential values 640s detected on the focusing boundary! 640s Convergence not guaranteed for NPBE/NRPBE calculations! 640s 640s ---------------------------------------- 640s CALCULATION #2 (complex-solv-fine): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 30.4176 A 640s Current memory usage: 102.625 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 0.225 x 0.225 x 0.225 640s Grid lengths: 14.400 x 14.400 x 14.400 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 1 640s Linearized traditional PBE 640s Boundary conditions from focusing 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 78.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 4.276523673491E+04 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s CALCULATION #3 (complex-ref-coarse): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 4.87072 A 640s Current memory usage: 102.625 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 1.500 x 1.500 x 1.500 640s Grid lengths: 96.000 x 96.000 x 96.000 640s Grid center: (25.875, 18.349, 19.112) 640s Multigrid levels: 5 640s Molecule ID: 1 640s Linearized traditional PBE 640s Multiple Debye-Huckel sphere boundary conditions 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 2.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 1.399234956777E+04 kJ/mol 640s Calculating forces... 640s [focusFillBound()]: WARNING: 640s Unusually large potential values 640s detected on the focusing boundary! 640s Convergence not guaranteed for NPBE/NRPBE calculations! 640s 640s ---------------------------------------- 640s CALCULATION #4 (complex-ref-fine): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 4.87072 A 640s Current memory usage: 102.625 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 0.225 x 0.225 x 0.225 640s Grid lengths: 14.400 x 14.400 x 14.400 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 1 640s Linearized traditional PBE 640s Boundary conditions from focusing 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 2.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 4.610066575192E+04 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 30.4176 A 640s Current memory usage: 62.396 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 1.500 x 1.500 x 1.500 640s Grid lengths: 96.000 x 96.000 x 96.000 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 2 640s Linearized traditional PBE 640s Multiple Debye-Huckel sphere boundary conditions 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 78.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 3.961107503213E+01 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s CALCULATION #6 (dmso-solv-fine): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 30.4176 A 640s Current memory usage: 62.396 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 0.225 x 0.225 x 0.225 640s Grid lengths: 14.400 x 14.400 x 14.400 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 2 640s Linearized traditional PBE 640s Boundary conditions from focusing 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 78.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 7.121048606059E+02 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 4.87072 A 640s Current memory usage: 62.396 MBTesting computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 640s *** PASSED *** 640s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 640s *** PASSED *** 640s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 640s *** PASSED *** 640s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 640s *** PASSED *** 640s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 640s *** PASSED *** 640s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 640s *** PASSED *** 640s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 640s *** PASSED *** 640s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 640s *** PASSED *** 640s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 640s *** PASSED *** 640s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 640s *** PASSED *** 640s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 640s *** PASSED *** 640s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 640s *** PASSED *** 640s Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) 640s *** PASSED *** 640s Elapsed time: 19.89225 seconds 640s -------------------------------------------------------------------------------- 640s -------------------------------------------------------------------------------- 640s Testing input file 1d7h-dmso-smol.in 640s 640s total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 1.500 x 1.500 x 1.500 640s Grid lengths: 96.000 x 96.000 x 96.000 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 2 640s Linearized traditional PBE 640s Multiple Debye-Huckel sphere boundary conditions 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 2.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 6.751571424823E+01 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s CALCULATION #8 (dmso-ref-fine): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 4.87072 A 640s Current memory usage: 62.396 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 0.225 x 0.225 x 0.225 640s Grid lengths: 14.400 x 14.400 x 14.400 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 2 640s Linearized traditional PBE 640s Boundary conditions from focusing 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 2.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 7.339101343121E+02 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 30.4176 A 640s Current memory usage: 102.404 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 1.500 x 1.500 x 1.500 640s Grid lengths: 96.000 x 96.000 x 96.000 640s Grid center: (25.875, 18.349, 19.112) 640s Multigrid levels: 5 640s Molecule ID: 3 640s Linearized traditional PBE 640s Multiple Debye-Huckel sphere boundary conditions 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 78.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 1.058410584089E+04 kJ/mol 640s Calculating forces... 640s [focusFillBound()]: WARNING: 640s Unusually large potential values 640s detected on the focusing boundary! 640s Convergence not guaranteed for NPBE/NRPBE calculations! 640s 640s ---------------------------------------- 640s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 30.4176 A 640s Current memory usage: 102.404 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 0.225 x 0.225 x 0.225 640s Grid lengths: 14.400 x 14.400 x 14.400 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 3 640s Linearized traditional PBE 640s Boundary conditions from focusing 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 78.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 4.205385249581E+04 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 4.87072 A 640s Current memory usage: 102.404 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 1.500 x 1.500 x 1.500 640s Grid lengths: 96.000 x 96.000 x 96.000 640s Grid center: (25.875, 18.349, 19.112) 640s Multigrid levels: 5 640s Molecule ID: 3 640s Linearized traditional PBE 640s Multiple Debye-Huckel sphere boundary conditions 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 2.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 1.395961902233E+04 kJ/mol 640s Calculating forces... 640s [focusFillBound()]: WARNING: 640s Unusually large potential values 640s detected on the focusing boundary! 640s Convergence not guaranteed for NPBE/NRPBE calculations! 640s 640s ---------------------------------------- 640s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 640s Setting up problem... 640s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 640s Debye length: 4.87072 A 640s Current memory usage: 102.404 MB total, 182.834 MB high water 640s Using linear spline charge discretization. 640s Grid dimensions: 65 x 65 x 65 640s Grid spacings: 0.225 x 0.225 x 0.225 640s Grid lengths: 14.400 x 14.400 x 14.400 640s Grid center: (17.751, 17.770, 20.492) 640s Multigrid levels: 5 640s Molecule ID: 3 640s Linearized traditional PBE 640s Boundary conditions from focusing 640s 2 ion species (0.010 M ionic strength): 640s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 640s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 640s Solute dielectric: 2.000 640s Solvent dielectric: 2.000 640s Using "molecular" surface definition; no smoothing 640s Solvent probe radius: 0.000 A 640s Temperature: 300.000 K 640s Electrostatic energies will be calculated 640s Total electrostatic energy = 4.538248433997E+04 kJ/mol 640s Calculating forces... 640s ---------------------------------------- 640s PRINT STATEMENTS 640s 640s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 640s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 640s Global net ELEC energy = -3.335429017008E+03 kJ/mol 640s 640s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 640s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 640s Global net ELEC energy = -2.180527370616E+01 kJ/mol 640s 640s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 640s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 640s Global net ELEC energy = -3.328631844166E+03 kJ/mol 640s 640s 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 640s Local net energy (PE 0) = 1.500810086371E+01 kJ/mol 640s Global net ELEC energy = 1.500810086371E+01 kJ/mol 640s ---------------------------------------- 640s CLEANING UP AND SHUTTING DOWN... 640s Destroying force arrays. 640s No energy arrays to destroy. 640s Destroying multigrid structures. 640s Destroying finite element structures. 640s Destroying 3 molecules 640s Final memory usage: 0.001 MB total, 182.834 MB high water 640s 640s 640s Thanks for using APBS! 640s 656s Checking for intermediate energies in input file 1d7h-dmso-mol.out 656s EXPECTED COMPUTED: 16 656s EXPECTED EXPECTED: 16 656s 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] 656s 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'] 656s COMPUTED RESULT 10608.99690259 656s COMPUTED RESULT 42765.23673491 656s COMPUTED RESULT 13992.34956777 656s COMPUTED RESULT 46100.66575192 656s COMPUTED RESULT 39.61107503213 656s COMPUTED RESULT 712.1048606059 656s COMPUTED RESULT 67.51571424823 656s COMPUTED RESULT 733.9101343121 656s COMPUTED RESULT 10584.10584089 656s COMPUTED RESULT 42053.85249581 656s COMPUTED RESULT 13959.61902233 656s COMPUTED RESULT 45382.48433997 656s COMPUTED RESULT -3335.429017008 656s COMPUTED RESULT -21.80527370616 656s COMPUTED RESULT -3328.631844166 656s COMPUTED RESULT 15.00810086371 656s BINARY: /usr/bin/apbs 656s INPUT: 1d7h-dmso-smol.in 656s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 656s asc_getToken: Error occurred (bailing out). 656s Vio_scanf: Format problem with input. 656s 656s 656s ---------------------------------------------------------------------- 656s APBS -- Adaptive Poisson-Boltzmann Solver 656s Version APBS 3.4.1 656s 656s Nathan A. Baker (nathan.baker@pnnl.gov) 656s Pacific Northwest National Laboratory 656s 656s Additional contributing authors listed in the code documentation. 656s 656s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 656s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 656s Northwest Division for the U.S. Department of Energy. 656s 656s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 656s Portions Copyright (c) 2002-2020, Nathan A. Baker. 656s Portions Copyright (c) 1999-2002, The Regents of the University of California. 656s Portions Copyright (c) 1995, Michael Holst. 656s All rights reserved. 656s 656s Redistribution and use in source and binary forms, with or without 656s modification, are permitted provided that the following conditions are met: 656s 656s * Redistributions of source code must retain the above copyright notice, this 656s list of conditions and the following disclaimer. 656s 656s * Redistributions in binary form must reproduce the above copyright notice, 656s this list of conditions and the following disclaimer in the documentation 656s and/or other materials provided with the distribution. 656s 656s * Neither the name of the developer nor the names of its contributors may be 656s used to endorse or promote products derived from this software without 656s specific prior written permission. 656s 656s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 656s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 656s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 656s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 656s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 656s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 656s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 656s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 656s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 656s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 656s ---------------------------------------------------------------------- 656s APBS uses FETK (the Finite Element ToolKit) to solve the 656s Poisson-Boltzmann equation numerically. FETK is a portable collection 656s of finite element modeling class libraries developed by the Michael Holst 656s research group and written in an object-oriented form of C. FEtk Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 656s *** PASSED *** 656s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 656s *** PASSED *** 656s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 656s *** PASSED *** 656s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 656s *** PASSED *** 656s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 656s *** PASSED *** 656s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 656s *** PASSED *** 656s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 656s *** PASSED *** 656s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 656s *** PASSED *** 656s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 656s *** PASSED *** 656s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 656s *** PASSED *** 656s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 656s *** PASSED *** 656s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 656s *** PASSED *** 656s Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) 656s *** PASSED *** 656s Elapsed time: 16.179755 seconds 656s -------------------------------------------------------------------------------- 656s -------------------------------------------------------------------------------- 656s Testing input file 1d7i-dss-mol.in 656s 656s is 656s designed to solve general coupled systems of nonlinear partial differential 656s equations using adaptive finite element methods, inexact Newton methods, 656s and algebraic multilevel methods. More information about FEtk may be found 656s at . 656s ---------------------------------------------------------------------- 656s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 656s Aqua is a modified form of the Holst group PMG library 656s which has been modified by Patrice Koehl 656s for improved efficiency and 656s memory usage when solving the Poisson-Boltzmann equation. 656s ---------------------------------------------------------------------- 656s Please cite your use of APBS as: 656s 656s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 656s nanosystems: application to microtubules and the ribosome. Proc. 656s Natl. Acad. Sci. USA 98, 10037-10041 2001. 656s 656s 656s This executable compiled on Jan 3 2025 at 11:01:42 656s 656s Parsing input file 1d7h-dmso-smol.in... 656s rank 0 size 1... 656s Parsed input file. 656s Got paths for 3 molecules 656s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 656s asc_getToken: Error occurred (bailing out). 656s Vio_scanf: Format problem with input. 656s 1673 atoms 656s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 656s Net charge 9.91e-01 e 656s Reading PQR-format atom data from dmso-min.pqr. 656s asc_getToken: Error occurred (bailing out). 656s Vio_scanf: Format problem with input. 656s 10 atoms 656s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 656s Net charge 2.78e-17 e 656s Reading PQR-format atom data from 1d7h-min.pqr. 656s 1663 atoms 656s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 656s Net charge 9.91e-01 e 656s Preparing to run 12 PBE calculations. 656s ---------------------------------------- 656s CALCULATION #1 (complex-solv-coarse): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 30.4176 A 656s Current memory usage: 102.625 MB total, 102.625 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 1.500 x 1.500 x 1.500 656s Grid lengths: 96.000 x 96.000 x 96.000 656s Grid center: (25.875, 18.349, 19.112) 656s Multigrid levels: 5 656s Molecule ID: 1 656s Linearized traditional PBE 656s Multiple Debye-Huckel sphere boundary conditions 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 78.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 1.074948704824E+04 kJ/mol 656s Calculating forces... 656s [focusFillBound()]: WARNING: 656s Unusually large potential values 656s detected on the focusing boundary! 656s Convergence not guaranteed for NPBE/NRPBE calculations! 656s 656s ---------------------------------------- 656s CALCULATION #2 (complex-solv-fine): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 30.4176 A 656s Current memory usage: 102.625 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 0.225 x 0.225 x 0.225 656s Grid lengths: 14.400 x 14.400 x 14.400 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 1 656s Linearized traditional PBE 656s Boundary conditions from focusing 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 78.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 4.289487256481E+04 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s CALCULATION #3 (complex-ref-coarse): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 4.87072 A 656s Current memory usage: 102.625 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 1.500 x 1.500 x 1.500 656s Grid lengths: 96.000 x 96.000 x 96.000 656s Grid center: (25.875, 18.349, 19.112) 656s Multigrid levels: 5 656s Molecule ID: 1 656s Linearized traditional PBE 656s Multiple Debye-Huckel sphere boundary conditions 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 2.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 1.399234956777E+04 kJ/mol 656s Calculating forces... 656s [focusFillBound()]: WARNING: 656s Unusually large potential values 656s detected on the focusing boundary! 656s Convergence not guaranteed for NPBE/NRPBE calculations! 656s 656s ---------------------------------------- 656s CALCULATION #4 (complex-ref-fine): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 4.87072 A 656s Current memory usage: 102.625 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 0.225 x 0.225 x 0.225 656s Grid lengths: 14.400 x 14.400 x 14.400 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 1 656s Linearized traditional PBE 656s Boundary conditions from focusing 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 2.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 4.610066575192E+04 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 30.4176 A 656s Current memory usage: 62.396 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 1.500 x 1.500 x 1.500 656s Grid lengths: 96.000 x 96.000 x 96.000 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 2 656s Linearized traditional PBE 656s Multiple Debye-Huckel sphere boundary conditions 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 78.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 3.719709905887E+01 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s CALCULATION #6 (dmso-solv-fine): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 30.4176 A 656s Current memory usage: 62.396 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 0.225 x 0.225 x 0.225 656s Grid lengths: 14.400 x 14.400 x 14.400 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 2 656s Linearized traditional PBE 656s Boundary conditions from focusing 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 78.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 7.125747080979E+02 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 4.87072 A 656s Current memory usage: 62.396 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 1.500 x 1.500 x 1.500 656s Grid lengths: 96.000 x 96.000 x 96.000 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 2 656s Linearized traditional PBE 656s Multiple Debye-Huckel sphere boundary conditions 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 2.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 6.751571424823E+01 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s CALCULATION #8 (dmso-ref-fine): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 4.87072 A 656s Current memory usage: 62.396 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 0.225 x 0.225 x 0.225 656s Grid lengths: 14.400 x 14.400 x 14.400 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 2 656s Linearized traditional PBE 656s Boundary conditions from focusing 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 2.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 7.339101343121E+02 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 30.4176 A 656s Current memory usage: 102.404 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 1.500 x 1.500 x 1.500 656s Grid lengths: 96.000 x 96.000 x 96.000 656s Grid center: (25.875, 18.349, 19.112) 656s Multigrid levels: 5 656s Molecule ID: 3 656s Linearized traditional PBE 656s Multiple Debye-Huckel sphere boundary conditions 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 78.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 1.071654753674E+04 kJ/mol 656s Calculating forces... 656s [focusFillBound()]: WARNING: 656s Unusually large potential values 656s detected on the focusing boundary! 656s Convergence not guaranteed for NPBE/NRPBE calculations! 656s 656s ---------------------------------------- 656s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 30.4176 A 656s Current memory usage: 102.404 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 0.225 x 0.225 x 0.225 656s Grid lengths: 14.400 x 14.400 x 14.400 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 3 656s Linearized traditional PBE 656s Boundary conditions from focusing 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 78.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 4.218178203716E+04 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 4.87072 A 656s Current memory usage: 102.404 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 1.500 x 1.500 x 1.500 656s Grid lengths: 96.000 x 96.000 x 96.000 656s Grid center: (25.875, 18.349, 19.112) 656s Multigrid levels: 5 656s Molecule ID: 3 656s Linearized traditional PBE 656s Multiple Debye-Huckel sphere boundary conditions 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 2.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 1.395961902233E+04 kJ/mol 656s Calculating forces... 656s [focusFillBound()]: WARNING: 656s Unusually large potential values 656s detected on the focusing boundary! 656s Convergence not guaranteed for NPBE/NRPBE calculations! 656s 656s ---------------------------------------- 656s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 656s Setting up problem... 656s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 656s Debye length: 4.87072 A 656s Current memory usage: 102.404 MB total, 182.834 MB high water 656s Using linear spline charge discretization. 656s Grid dimensions: 65 x 65 x 65 656s Grid spacings: 0.225 x 0.225 x 0.225 656s Grid lengths: 14.400 x 14.400 x 14.400 656s Grid center: (17.751, 17.770, 20.492) 656s Multigrid levels: 5 656s Molecule ID: 3 656s Linearized traditional PBE 656s Boundary conditions from focusing 656s 2 ion species (0.010 M ionic strength): 656s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 656s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 656s Solute dielectric: 2.000 656s Solvent dielectric: 2.000 656s Using "molecular" surface definition;harmonic average smoothing 656s Solvent probe radius: 0.000 A 656s Temperature: 300.000 K 656s Electrostatic energies will be calculated 656s Total electrostatic energy = 4.538248433997E+04 kJ/mol 656s Calculating forces... 656s ---------------------------------------- 656s PRINT STATEMENTS 656s 656s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 656s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 656s Global net ELEC energy = -3.205793187109E+03 kJ/mol 656s 656s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 656s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 656s Global net ELEC energy = -2.133542621421E+01 kJ/mol 656s 656s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 656s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 656s Global net ELEC energy = -3.200702302816E+03 kJ/mol 656s 656s 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 656s Local net energy (PE 0) = 1.624454192073E+01 kJ/mol 656s Global net ELEC energy = 1.624454192073E+01 kJ/mol 656s ---------------------------------------- 656s CLEANING UP AND SHUTTING DOWN... 656s Destroying force arrays. 656s No energy arrays to destroy. 656s Destroying multigrid structures. 656s Destroying finite element structures. 656s Destroying 3 molecules 656s Final memory usage: 0.001 MB total, 182.834 MB high water 656s 656s 656s Thanks for using APBS! 656s 676s Checking for intermediate energies in input file 1d7h-dmso-smol.out 676s EXPECTED COMPUTED: 16 676s EXPECTED EXPECTED: 16 676s 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] 676s 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'] 676s COMPUTED RESULT 10749.48704824 676s COMPUTED RESULT 42894.87256481 676s COMPUTED RESULT 13992.34956777 676s COMPUTED RESULT 46100.66575192 676s COMPUTED RESULT 37.19709905887 676s COMPUTED RESULT 712.5747080979 676s COMPUTED RESULT 67.51571424823 676s COMPUTED RESULT 733.9101343121 676s COMPUTED RESULT 10716.54753674 676s COMPUTED RESULT 42181.78203716 676s COMPUTED RESULT 13959.61902233 676s COMPUTED RESULT 45382.48433997 676s COMPUTED RESULT -3205.793187109 676s COMPUTED RESULT -21.33542621421 676s COMPUTED RESULT -3200.702302816 676s COMPUTED RESULT 16.24454192073 676s BINARY: /usr/bin/apbs 676s INPUT: 1d7i-dss-mol.in 676s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 676s asc_getToken: Error occurred (bailing out). 676s Vio_scanf: Format problem with input. 676s 676s 676s ---------------------------------------------------------------------- 676s APBS -- Adaptive Poisson-Boltzmann Solver 676s Version APBS 3.4.1 676s 676s Nathan A. Baker (nathan.baker@pnnl.gov) 676s Pacific Northwest National Laboratory 676s 676s Additional contributing authors listed in the code documentation. 676s 676s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 676s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 676s Northwest Division for the U.S. Department of Energy. 676s 676s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 676s Portions Copyright (c) 2002-2020, Nathan A. Baker. 676s Portions Copyright (c) 1999-2002, The Regents of the University of California. 676s Portions Copyright (c) 1995, Michael Holst. 676s All rights reserved. 676s 676s Redistribution and use in source and binary forms, with or without 676s modification, are permitted provided that the following conditions are met: 676s 676s * Redistributions of source code must retain the above copyright notice, this 676s list of conditions and the following disclaimer. 676s 676s * Redistributions in binary form must reproduce the above copyright notice, 676s this list of conditions and the following disclaimer in the documentation 676s and/or other materials provided with the distribution. 676s 676s * Neither the name of the developer nor the names of its contributors may be 676s used to endorse or promote products derived from this software without 676s specific prior written permission. 676s 676s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 676s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 676s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 676s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 676s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 676s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 676s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 676s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 676s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 676s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 676s ---------------------------------------------------------------------- 676s APBS uses FETK (the Finite Element ToolKit) to solve the 676s Poisson-Boltzmann equation numerically. FETK is a portable collection 676s of finite element modeling class libraries developed by the Michael Holst 676s research group and written in an object-oriented form of C. FEtk is 676s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 676s *** PASSED *** 676s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 676s *** PASSED *** 676s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 676s *** PASSED *** 676s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 676s *** PASSED *** 676s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 676s *** PASSED *** 676s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 676s *** PASSED *** 676s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 676s *** PASSED *** 676s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 676s *** PASSED *** 676s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 676s *** PASSED *** 676s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 676s *** PASSED *** 676s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 676s *** PASSED *** 676s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 676s *** PASSED *** 676s Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) 676s *** PASSED *** 676s Elapsed time: 20.106743 seconds 676s -------------------------------------------------------------------------------- 676s -------------------------------------------------------------------------------- 676s Testing input file 1d7i-dss-smol.in 676s 676s designed to solve general coupled systems of nonlinear partial differential 676s equations using adaptive finite element methods, inexact Newton methods, 676s and algebraic multilevel methods. More information about FEtk may be found 676s at . 676s ---------------------------------------------------------------------- 676s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 676s Aqua is a modified form of the Holst group PMG library 676s which has been modified by Patrice Koehl 676s for improved efficiency and 676s memory usage when solving the Poisson-Boltzmann equation. 676s ---------------------------------------------------------------------- 676s Please cite your use of APBS as: 676s 676s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 676s nanosystems: application to microtubules and the ribosome. Proc. 676s Natl. Acad. Sci. USA 98, 10037-10041 2001. 676s 676s 676s This executable compiled on Jan 3 2025 at 11:01:42 676s 676s Parsing input file 1d7i-dss-mol.in... 676s rank 0 size 1... 676s Parsed input file. 676s Got paths for 3 molecules 676s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 676s asc_getToken: Error occurred (bailing out). 676s Vio_scanf: Format problem with input. 676s 1677 atoms 676s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 676s Net charge 9.91e-01 e 676s Reading PQR-format atom data from dss-min.pqr. 676s asc_getToken: Error occurred (bailing out). 676s Vio_scanf: Format problem with input. 676s 14 atoms 676s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 676s Net charge -8.33e-17 e 676s Reading PQR-format atom data from 1d7i-min.pqr. 676s 1663 atoms 676s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 676s Net charge 9.91e-01 e 676s Preparing to run 12 PBE calculations. 676s ---------------------------------------- 676s CALCULATION #1 (complex-solv-coarse): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 30.4176 A 676s Current memory usage: 102.869 MB total, 102.869 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 1.500 x 1.500 x 1.500 676s Grid lengths: 96.000 x 96.000 x 96.000 676s Grid center: (25.264, 18.988, 19.122) 676s Multigrid levels: 5 676s Molecule ID: 1 676s Linearized traditional PBE 676s Multiple Debye-Huckel sphere boundary conditions 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 78.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 9.160578033846E+03 kJ/mol 676s Calculating forces... 676s [focusFillBound()]: WARNING: 676s Unusually large potential values 676s detected on the focusing boundary! 676s Convergence not guaranteed for NPBE/NRPBE calculations! 676s 676s ---------------------------------------- 676s CALCULATION #2 (complex-solv-fine): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 30.4176 A 676s Current memory usage: 102.869 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 0.225 x 0.225 x 0.225 676s Grid lengths: 14.400 x 14.400 x 14.400 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 1 676s Linearized traditional PBE 676s Boundary conditions from focusing 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 78.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 3.955701871716E+04 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #3 (complex-ref-coarse): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 4.87072 A 676s Current memory usage: 102.869 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 1.500 x 1.500 x 1.500 676s Grid lengths: 96.000 x 96.000 x 96.000 676s Grid center: (25.264, 18.988, 19.122) 676s Multigrid levels: 5 676s Molecule ID: 1 676s Linearized traditional PBE 676s Multiple Debye-Huckel sphere boundary conditions 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 2.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.264965939588E+04 kJ/mol 676s Calculating forces... 676s [focusFillBound()]: WARNING: 676s Unusually large potential values 676s detected on the focusing boundary! 676s Convergence not guaranteed for NPBE/NRPBE calculations! 676s 676s ---------------------------------------- 676s CALCULATION #4 (complex-ref-fine): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 4.87072 A 676s Current memory usage: 102.869 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 0.225 x 0.225 x 0.225 676s Grid lengths: 14.400 x 14.400 x 14.400 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 1 676s Linearized traditional PBE 676s Boundary conditions from focusing 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 2.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 4.301801664829E+04 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #5 (dss-solv-coarse): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 30.4176 A 676s Current memory usage: 62.482 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 1.500 x 1.500 x 1.500 676s Grid lengths: 96.000 x 96.000 x 96.000 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 2 676s Linearized traditional PBE 676s Multiple Debye-Huckel sphere boundary conditions 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 78.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 9.431133325426E+01 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #6 (dss-solv-fine): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 30.4176 A 676s Current memory usage: 62.482 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 0.225 x 0.225 x 0.225 676s Grid lengths: 14.400 x 14.400 x 14.400 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 2 676s Linearized traditional PBE 676s Boundary conditions from focusing 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 78.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.677348113184E+03 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #7 (dss-ref-coarse): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 4.87072 A 676s Current memory usage: 62.482 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 1.500 x 1.500 x 1.500 676s Grid lengths: 96.000 x 96.000 x 96.000 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 2 676s Linearized traditional PBE 676s Multiple Debye-Huckel sphere boundary conditions 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 2.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.171079106781E+02 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #8 (dss-ref-fine): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 4.87072 A 676s Current memory usage: 62.482 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 0.225 x 0.225 x 0.225 676s Grid lengths: 14.400 x 14.400 x 14.400 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 2 676s Linearized traditional PBE 676s Boundary conditions from focusing 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 2.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.697869784185E+03 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 30.4176 A 676s Current memory usage: 102.566 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 1.500 x 1.500 x 1.500 676s Grid lengths: 96.000 x 96.000 x 96.000 676s Grid center: (25.264, 18.988, 19.122) 676s Multigrid levels: 5 676s Molecule ID: 3 676s Linearized traditional PBE 676s Multiple Debye-Huckel sphere boundary conditions 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 78.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 9.040108332204E+03 kJ/mol 676s Calculating forces... 676s [focusFillBound()]: WARNING: 676s Unusually large potential values 676s detected on the focusing boundary! 676s Convergence not guaranteed for NPBE/NRPBE calculations! 676s 676s ---------------------------------------- 676s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 30.4176 A 676s Current memory usage: 102.566 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 0.225 x 0.225 x 0.225 676s Grid lengths: 14.400 x 14.400 x 14.400 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 3 676s Linearized traditional PBE 676s Boundary conditions from focusing 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 78.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 3.787747796627E+04 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 4.87072 A 676s Current memory usage: 102.566 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 1.500 x 1.500 x 1.500 676s Grid lengths: 96.000 x 96.000 x 96.000 676s Grid center: (25.264, 18.988, 19.122) 676s Multigrid levels: 5 676s Molecule ID: 3 676s Linearized traditional PBE 676s Multiple Debye-Huckel sphere boundary conditions 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 2.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.252495566243E+04 kJ/mol 676s Calculating forces... 676s [focusFillBound()]: WARNING: 676s Unusually large potential values 676s detected on the focusing boundary! 676s Convergence not guaranteed for NPBE/NRPBE calculations! 676s 676s ---------------------------------------- 676s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 676s Setting up problem... 676s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 676s Debye length: 4.87072 A 676s Current memory usage: 102.566 MB total, 183.200 MB high water 676s Using linear spline charge discretization. 676s Grid dimensions: 65 x 65 x 65 676s Grid spacings: 0.225 x 0.225 x 0.225 676s Grid lengths: 14.400 x 14.400 x 14.400 676s Grid center: (17.340, 19.211, 20.503) 676s Multigrid levels: 5 676s Molecule ID: 3 676s Linearized traditional PBE 676s Boundary conditions from focusing 676s 2 ion species (0.010 M ionic strength): 676s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 676s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 676s Solute dielectric: 2.000 676s Solvent dielectric: 2.000 676s Using "molecular" surface definition; no smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 4.133237922574E+04 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s PRINT STATEMENTS 676s 676s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 676s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 676s Global net ELEC energy = -3.460997931137E+03 kJ/mol 676s 676s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 676s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 676s Global net ELEC energy = -2.052167100108E+01 kJ/mol 676s 676s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 676s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 676s Global net ELEC energy = -3.454901259473E+03 kJ/mol 676s 676s 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 676s Local net energy (PE 0) = 1.442499933668E+01 kJ/mol 676s Global net ELEC energy = 1.442499933668E+01 kJ/mol 676s ---------------------------------------- 676s CLEANING UP AND SHUTTING DOWN... 676s Destroying force arrays. 676s No energy arrays to destroy. 676s Destroying multigrid structures. 676s Destroying finite element structures. 676s Destroying 3 molecules 676s Final memory usage: 0.001 MB total, 183.200 MB high water 676s 676s 676s Thanks for using APBS! 676s 692s Checking for intermediate energies in input file 1d7i-dss-mol.out 692s EXPECTED COMPUTED: 16 692s EXPECTED EXPECTED: 16 692s 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] 692s 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'] 692s COMPUTED RESULT 9160.578033846 692s COMPUTED RESULT 39557.01871716 692s COMPUTED RESULT 12649.65939588 692s COMPUTED RESULT 43018.01664829 692s COMPUTED RESULT 94.31133325426 692s COMPUTED RESULT 1677.348113184 692s COMPUTED RESULT 117.1079106781 692s COMPUTED RESULT 1697.869784185 692s COMPUTED RESULT 9040.108332204 692s COMPUTED RESULT 37877.47796627 692s COMPUTED RESULT 12524.95566243 692s COMPUTED RESULT 41332.37922574 692s COMPUTED RESULT -3460.997931137 692s COMPUTED RESULT -20.52167100108 692s COMPUTED RESULT -3454.901259473 692s COMPUTED RESULT 14.42499933668 692s BINARY: /usr/bin/apbs 692s INPUT: 1d7i-dss-smol.in 692s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 692s asc_getToken: Error occurred (bailing out). 692s Vio_scanf: Format problem with input. 692s 692s 692s ---------------------------------------------------------------------- 692s APBS -- Adaptive Poisson-Boltzmann Solver 692s Version APBS 3.4.1 692s 692s Nathan A. Baker (nathan.baker@pnnl.gov) 692s Pacific Northwest National Laboratory 692s 692s Additional contributing authors listed in the code documentation. 692s 692s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 692s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 692s Northwest Division for the U.S. Department of Energy. 692s 692s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 692s Portions Copyright (c) 2002-2020, Nathan A. Baker. 692s Portions Copyright (c) 1999-2002, The Regents of the University of California. 692s Portions Copyright (c) 1995, Michael Holst. 692s All rights reserved. 692s 692s Redistribution and use in source and binary forms, with or without 692s modification, are permitted provided that the following conditions are met: 692s 692s * Redistributions of source code must retain the above copyright notice, this 692s list of conditions and the following disclaimer. 692s 692s * Redistributions in binary form must reproduce the above copyright notice, 692s this list of conditions and the following disclaimer in the documentation 692s and/or other materials provided with the distribution. 692s 692s * Neither the name of the developer nor the names of its contributors may be 692s used to endorse or promote products derived from this software without 692s specific prior written permission. 692s 692s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 692s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 692s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 692s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 692s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 692s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 692s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 692s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 692s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 692s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 692s ---------------------------------------------------------------------- 692s APBS uses FETK (the Finite Element ToolKit) to solve the 692s Poisson-Boltzmann equation numerically. FETK is a portable collection 692s of finite element modeling class libraries developed by the Michael Holst 692s research group and written in an object-oriented form of C. FEtk is 692s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 692s *** PASSED *** 692s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 692s *** PASSED *** 692s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 692s *** PASSED *** 692s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 692s *** PASSED *** 692s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 692s *** PASSED *** 692s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 692s *** PASSED *** 692s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 692s *** PASSED *** 692s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 692s *** PASSED *** 692s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 692s *** PASSED *** 692s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 692s *** PASSED *** 692s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 692s *** PASSED *** 692s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 692s *** PASSED *** 692s Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) 692s *** PASSED *** 692s Elapsed time: 16.466135 seconds 692s -------------------------------------------------------------------------------- 692s Total elapsed time: 72.644883 seconds 692s Test results have been logged 692s -------------------------------------------------------------------------------- 692s -------------------------------------------------------------------------------- 692s Testing input file apbs-mol.in 692s 692s designed to solve general coupled systems of nonlinear partial differential 692s equations using adaptive finite element methods, inexact Newton methods, 692s and algebraic multilevel methods. More information about FEtk may be found 692s at . 692s ---------------------------------------------------------------------- 692s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 692s Aqua is a modified form of the Holst group PMG library 692s which has been modified by Patrice Koehl 692s for improved efficiency and 692s memory usage when solving the Poisson-Boltzmann equation. 692s ---------------------------------------------------------------------- 692s Please cite your use of APBS as: 692s 692s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 692s nanosystems: application to microtubules and the ribosome. Proc. 692s Natl. Acad. Sci. USA 98, 10037-10041 2001. 692s 692s 692s This executable compiled on Jan 3 2025 at 11:01:42 692s 692s Parsing input file 1d7i-dss-smol.in... 692s rank 0 size 1... 692s Parsed input file. 692s Got paths for 3 molecules 692s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 692s asc_getToken: Error occurred (bailing out). 692s Vio_scanf: Format problem with input. 692s 1677 atoms 692s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 692s Net charge 9.91e-01 e 692s Reading PQR-format atom data from dss-min.pqr. 692s asc_getToken: Error occurred (bailing out). 692s Vio_scanf: Format problem with input. 692s 14 atoms 692s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 692s Net charge -8.33e-17 e 692s Reading PQR-format atom data from 1d7i-min.pqr. 692s 1663 atoms 692s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 692s Net charge 9.91e-01 e 692s Preparing to run 12 PBE calculations. 692s ---------------------------------------- 692s CALCULATION #1 (complex-solv-coarse): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 30.4176 A 692s Current memory usage: 102.869 MB total, 102.869 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 1.500 x 1.500 x 1.500 692s Grid lengths: 96.000 x 96.000 x 96.000 692s Grid center: (25.264, 18.988, 19.122) 692s Multigrid levels: 5 692s Molecule ID: 1 692s Linearized traditional PBE 692s Multiple Debye-Huckel sphere boundary conditions 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 78.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 9.634884642408E+03 kJ/mol 692s Calculating forces... 692s [focusFillBound()]: WARNING: 692s Unusually large potential values 692s detected on the focusing boundary! 692s Convergence not guaranteed for NPBE/NRPBE calculations! 692s 692s ---------------------------------------- 692s CALCULATION #2 (complex-solv-fine): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 30.4176 A 692s Current memory usage: 102.869 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 0.225 x 0.225 x 0.225 692s Grid lengths: 14.400 x 14.400 x 14.400 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 1 692s Linearized traditional PBE 692s Boundary conditions from focusing 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 78.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 4.003177540425E+04 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s CALCULATION #3 (complex-ref-coarse): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 4.87072 A 692s Current memory usage: 102.869 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 1.500 x 1.500 x 1.500 692s Grid lengths: 96.000 x 96.000 x 96.000 692s Grid center: (25.264, 18.988, 19.122) 692s Multigrid levels: 5 692s Molecule ID: 1 692s Linearized traditional PBE 692s Multiple Debye-Huckel sphere boundary conditions 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 2.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 1.264965939588E+04 kJ/mol 692s Calculating forces... 692s [focusFillBound()]: WARNING: 692s Unusually large potential values 692s detected on the focusing boundary! 692s Convergence not guaranteed for NPBE/NRPBE calculations! 692s 692s ---------------------------------------- 692s CALCULATION #4 (complex-ref-fine): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 4.87072 A 692s Current memory usage: 102.869 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 0.225 x 0.225 x 0.225 692s Grid lengths: 14.400 x 14.400 x 14.400 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 1 692s Linearized traditional PBE 692s Boundary conditions from focusing 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 2.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 4.301801664829E+04 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s CALCULATION #5 (dss-solv-coarse): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 30.4176 A 692s Current memory usage: 62.482 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 1.500 x 1.500 x 1.500 692s Grid lengths: 96.000 x 96.000 x 96.000 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 2 692s Linearized traditional PBE 692s Multiple Debye-Huckel sphere boundary conditions 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 78.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 7.942232645345E+01 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s CALCULATION #6 (dss-solv-fine): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 30.4176 A 692s Current memory usage: 62.482 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 0.225 x 0.225 x 0.225 692s Grid lengths: 14.400 x 14.400 x 14.400 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 2 692s Linearized traditional PBE 692s Boundary conditions from focusing 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 78.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 1.677798535473E+03 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s CALCULATION #7 (dss-ref-coarse): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 4.87072 A 692s Current memory usage: 62.482 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 1.500 x 1.500 x 1.500 692s Grid lengths: 96.000 x 96.000 x 96.000 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 2 692s Linearized traditional PBE 692s Multiple Debye-Huckel sphere boundary conditions 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 2.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 1.171079106781E+02 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s CALCULATION #8 (dss-ref-fine): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 4.87072 A 692s Current memory usage: 62.482 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 0.225 x 0.225 x 0.225 692s Grid lengths: 14.400 x 14.400 x 14.400 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 2 692s Linearized traditional PBE 692s Boundary conditions from focusing 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 2.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 1.697869784185E+03 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 30.4176 A 692s Current memory usage: 102.566 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 1.500 x 1.500 x 1.500 692s Grid lengths: 96.000 x 96.000 x 96.000 692s Grid center: (25.264, 18.988, 19.122) 692s Multigrid levels: 5 692s Molecule ID: 3 692s Linearized traditional PBE 692s Multiple Debye-Huckel sphere boundary conditions 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 78.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 9.507068451372E+03 kJ/mol 692s Calculating forces... 692s [focusFillBound()]: WARNING: 692s Unusually large potential values 692s detected on the focusing boundary! 692s Convergence not guaranteed for NPBE/NRPBE calculations! 692s 692s ---------------------------------------- 692s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 30.4176 A 692s Current memory usage: 102.566 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 0.225 x 0.225 x 0.225 692s Grid lengths: 14.400 x 14.400 x 14.400 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 3 692s Linearized traditional PBE 692s Boundary conditions from focusing 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 78.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 3.835075772299E+04 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 4.87072 A 692s Current memory usage: 102.566 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 1.500 x 1.500 x 1.500 692s Grid lengths: 96.000 x 96.000 x 96.000 692s Grid center: (25.264, 18.988, 19.122) 692s Multigrid levels: 5 692s Molecule ID: 3 692s Linearized traditional PBE 692s Multiple Debye-Huckel sphere boundary conditions 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 2.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 1.252495566243E+04 kJ/mol 692s Calculating forces... 692s [focusFillBound()]: WARNING: 692s Unusually large potential values 692s detected on the focusing boundary! 692s Convergence not guaranteed for NPBE/NRPBE calculations! 692s 692s ---------------------------------------- 692s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 692s Setting up problem... 692s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 692s Debye length: 4.87072 A 692s Current memory usage: 102.566 MB total, 183.200 MB high water 692s Using linear spline charge discretization. 692s Grid dimensions: 65 x 65 x 65 692s Grid spacings: 0.225 x 0.225 x 0.225 692s Grid lengths: 14.400 x 14.400 x 14.400 692s Grid center: (17.340, 19.211, 20.503) 692s Multigrid levels: 5 692s Molecule ID: 3 692s Linearized traditional PBE 692s Boundary conditions from focusing 692s 2 ion species (0.010 M ionic strength): 692s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 692s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 692s Solute dielectric: 2.000 692s Solvent dielectric: 2.000 692s Using "molecular" surface definition;harmonic average smoothing 692s Solvent probe radius: 0.000 A 692s Temperature: 300.000 K 692s Electrostatic energies will be calculated 692s Total electrostatic energy = 4.133237922574E+04 kJ/mol 692s Calculating forces... 692s ---------------------------------------- 692s PRINT STATEMENTS 692s 692s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 692s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 692s Global net ELEC energy = -2.986241244040E+03 kJ/mol 692s 692s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 692s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 692s Global net ELEC energy = -2.007124871262E+01 kJ/mol 692s 692s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 692s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 692s Global net ELEC energy = -2.981621502756E+03 kJ/mol 692s 692s 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 692s Local net energy (PE 0) = 1.545150742844E+01 kJ/mol 692s Global net ELEC energy = 1.545150742844E+01 kJ/mol 692s ---------------------------------------- 692s CLEANING UP AND SHUTTING DOWN... 692s Destroying force arrays. 692s No energy arrays to destroy. 692s Destroying multigrid structures. 692s Destroying finite element structures. 692s Destroying 3 molecules 692s Final memory usage: 0.001 MB total, 183.200 MB high water 692s 692s 692s Thanks for using APBS! 692s 711s Checking for intermediate energies in input file 1d7i-dss-smol.out 711s EXPECTED COMPUTED: 16 711s EXPECTED EXPECTED: 16 711s 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] 711s 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'] 711s COMPUTED RESULT 9634.884642408 711s COMPUTED RESULT 40031.77540425 711s COMPUTED RESULT 12649.65939588 711s COMPUTED RESULT 43018.01664829 711s COMPUTED RESULT 79.42232645345 711s COMPUTED RESULT 1677.798535473 711s COMPUTED RESULT 117.1079106781 711s COMPUTED RESULT 1697.869784185 711s COMPUTED RESULT 9507.068451372 711s COMPUTED RESULT 38350.75772299 711s COMPUTED RESULT 12524.95566243 711s COMPUTED RESULT 41332.37922574 711s COMPUTED RESULT -2986.24124404 711s COMPUTED RESULT -20.07124871262 711s COMPUTED RESULT -2981.621502756 711s COMPUTED RESULT 15.45150742844 711s Running tests for hca-bind section 711s BINARY: /usr/bin/apbs 711s INPUT: apbs-mol.in 711s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 711s asc_getToken: Error occurred (bailing out). 711s Vio_scanf: Format problem with input. 711s 711s 711s ---------------------------------------------------------------------- 711s APBS -- Adaptive Poisson-Boltzmann Solver 711s Version APBS 3.4.1 711s 711s Nathan A. Baker (nathan.baker@pnnl.gov) 711s Pacific Northwest National Laboratory 711s 711s Additional contributing authors listed in the code documentation. 711s 711s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 711s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 711s Northwest Division for the U.S. Department of Energy. 711s 711s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 711s Portions Copyright (c) 2002-2020, Nathan A. Baker. 711s Portions Copyright (c) 1999-2002, The Regents of the University of California. 711s Portions Copyright (c) 1995, Michael Holst. 711s All rights reserved. 711s 711s Redistribution and use in source and binary forms, with or without 711s modification, are permitted provided that the following conditions are met: 711s 711s * Redistributions of source code must retain the above copyright notice, this 711s list of conditions and the following disclaimer. 711s 711s * Redistributions in binary form must reproduce the above copyright notice, 711s this list of conditions and the following disclaimer in the documentation 711s and/or other materials provided with the distribution. 711s 711s * Neither the name of the developer nor the names of its contributors may be 711s used to endorse or promote products derived from this software without 711s specific prior written permission. 711s 711s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 711s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 711s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 711s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 711s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 711s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 711s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 711s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 711s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 711s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 711s ---------------------------------------------------------------------- 711s APBS uses FETK (the Finite Element ToolKit) to solve the 711s Poisson-Boltzmann equation numerically. FETK is a portable collection 711s of finite element modeling class libraries developed by the Michael Holst 711s research group and written in an object-orienTesting computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 711s *** PASSED *** 711s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 711s *** PASSED *** 711s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 711s *** PASSED *** 711s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 711s *** PASSED *** 711s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 711s *** PASSED *** 711s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 711s *** PASSED *** 711s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 711s *** PASSED *** 711s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 711s *** PASSED *** 711s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 711s *** PASSED *** 711s Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) 711s *** PASSED *** 711s Elapsed time: 18.322811 seconds 711s -------------------------------------------------------------------------------- 711s -------------------------------------------------------------------------------- 711s Testing input file apbs-smol.in 711s 711s ted form of C. FEtk is 711s designed to solve general coupled systems of nonlinear partial differential 711s equations using adaptive finite element methods, inexact Newton methods, 711s and algebraic multilevel methods. More information about FEtk may be found 711s at . 711s ---------------------------------------------------------------------- 711s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 711s Aqua is a modified form of the Holst group PMG library 711s which has been modified by Patrice Koehl 711s for improved efficiency and 711s memory usage when solving the Poisson-Boltzmann equation. 711s ---------------------------------------------------------------------- 711s Please cite your use of APBS as: 711s 711s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 711s nanosystems: application to microtubules and the ribosome. Proc. 711s Natl. Acad. Sci. USA 98, 10037-10041 2001. 711s 711s 711s This executable compiled on Jan 3 2025 at 11:01:42 711s 711s Parsing input file apbs-mol.in... 711s rank 0 size 1... 711s Parsed input file. 711s Got paths for 3 molecules 711s Reading PQR-format atom data from acet.pqr. 711s asc_getToken: Error occurred (bailing out). 711s Vio_scanf: Format problem with input. 711s 18 atoms 711s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 711s Net charge -1.00e+00 e 711s Reading PQR-format atom data from hca.pqr. 711s asc_getToken: Error occurred (bailing out). 711s Vio_scanf: Format problem with input. 711s 2482 atoms 711s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 711s Net charge 1.00e+00 e 711s Reading PQR-format atom data from complex.pqr. 711s 2500 atoms 711s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 711s Net charge -1.02e-14 e 711s Preparing to run 9 PBE calculations. 711s ---------------------------------------- 711s CALCULATION #1 (acet): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 62.632 MB total, 62.632 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 1.500 x 1.500 x 1.500 711s Grid lengths: 96.000 x 96.000 x 96.000 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 1 711s Linearized traditional PBE 711s Single Debye-Huckel sphere boundary conditions 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 2.213600726771E+02 kJ/mol 711s Calculating forces... 711s ---------------------------------------- 711s CALCULATION #2 (acet): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 62.632 MB total, 123.513 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 0.581 x 0.581 x 0.581 711s Grid lengths: 37.181 x 37.181 x 37.181 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 1 711s Linearized traditional PBE 711s Boundary conditions from focusing 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 1.825764811255E+03 kJ/mol 711s Calculating forces... 711s ---------------------------------------- 711s CALCULATION #3 (acet): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 62.632 MB total, 123.513 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 0.225 x 0.225 x 0.225 711s Grid lengths: 14.400 x 14.400 x 14.400 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 1 711s Linearized traditional PBE 711s Boundary conditions from focusing 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 6.458471211905E+03 kJ/mol 711s Calculating forces... 711s ---------------------------------------- 711s CALCULATION #4 (hca): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 127.616 MB total, 127.616 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 1.500 x 1.500 x 1.500 711s Grid lengths: 96.000 x 96.000 x 96.000 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 2 711s Linearized traditional PBE 711s Single Debye-Huckel sphere boundary conditions 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 2.093606095527E+04 kJ/mol 711s Calculating forces... 711s [focusFillBound()]: WARNING: 711s Unusually large potential values 711s detected on the focusing boundary! 711s Convergence not guaranteed for NPBE/NRPBE calculations! 711s 711s ---------------------------------------- 711s CALCULATION #5 (hca): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 127.616 MB total, 207.303 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 0.581 x 0.581 x 0.581 711s Grid lengths: 37.181 x 37.181 x 37.181 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 2 711s Linearized traditional PBE 711s Boundary conditions from focusing 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 1.515433544464E+05 kJ/mol 711s Calculating forces... 711s [focusFillBound()]: WARNING: 711s Unusually large potential values 711s detected on the focusing boundary! 711s Convergence not guaranteed for NPBE/NRPBE calculations! 711s 711s ---------------------------------------- 711s CALCULATION #6 (hca): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 127.616 MB total, 207.303 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 0.225 x 0.225 x 0.225 711s Grid lengths: 14.400 x 14.400 x 14.400 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 2 711s Linearized traditional PBE 711s Boundary conditions from focusing 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 1.786369323561E+05 kJ/mol 711s Calculating forces... 711s ---------------------------------------- 711s CALCULATION #7 (complex): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 127.915 MB total, 207.303 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 1.500 x 1.500 x 1.500 711s Grid lengths: 96.000 x 96.000 x 96.000 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 3 711s Linearized traditional PBE 711s Single Debye-Huckel sphere boundary conditions 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 2.105322784838E+04 kJ/mol 711s Calculating forces... 711s [focusFillBound()]: WARNING: 711s Unusually large potential values 711s detected on the focusing boundary! 711s Convergence not guaranteed for NPBE/NRPBE calculations! 711s 711s ---------------------------------------- 711s CALCULATION #8 (complex): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 127.915 MB total, 207.713 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 0.581 x 0.581 x 0.581 711s Grid lengths: 37.181 x 37.181 x 37.181 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 3 711s Linearized traditional PBE 711s Boundary conditions from focusing 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 1.533304996252E+05 kJ/mol 711s Calculating forces... 711s [focusFillBound()]: WARNING: 711s Unusually large potential values 711s detected on the focusing boundary! 711s Convergence not guaranteed for NPBE/NRPBE calculations! 711s 711s ---------------------------------------- 711s CALCULATION #9 (complex): MULTIGRID 711s Setting up problem... 711s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 711s Debye length: 0 A 711s Current memory usage: 127.915 MB total, 207.713 MB high water 711s Using linear spline charge discretization. 711s Grid dimensions: 65 x 65 x 65 711s Grid spacings: 0.225 x 0.225 x 0.225 711s Grid lengths: 14.400 x 14.400 x 14.400 711s Grid center: (-6.028, 3.898, 15.179) 711s Multigrid levels: 5 711s Molecule ID: 3 711s Linearized traditional PBE 711s Boundary conditions from focusing 711s 2 ion species (0.000 M ionic strength): 711s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 711s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 711s Solute dielectric: 2.000 711s Solvent dielectric: 78.540 711s Using "molecular" surface definition; no smoothing 711s Solvent probe radius: 0.000 A 711s Temperature: 298.150 K 711s Electrostatic energies will be calculated 711s Total electrostatic energy = 1.850429388099E+05 kJ/mol 711s Calculating forces... 711s ---------------------------------------- 711s PRINT STATEMENTS 711s 711s print energy 3 (complex) - 1 (acet) - 2 (hca) end 711s Local net energy (PE 0) = -5.246475812665E+01 kJ/mol 711s Global net ELEC energy = -5.246475812665E+01 kJ/mol 711s ---------------------------------------- 711s CLEANING UP AND SHUTTING DOWN... 711s Destroying force arrays. 711s No energy arrays to destroy. 711s Destroying multigrid structures. 711s Destroying finite element structures. 711s Destroying 3 molecules 711s Final memory usage: 0.001 MB total, 207.713 MB high water 711s 711s 711s Thanks for using APBS! 711s 725s Checking for intermediate energies in input file apbs-mol.out 725s EXPECTED COMPUTED: 10 725s EXPECTED EXPECTED: 10 725s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] 725s 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'] 725s COMPUTED RESULT 221.3600726771 725s COMPUTED RESULT 1825.764811255 725s COMPUTED RESULT 6458.471211905 725s COMPUTED RESULT 20936.06095527 725s COMPUTED RESULT 151543.3544464 725s COMPUTED RESULT 178636.9323561 725s COMPUTED RESULT 21053.22784838 725s COMPUTED RESULT 153330.4996252 725s COMPUTED RESULT 185042.9388099 725s COMPUTED RESULT -52.46475812665 725s BINARY: /usr/bin/apbs 725s INPUT: apbs-smol.in 725s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 725s asc_getToken: Error occurred (bailing out). 725s Vio_scanf: Format problem with input. 725s 725s 725s ---------------------------------------------------------------------- 725s APBS -- Adaptive Poisson-Boltzmann Solver 725s Version APBS 3.4.1 725s 725s Nathan A. Baker (nathan.baker@pnnl.gov) 725s Pacific Northwest National Laboratory 725s 725s Additional contributing authors listed in the code documentation. 725s 725s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 725s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 725s Northwest Division for the U.S. Department of Energy. 725s 725s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 725s Portions Copyright (c) 2002-2020, Nathan A. Baker. 725s Portions Copyright (c) 1999-2002, The Regents of the University of California. 725s Portions Copyright (c) 1995, Michael Holst. 725s All rights reserved. 725s 725s Redistribution and use in source and binary forms, with or without 725s modification, are permitted provided that the following conditions are met: 725s 725s * Redistributions of source code must retain the above copyright notice, this 725s list of conditions and the following disclaimer. 725s 725s * Redistributions in binary form must reproduce the above copyright notice, 725s this list of conditions and the following disclaimer in the documentation 725s and/or other materials provided with the distribution. 725s 725s * Neither the name of the developer nor the names of its contributors may be 725s used to endorse or promote products derived from this software without 725s specific prior written permission. 725s 725s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 725s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 725s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 725s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 725s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 725s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 725s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 725s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 725s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 725s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 725s ---------------------------------------------------------------------- 725s APBS uses FETK (the Finite Element ToolKit) to solve the 725s Poisson-Boltzmann equation numerically. FETK is a portable collection 725s of finite element modeling class libraries developed by the Michael Holst 725s research group and written in an object-oriented form of C. FEtk is 725s designed to solve general coupled systems of nonlinear partial differential 725s equations using adaptive finite element methods, inexact Newton methods, 725s and algebraic multilevel methods. More information about FEtk may be found 725s at . 725s ---------------------------------------------------------------------- 725s APBS also uses Aqua to solve the PoiTesting computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 725s *** PASSED *** 725s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 725s *** PASSED *** 725s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 725s *** PASSED *** 725s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 725s *** PASSED *** 725s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 725s *** PASSED *** 725s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 725s *** PASSED *** 725s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 725s *** PASSED *** 725s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 725s *** PASSED *** 725s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 725s *** PASSED *** 725s Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) 725s *** PASSED *** 725s Elapsed time: 14.394325 seconds 725s -------------------------------------------------------------------------------- 725s Total elapsed time: 32.717135999999996 seconds 725s Test results have been logged 725s -------------------------------------------------------------------------------- 725s -------------------------------------------------------------------------------- 725s Testing input file apbs-mol.in 725s 725s sson-Boltzmann equation numerically. 725s Aqua is a modified form of the Holst group PMG library 725s which has been modified by Patrice Koehl 725s for improved efficiency and 725s memory usage when solving the Poisson-Boltzmann equation. 725s ---------------------------------------------------------------------- 725s Please cite your use of APBS as: 725s 725s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 725s nanosystems: application to microtubules and the ribosome. Proc. 725s Natl. Acad. Sci. USA 98, 10037-10041 2001. 725s 725s 725s This executable compiled on Jan 3 2025 at 11:01:42 725s 725s Parsing input file apbs-smol.in... 725s rank 0 size 1... 725s Parsed input file. 725s Got paths for 3 molecules 725s Reading PQR-format atom data from acet.pqr. 725s asc_getToken: Error occurred (bailing out). 725s Vio_scanf: Format problem with input. 725s 18 atoms 725s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 725s Net charge -1.00e+00 e 725s Reading PQR-format atom data from hca.pqr. 725s asc_getToken: Error occurred (bailing out). 725s Vio_scanf: Format problem with input. 725s 2482 atoms 725s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 725s Net charge 1.00e+00 e 725s Reading PQR-format atom data from complex.pqr. 725s 2500 atoms 725s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 725s Net charge -1.02e-14 e 725s Preparing to run 9 PBE calculations. 725s ---------------------------------------- 725s CALCULATION #1 (acet): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 62.632 MB total, 62.632 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 1.500 x 1.500 x 1.500 725s Grid lengths: 96.000 x 96.000 x 96.000 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 1 725s Linearized traditional PBE 725s Single Debye-Huckel sphere boundary conditions 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 1.884888131017E+02 kJ/mol 725s Calculating forces... 725s ---------------------------------------- 725s CALCULATION #2 (acet): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 62.632 MB total, 123.513 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 0.581 x 0.581 x 0.581 725s Grid lengths: 37.181 x 37.181 x 37.181 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 1 725s Linearized traditional PBE 725s Boundary conditions from focusing 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 1.820045922544E+03 kJ/mol 725s Calculating forces... 725s ---------------------------------------- 725s CALCULATION #3 (acet): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 62.632 MB total, 123.513 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 0.225 x 0.225 x 0.225 725s Grid lengths: 14.400 x 14.400 x 14.400 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 1 725s Linearized traditional PBE 725s Boundary conditions from focusing 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 6.460002606908E+03 kJ/mol 725s Calculating forces... 725s ---------------------------------------- 725s CALCULATION #4 (hca): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 127.616 MB total, 127.616 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 1.500 x 1.500 x 1.500 725s Grid lengths: 96.000 x 96.000 x 96.000 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 2 725s Linearized traditional PBE 725s Single Debye-Huckel sphere boundary conditions 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 2.189161497021E+04 kJ/mol 725s Calculating forces... 725s [focusFillBound()]: WARNING: 725s Unusually large potential values 725s detected on the focusing boundary! 725s Convergence not guaranteed for NPBE/NRPBE calculations! 725s 725s ---------------------------------------- 725s CALCULATION #5 (hca): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 127.616 MB total, 207.303 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 0.581 x 0.581 x 0.581 725s Grid lengths: 37.181 x 37.181 x 37.181 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 2 725s Linearized traditional PBE 725s Boundary conditions from focusing 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 1.520000494925E+05 kJ/mol 725s Calculating forces... 725s [focusFillBound()]: WARNING: 725s Unusually large potential values 725s detected on the focusing boundary! 725s Convergence not guaranteed for NPBE/NRPBE calculations! 725s 725s ---------------------------------------- 725s CALCULATION #6 (hca): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 127.616 MB total, 207.303 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 0.225 x 0.225 x 0.225 725s Grid lengths: 14.400 x 14.400 x 14.400 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 2 725s Linearized traditional PBE 725s Boundary conditions from focusing 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 1.790436191580E+05 kJ/mol 725s Calculating forces... 725s ---------------------------------------- 725s CALCULATION #7 (complex): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 127.915 MB total, 207.303 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 1.500 x 1.500 x 1.500 725s Grid lengths: 96.000 x 96.000 x 96.000 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 3 725s Linearized traditional PBE 725s Single Debye-Huckel sphere boundary conditions 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 2.195842512312E+04 kJ/mol 725s Calculating forces... 725s [focusFillBound()]: WARNING: 725s Unusually large potential values 725s detected on the focusing boundary! 725s Convergence not guaranteed for NPBE/NRPBE calculations! 725s 725s ---------------------------------------- 725s CALCULATION #8 (complex): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 127.915 MB total, 207.713 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 0.581 x 0.581 x 0.581 725s Grid lengths: 37.181 x 37.181 x 37.181 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 3 725s Linearized traditional PBE 725s Boundary conditions from focusing 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 1.537771604355E+05 kJ/mol 725s Calculating forces... 725s [focusFillBound()]: WARNING: 725s Unusually large potential values 725s detected on the focusing boundary! 725s Convergence not guaranteed for NPBE/NRPBE calculations! 725s 725s ---------------------------------------- 725s CALCULATION #9 (complex): MULTIGRID 725s Setting up problem... 725s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 725s Debye length: 0 A 725s Current memory usage: 127.915 MB total, 207.713 MB high water 725s Using linear spline charge discretization. 725s Grid dimensions: 65 x 65 x 65 725s Grid spacings: 0.225 x 0.225 x 0.225 725s Grid lengths: 14.400 x 14.400 x 14.400 725s Grid center: (-6.028, 3.898, 15.179) 725s Multigrid levels: 5 725s Molecule ID: 3 725s Linearized traditional PBE 725s Boundary conditions from focusing 725s 2 ion species (0.000 M ionic strength): 725s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 725s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 725s Solute dielectric: 2.000 725s Solvent dielectric: 78.540 725s Using "molecular" surface definition;harmonic average smoothing 725s Solvent probe radius: 0.000 A 725s Temperature: 298.150 K 725s Electrostatic energies will be calculated 725s Total electrostatic energy = 1.854495619747E+05 kJ/mol 725s Calculating forces... 725s ---------------------------------------- 725s PRINT STATEMENTS 725s 725s print energy 3 (complex) - 1 (acet) - 2 (hca) end 725s Local net energy (PE 0) = -5.405979017066E+01 kJ/mol 725s Global net ELEC energy = -5.405979017066E+01 kJ/mol 725s ---------------------------------------- 725s CLEANING UP AND SHUTTING DOWN... 725s Destroying force arrays. 725s No energy arrays to destroy. 725s Destroying multigrid structures. 725s Destroying finite element structures. 725s Destroying 3 molecules 725s Final memory usage: 0.001 MB total, 207.713 MB high water 725s 725s 725s Thanks for using APBS! 725s 736s Checking for intermediate energies in input file apbs-smol.out 736s EXPECTED COMPUTED: 10 736s EXPECTED EXPECTED: 10 736s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] 736s 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'] 736s COMPUTED RESULT 188.4888131017 736s COMPUTED RESULT 1820.045922544 736s COMPUTED RESULT 6460.002606908 736s COMPUTED RESULT 21891.61497021 736s COMPUTED RESULT 152000.0494925 736s COMPUTED RESULT 179043.619158 736s COMPUTED RESULT 21958.42512312 736s COMPUTED RESULT 153777.1604355 736s COMPUTED RESULT 185449.5619747 736s COMPUTED RESULT -54.05979017066 736s Running tests for ionize section 736s BINARY: /usr/bin/apbs 736s INPUT: apbs-mol.in 736s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 736s asc_getToken: Error occurred (bailing out). 736s Vio_scanf: Format problem with input. 736s 736s 736s ---------------------------------------------------------------------- 736s APBS -- Adaptive Poisson-Boltzmann Solver 736s Version APBS 3.4.1 736s 736s Nathan A. Baker (nathan.baker@pnnl.gov) 736s Pacific Northwest National Laboratory 736s 736s Additional contributing authors listed in the code documentation. 736s 736s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 736s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 736s Northwest Division for the U.S. Department of Energy. 736s 736s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 736s Portions Copyright (c) 2002-2020, Nathan A. Baker. 736s Portions Copyright (c) 1999-2002, The Regents of the University of California. 736s Portions Copyright (c) 1995, Michael Holst. 736s All rights reserved. 736s 736s Redistribution and use in source and binary forms, with or without 736s modification, are permitted provided that the following conditions are met: 736s 736s * Redistributions of source code must retain the above copyright notice, this 736s list of conditions and the following disclaimer. 736s 736s * Redistributions in binary form must reproduce the above copyright notice, 736s this list of conditions and the following disclaimer in the documentation 736s and/or other materials provided with the distribution. 736s 736s * Neither the name of the developer nor the names of its contributors may be 736s used to endorse or promote products derived from this software without 736s specific prior written permission. 736s 736s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 736s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 736s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 736s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 736s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 736s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 736s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 736s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 736s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 736s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 736s ---------------------------------------------------------------------- 736s APBS uses FETK (the Finite Element ToolKit) to solve the 736s Poisson-Boltzmann equation numerically. FETK is a portable collection 736s of finite element modeling class libraries developed by the Michael Holst 736s research group and written in an object-oriented form of C. FEtk is 736s designed to solve general coupled systems of nonlinear partial differential 736s equations using adaptive finite element methods, inexact Newton methods, 736s and algebraic multilevel methods. More information about FEtk may be found 736s at . 736s ---------------------------------------------------------------------- 736s APBS aTesting computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 736s *** PASSED *** 736s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 736s *** PASSED *** 736s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 736s *** PASSED *** 736s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 736s *** PASSED *** 736s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 736s *** PASSED *** 736s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 736s *** PASSED *** 736s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 736s *** PASSED *** 736s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 736s *** PASSED *** 736s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 736s *** PASSED *** 736s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 736s *** PASSED *** 736s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 736s *** PASSED *** 736s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 736s *** PASSED *** 736s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 736s *** PASSED *** 736s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 736s *** PASSED *** 736s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 736s *** PASSED *** 736s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 736s *** PASSED *** 736s Elapsed time: 11.417086 seconds 736s -------------------------------------------------------------------------------- 736s -------------------------------------------------------------------------------- 736s Testing input file apbs-smol.in 736s 736s lso uses Aqua to solve the Poisson-Boltzmann equation numerically. 736s Aqua is a modified form of the Holst group PMG library 736s which has been modified by Patrice Koehl 736s for improved efficiency and 736s memory usage when solving the Poisson-Boltzmann equation. 736s ---------------------------------------------------------------------- 736s Please cite your use of APBS as: 736s 736s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 736s nanosystems: application to microtubules and the ribosome. Proc. 736s Natl. Acad. Sci. USA 98, 10037-10041 2001. 736s 736s 736s This executable compiled on Jan 3 2025 at 11:01:42 736s 736s Parsing input file apbs-mol.in... 736s rank 0 size 1... 736s Parsed input file. 736s Got paths for 3 molecules 736s Reading PQR-format atom data from acetic-acid.pqr. 736s asc_getToken: Error occurred (bailing out). 736s Vio_scanf: Format problem with input. 736s 8 atoms 736s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 736s Net charge -1.67e-16 e 736s Reading PQR-format atom data from acetate.pqr. 736s asc_getToken: Error occurred (bailing out). 736s Vio_scanf: Format problem with input. 736s 8 atoms 736s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 736s Net charge -1.00e+00 e 736s Reading PQR-format atom data from proton.pqr. 736s 1 atoms 736s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 736s Net charge 1.00e+00 e 736s Preparing to run 12 PBE calculations. 736s ---------------------------------------- 736s CALCULATION #1 (acetic-solv): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 7.76163 A 736s Current memory usage: 61.581 MB total, 61.581 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.188 x 0.188 x 0.188 736s Grid lengths: 12.000 x 12.000 x 12.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 1 736s Linearized traditional PBE 736s Multiple Debye-Huckel sphere boundary conditions 736s 2 ion species (0.150 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 78.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 5.823898055191E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #2 (acetic-solv): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 7.76163 A 736s Current memory usage: 61.581 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.094 x 0.094 x 0.094 736s Grid lengths: 6.000 x 6.000 x 6.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 1 736s Linearized traditional PBE 736s Boundary conditions from focusing 736s 2 ion species (0.150 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 78.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 9.793274462353E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #3 (acetic-ref): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 0 A 736s Current memory usage: 61.405 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.188 x 0.188 x 0.188 736s Grid lengths: 12.000 x 12.000 x 12.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 1 736s Linearized traditional PBE 736s Multiple Debye-Huckel sphere boundary conditions 736s 2 ion species (0.000 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 2.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 5.846917564309E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #4 (acetic-ref): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 0 A 736s Current memory usage: 61.405 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.094 x 0.094 x 0.094 736s Grid lengths: 6.000 x 6.000 x 6.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 1 736s Linearized traditional PBE 736s Boundary conditions from focusing 736s 2 ion species (0.000 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 2.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 9.815953282539E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #5 (acetate-solv): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 7.76163 A 736s Current memory usage: 61.581 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.188 x 0.188 x 0.188 736s Grid lengths: 12.000 x 12.000 x 12.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 2 736s Linearized traditional PBE 736s Multiple Debye-Huckel sphere boundary conditions 736s 2 ion species (0.150 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 78.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 8.219846763777E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #6 (acetate-solv): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 7.76163 A 736s Current memory usage: 61.581 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.094 x 0.094 x 0.094 736s Grid lengths: 6.000 x 6.000 x 6.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 2 736s Linearized traditional PBE 736s Boundary conditions from focusing 736s 2 ion species (0.150 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 78.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 1.392741988698E+04 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #7 (acetate-ref): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 0 A 736s Current memory usage: 61.405 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.188 x 0.188 x 0.188 736s Grid lengths: 12.000 x 12.000 x 12.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 2 736s Linearized traditional PBE 736s Multiple Debye-Huckel sphere boundary conditions 736s 2 ion species (0.000 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 2.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 8.420373979905E+03 kJ/mol 736s Calculating forces... 736s [focusFillBound()]: WARNING: 736s Unusually large potential values 736s detected on the focusing boundary! 736s Convergence not guaranteed for NPBE/NRPBE calculations! 736s 736s ---------------------------------------- 736s CALCULATION #8 (acetate-ref): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 0 A 736s Current memory usage: 61.405 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.094 x 0.094 x 0.094 736s Grid lengths: 6.000 x 6.000 x 6.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 2 736s Linearized traditional PBE 736s Boundary conditions from focusing 736s 2 ion species (0.000 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 2.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 1.412716615065E+04 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #9 (proton-solv): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 7.76163 A 736s Current memory usage: 61.410 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.188 x 0.188 x 0.188 736s Grid lengths: 12.000 x 12.000 x 12.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 3 736s Linearized traditional PBE 736s Multiple Debye-Huckel sphere boundary conditions 736s 2 ion species (0.150 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 78.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 3.862359524598E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #10 (proton-solv): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 7.76163 A 736s Current memory usage: 61.410 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.094 x 0.094 x 0.094 736s Grid lengths: 6.000 x 6.000 x 6.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 3 736s Linearized traditional PBE 736s Boundary conditions from focusing 736s 2 ion species (0.150 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 78.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 6.288156251610E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s CALCULATION #11 (proton-ref): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 0 A 736s Current memory usage: 61.371 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.188 x 0.188 x 0.188 736s Grid lengths: 12.000 x 12.000 x 12.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 3 736s Linearized traditional PBE 736s Multiple Debye-Huckel sphere boundary conditions 736s 2 ion species (0.000 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 2.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 4.162533113906E+03 kJ/mol 736s Calculating forces... 736s [focusFillBound()]: WARNING: 736s Unusually large potential values 736s detected on the focusing boundary! 736s Convergence not guaranteed for NPBE/NRPBE calculations! 736s 736s ---------------------------------------- 736s CALCULATION #12 (proton-ref): MULTIGRID 736s Setting up problem... 736s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 736s Debye length: 0 A 736s Current memory usage: 61.371 MB total, 122.371 MB high water 736s Using linear spline charge discretization. 736s Grid dimensions: 65 x 65 x 65 736s Grid spacings: 0.094 x 0.094 x 0.094 736s Grid lengths: 6.000 x 6.000 x 6.000 736s Grid center: (0.000, -0.154, 1.287) 736s Multigrid levels: 5 736s Molecule ID: 3 736s Linearized traditional PBE 736s Boundary conditions from focusing 736s 2 ion species (0.000 M ionic strength): 736s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 736s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 736s Solute dielectric: 2.000 736s Solvent dielectric: 2.000 736s Using "molecular" surface definition; no smoothing 736s Solvent probe radius: 0.000 A 736s Temperature: 293.000 K 736s Electrostatic energies will be calculated 736s Total electrostatic energy = 6.585616091973E+03 kJ/mol 736s Calculating forces... 736s ---------------------------------------- 736s PRINT STATEMENTS 736s 736s print energy 1 (acetic-solv) - 2 (acetic-ref) end 736s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 736s Global net ELEC energy = -2.267882018629E+01 kJ/mol 736s 736s print energy 3 (acetate-solv) - 4 (acetate-ref) end 736s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 736s Global net ELEC energy = -1.997462636633E+02 kJ/mol 736s 736s print energy 5 (proton-solv) - 6 (proton-ref) end 736s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 736s Global net ELEC energy = -2.974598403628E+02 kJ/mol 736s 736s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 736s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 736s Global net ELEC energy = -4.745272838398E+02 kJ/mol 736s ---------------------------------------- 736s CLEANING UP AND SHUTTING DOWN... 736s Destroying force arrays. 736s No energy arrays to destroy. 736s Destroying multigrid structures. 736s Destroying finite element structures. 736s Destroying 3 molecules 736s Final memory usage: 0.001 MB total, 122.371 MB high water 736s 736s 736s Thanks for using APBS! 736s 746s Checking for intermediate energies in input file apbs-mol.out 746s EXPECTED COMPUTED: 16 746s EXPECTED EXPECTED: 16 746s 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] 746s 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'] 746s COMPUTED RESULT 5823.898055191 746s COMPUTED RESULT 9793.274462353 746s COMPUTED RESULT 5846.917564309 746s COMPUTED RESULT 9815.953282539 746s COMPUTED RESULT 8219.846763777 746s COMPUTED RESULT 13927.41988698 746s COMPUTED RESULT 8420.373979905 746s COMPUTED RESULT 14127.16615065 746s COMPUTED RESULT 3862.359524598 746s COMPUTED RESULT 6288.15625161 746s COMPUTED RESULT 4162.533113906 746s COMPUTED RESULT 6585.616091973 746s COMPUTED RESULT -22.67882018629 746s COMPUTED RESULT -199.7462636633 746s COMPUTED RESULT -297.4598403628 746s COMPUTED RESULT -474.5272838398 746s BINARY: /usr/bin/apbs 746s INPUT: apbs-smol.in 746s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 746s asc_getToken: Error occurred (bailing out). 746s Vio_scanf: Format problem with input. 746s 746s 746s ---------------------------------------------------------------------- 746s APBS -- Adaptive Poisson-Boltzmann Solver 746s Version APBS 3.4.1 746s 746s Nathan A. Baker (nathan.baker@pnnl.gov) 746s Pacific Northwest National Laboratory 746s 746s Additional contributing authors listed in the code documentation. 746s 746s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 746s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 746s Northwest Division for the U.S. Department of Energy. 746s 746s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 746s Portions Copyright (c) 2002-2020, Nathan A. Baker. 746s Portions Copyright (c) 1999-2002, The Regents of the University of California. 746s Portions Copyright (c) 1995, Michael Holst. 746s All rights reserved. 746s 746s Redistribution and use in source and binary forms, with or without 746s modification, are permitted provided that the following conditions are met: 746s 746s * Redistributions of source code must retain the above copyright notice, this 746s list of conditions and the following disclaimer. 746s 746s * Redistributions in binary form must reproduce the above copyright notice, 746s this list of conditions and the following disclaimer in the documentation 746s and/or other materials provided with the distribution. 746s 746s * Neither the name of the developer nor the names of its contributors may be 746s used to endorse or promote products derived from this software without 746s specific prior written permission. 746s 746s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 746s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 746s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 746s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 746s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 746s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 746s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 746s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 746s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 746s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 746s ---------------------------------------------------------------------- 746s APBS uses FETK (the Finite Element ToolKit) to solve the 746s Poisson-Boltzmann equation numerically. FETK is a portable collection 746s of finite element modeling class libraries developed by the Michael Holst 746s research group and writtenTesting computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 746s *** PASSED *** 746s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 746s *** PASSED *** 746s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 746s *** PASSED *** 746s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 746s *** PASSED *** 746s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 746s *** PASSED *** 746s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 746s *** PASSED *** 746s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 746s *** PASSED *** 746s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 746s *** PASSED *** 746s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 746s *** PASSED *** 746s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 746s *** PASSED *** 746s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 746s *** PASSED *** 746s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 746s *** PASSED *** 746s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 746s *** PASSED *** 746s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 746s *** PASSED *** 746s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 746s *** PASSED *** 746s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 746s *** PASSED *** 746s Elapsed time: 9.905914 seconds 746s -------------------------------------------------------------------------------- 746s Total elapsed time: 21.323 seconds 746s Test results have been logged 746s -------------------------------------------------------------------------------- 746s -------------------------------------------------------------------------------- 746s Testing input file ion-pmf.in 746s 746s in an object-oriented form of C. FEtk is 746s designed to solve general coupled systems of nonlinear partial differential 746s equations using adaptive finite element methods, inexact Newton methods, 746s and algebraic multilevel methods. More information about FEtk may be found 746s at . 746s ---------------------------------------------------------------------- 746s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 746s Aqua is a modified form of the Holst group PMG library 746s which has been modified by Patrice Koehl 746s for improved efficiency and 746s memory usage when solving the Poisson-Boltzmann equation. 746s ---------------------------------------------------------------------- 746s Please cite your use of APBS as: 746s 746s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 746s nanosystems: application to microtubules and the ribosome. Proc. 746s Natl. Acad. Sci. USA 98, 10037-10041 2001. 746s 746s 746s This executable compiled on Jan 3 2025 at 11:01:42 746s 746s Parsing input file apbs-smol.in... 746s rank 0 size 1... 746s Parsed input file. 746s Got paths for 3 molecules 746s Reading PQR-format atom data from acetic-acid.pqr. 746s asc_getToken: Error occurred (bailing out). 746s Vio_scanf: Format problem with input. 746s 8 atoms 746s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 746s Net charge -1.67e-16 e 746s Reading PQR-format atom data from acetate.pqr. 746s asc_getToken: Error occurred (bailing out). 746s Vio_scanf: Format problem with input. 746s 8 atoms 746s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 746s Net charge -1.00e+00 e 746s Reading PQR-format atom data from proton.pqr. 746s 1 atoms 746s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 746s Net charge 1.00e+00 e 746s Preparing to run 12 PBE calculations. 746s ---------------------------------------- 746s CALCULATION #1 (acetic-solv): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 7.76163 A 746s Current memory usage: 61.581 MB total, 61.581 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.188 x 0.188 x 0.188 746s Grid lengths: 12.000 x 12.000 x 12.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 1 746s Linearized traditional PBE 746s Multiple Debye-Huckel sphere boundary conditions 746s 2 ion species (0.150 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 78.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 5.824172730822E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #2 (acetic-solv): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 7.76163 A 746s Current memory usage: 61.581 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.094 x 0.094 x 0.094 746s Grid lengths: 6.000 x 6.000 x 6.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 1 746s Linearized traditional PBE 746s Boundary conditions from focusing 746s 2 ion species (0.150 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 78.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 9.793622759239E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #3 (acetic-ref): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 0 A 746s Current memory usage: 61.405 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.188 x 0.188 x 0.188 746s Grid lengths: 12.000 x 12.000 x 12.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 1 746s Linearized traditional PBE 746s Multiple Debye-Huckel sphere boundary conditions 746s 2 ion species (0.000 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 2.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 5.846917564309E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #4 (acetic-ref): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 0 A 746s Current memory usage: 61.405 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.094 x 0.094 x 0.094 746s Grid lengths: 6.000 x 6.000 x 6.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 1 746s Linearized traditional PBE 746s Boundary conditions from focusing 746s 2 ion species (0.000 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 2.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 9.815953282539E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #5 (acetate-solv): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 7.76163 A 746s Current memory usage: 61.581 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.188 x 0.188 x 0.188 746s Grid lengths: 12.000 x 12.000 x 12.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 2 746s Linearized traditional PBE 746s Multiple Debye-Huckel sphere boundary conditions 746s 2 ion species (0.150 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 78.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 8.221328580569E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #6 (acetate-solv): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 7.76163 A 746s Current memory usage: 61.581 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.094 x 0.094 x 0.094 746s Grid lengths: 6.000 x 6.000 x 6.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 2 746s Linearized traditional PBE 746s Boundary conditions from focusing 746s 2 ion species (0.150 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 78.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 1.392867783119E+04 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #7 (acetate-ref): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 0 A 746s Current memory usage: 61.405 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.188 x 0.188 x 0.188 746s Grid lengths: 12.000 x 12.000 x 12.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 2 746s Linearized traditional PBE 746s Multiple Debye-Huckel sphere boundary conditions 746s 2 ion species (0.000 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 2.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 8.420373979905E+03 kJ/mol 746s Calculating forces... 746s [focusFillBound()]: WARNING: 746s Unusually large potential values 746s detected on the focusing boundary! 746s Convergence not guaranteed for NPBE/NRPBE calculations! 746s 746s ---------------------------------------- 746s CALCULATION #8 (acetate-ref): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 0 A 746s Current memory usage: 61.405 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.094 x 0.094 x 0.094 746s Grid lengths: 6.000 x 6.000 x 6.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 2 746s Linearized traditional PBE 746s Boundary conditions from focusing 746s 2 ion species (0.000 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 2.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 1.412716615065E+04 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #9 (proton-solv): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 7.76163 A 746s Current memory usage: 61.410 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.188 x 0.188 x 0.188 746s Grid lengths: 12.000 x 12.000 x 12.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 3 746s Linearized traditional PBE 746s Multiple Debye-Huckel sphere boundary conditions 746s 2 ion species (0.150 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 78.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 3.863066835285E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #10 (proton-solv): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 7.76163 A 746s Current memory usage: 61.410 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.094 x 0.094 x 0.094 746s Grid lengths: 6.000 x 6.000 x 6.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 3 746s Linearized traditional PBE 746s Boundary conditions from focusing 746s 2 ion species (0.150 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 78.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 6.289649216644E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s CALCULATION #11 (proton-ref): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 0 A 746s Current memory usage: 61.371 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.188 x 0.188 x 0.188 746s Grid lengths: 12.000 x 12.000 x 12.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 3 746s Linearized traditional PBE 746s Multiple Debye-Huckel sphere boundary conditions 746s 2 ion species (0.000 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 2.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 4.162533113906E+03 kJ/mol 746s Calculating forces... 746s [focusFillBound()]: WARNING: 746s Unusually large potential values 746s detected on the focusing boundary! 746s Convergence not guaranteed for NPBE/NRPBE calculations! 746s 746s ---------------------------------------- 746s CALCULATION #12 (proton-ref): MULTIGRID 746s Setting up problem... 746s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 746s Debye length: 0 A 746s Current memory usage: 61.371 MB total, 122.371 MB high water 746s Using linear spline charge discretization. 746s Grid dimensions: 65 x 65 x 65 746s Grid spacings: 0.094 x 0.094 x 0.094 746s Grid lengths: 6.000 x 6.000 x 6.000 746s Grid center: (0.000, -0.154, 1.287) 746s Multigrid levels: 5 746s Molecule ID: 3 746s Linearized traditional PBE 746s Boundary conditions from focusing 746s 2 ion species (0.000 M ionic strength): 746s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 746s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 746s Solute dielectric: 2.000 746s Solvent dielectric: 2.000 746s Using "molecular" surface definition;harmonic average smoothing 746s Solvent probe radius: 0.000 A 746s Temperature: 293.000 K 746s Electrostatic energies will be calculated 746s Total electrostatic energy = 6.585616091973E+03 kJ/mol 746s Calculating forces... 746s ---------------------------------------- 746s PRINT STATEMENTS 746s 746s print energy 1 (acetic-solv) - 2 (acetic-ref) end 746s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 746s Global net ELEC energy = -2.233052329981E+01 kJ/mol 746s 746s print energy 3 (acetate-solv) - 4 (acetate-ref) end 746s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 746s Global net ELEC energy = -1.984883194538E+02 kJ/mol 746s 746s print energy 5 (proton-solv) - 6 (proton-ref) end 746s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 746s Global net ELEC energy = -2.959668753288E+02 kJ/mol 746s 746s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 746s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 746s Global net ELEC energy = -4.721246714828E+02 kJ/mol 746s ---------------------------------------- 746s CLEANING UP AND SHUTTING DOWN... 746s Destroying force arrays. 746s No energy arrays to destroy. 746s Destroying multigrid structures. 746s Destroying finite element structures. 746s Destroying 3 molecules 746s Final memory usage: 0.001 MB total, 122.371 MB high water 746s 746s 746s Thanks for using APBS! 746s 755s Checking for intermediate energies in input file apbs-smol.out 755s EXPECTED COMPUTED: 16 755s EXPECTED EXPECTED: 16 755s 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] 755s 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'] 755s COMPUTED RESULT 5824.172730822 755s COMPUTED RESULT 9793.622759239 755s COMPUTED RESULT 5846.917564309 755s COMPUTED RESULT 9815.953282539 755s COMPUTED RESULT 8221.328580569 755s COMPUTED RESULT 13928.67783119 755s COMPUTED RESULT 8420.373979905 755s COMPUTED RESULT 14127.16615065 755s COMPUTED RESULT 3863.066835285 755s COMPUTED RESULT 6289.649216644 755s COMPUTED RESULT 4162.533113906 755s COMPUTED RESULT 6585.616091973 755s COMPUTED RESULT -22.33052329981 755s COMPUTED RESULT -198.4883194538 755s COMPUTED RESULT -295.9668753288 755s COMPUTED RESULT -472.1246714828 755s Running tests for ion-pmf section 755s BINARY: /usr/bin/apbs 755s INPUT: ion-pmf.in 755s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 755s asc_getToken: Error occurred (bailing out). 755s Vio_scanf: Format problem with input. 755s asc_getToken: Error occurred (bailing out). 755s Vio_scanf: Format problem with input. 755s 755s 755s ---------------------------------------------------------------------- 755s APBS -- Adaptive Poisson-Boltzmann Solver 755s Version APBS 3.4.1 755s 755s Nathan A. Baker (nathan.baker@pnnl.gov) 755s Pacific Northwest National Laboratory 755s 755s Additional contributing authors listed in the code documentation. 755s 755s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 755s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 755s Northwest Division for the U.S. Department of Energy. 755s 755s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 755s Portions Copyright (c) 2002-2020, Nathan A. Baker. 755s Portions Copyright (c) 1999-2002, The Regents of the University of California. 755s Portions Copyright (c) 1995, Michael Holst. 755s All rights reserved. 755s 755s Redistribution and use in source and binary forms, with or without 755s modification, are permitted provided that the following conditions are met: 755s 755s * Redistributions of source code must retain the above copyright notice, this 755s list of conditions and the following disclaimer. 755s 755s * Redistributions in binary form must reproduce the above copyright notice, 755s this list of conditions and the following disclaimer in the documentation 755s and/or other materials provided with the distribution. 755s 755s * Neither the name of the developer nor the names of its contributors may be 755s used to endorse or promote products derived from this software without 755s specific prior written permission. 755s 755s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 755s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 755s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 755s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 755s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 755s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 755s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 755s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 755s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 755s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 755s ---------------------------------------------------------------------- 755s APBS uses FETK (the Finite Element ToolKit) to solve the 755s Poisson-Boltzmann equation numerically. FETK is a portable collection 755s of finite element modeling class libraries developed by the Michael Holst 755s research group and written in an object-oriented form of C. FEtk is 755s designed to solve general coupled systems of nonlinear partial differential 755s equations using adaptive finite element methods, inexact Newton methods, 755s and algebraic multilevel methods. More information about FEtk may be found 755s at . 755s ---------------------------------------------------------------------- 755s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 755s Aqua is a modified form of the Holst group PMG library 755s which has been modified by Patrice Koehl 755s for improved efficiency and 755s memory usage when solving the Poisson-Boltzmann equation. 755s ---------------------------------------------------------------------- 755s Please cite your use of APBS as: 755s 755s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 755s nanosystems: application to microtubules and the ribosome. Proc. 755s Natl. Acad. Sci. USA 98, 10037-10041 2001. 755s 755s 755s This executable compiled on Jan 3 2025 at 11:01:42 755s 755s Parsing input file ion-pmf.in... 755s rank 0 size 1... 755s Parsed input file. 755s Reading parameter data from parm.dat. 755s Got paths for 1 molecules 755s Reading PDB-format atom data from ion-pmf.pdb. 755s Vpmg_ibForce: No force for zero ionic strength! 755s Vpmg_ibForce: No force for zero ionic strength! 755s 2 atoms 755s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 755s Net charge 2.00e+00 e 755s Preparing to run 3 PBE calculations. 755s ---------------------------------------- 755s CALCULATION #1 (solv): MULTIGRID 755s Setting up problem... 755s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 755s Debye length: 0 A 755s Current memory usage: 61.094 MB total, 61.094 MB high water 755s Using cubic spline charge discretization. 755s Grid dimensions: 65 x 65 x 65 755s Grid spacings: 0.210 x 0.210 x 0.210 755s Grid lengths: 13.440 x 13.440 x 13.440 755s Grid center: (0.000, 0.000, 0.000) 755s Multigrid levels: 5 755s Molecule ID: 1 755s Linearized traditional PBE 755s Multiple Debye-Huckel sphere boundary conditions 755s 0 ion species (0.000 M ionic strength): 755s Solute dielectric: 1.000 755s Solvent dielectric: 78.540 755s Using spline-based surface definition;window = 0.300 755s Temperature: 298.150 K 755s Electrostatic energies will be calculated 755s All-atom solvent forces will be calculated 755s Total electrostatic energy = 7.839535983197E+03 kJ/mol 755s Calculating forces... 755s Printing per-atom forces for molecule 1 (kJ/mol/A) 755s Legend: 755s tot n -- total force for atom n 755s qf n -- fixed charge force for atom n 755s db n -- dielectric boundary force for atom n 755s ib n -- ionic boundary force for atom n 755s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 755s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 755s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 755s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 755s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 755s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 755s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 755s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 755s Vpmg_ibForce: No force for zero ionic strength! 755s Vpmg_ibForce: No force for zero ionic strength! 755s ---------------------------------------- 755s CALCULATION #2 (ref): MULTIGRID 755s Setting up problem... 755s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 755s Debye length: 0 A 755s Current memory usage: 61.095 MB total, 61.134 MB high water 755s Using cubic spline charge discretization. 755s Grid dimensions: 65 x 65 x 65 755s Grid spacings: 0.210 x 0.210 x 0.210 755s Grid lengths: 13.440 x 13.440 x 13.440 755s Grid center: (0.000, 0.000, 0.000) 755s Multigrid levels: 5 755s Molecule ID: 1 755s Linearized traditional PBE 755s Multiple Debye-Huckel sphere boundary conditions 755s 0 ion species (0.000 M ionic strength): 755s Solute dielectric: 1.000 755s Solvent dielectric: 1.000 755s Using spline-based surface definition;window = 0.300 755s Temperature: 298.150 K 755s Electrostatic energies will be calculated 755s All-atom solvent forces will be calculated 755s Total electrostatic energy = 8.964727588811E+03 kJ/mol 755s Calculating forces... 755s Printing per-atom forces for molecule 1 (kJ/mol/A) 755s Legend: 755s tot n -- total force for atom n 755s qf n -- fixed charge force for atom n 755s db n -- dielectric boundary force for atom n 755s ib n -- ionic boundary force for atom n 755s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 755s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 755s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 755s mgF db 0 0.000e+00 0.000e+00 0.000e+00 755s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 755s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 755s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 755s mgF db 1 0.000e+00 0.000e+00 0.000e+00 755s ---------------------------------------- 755s CALCULATION #3 (asolv): APOLAR 755s Printing per atom forces (kJ/mol/A) 755s Legend: 755s tot n -- Total force for atom n 755s sasa n -- SASA force for atom n 755s sav n -- SAV force for atom n 755s wca n -- WCA force for atom n 755s 755s gamma 0.000720 755s pressure 0.000000 755s bconc 0.033000 755s 755s tot 0 2.715e-02 9.130e-07 9.130e-07 755s sasa 0 -1.100e+01 0.000e+00 0.000e+00 755s sav 0 0.000e+00 0.000e+00 0.000e+00 755s wca 0 -5.827e-01 -2.767e-05 -2.767e-05 755s tot 1 -2.723e-02 9.133e-07 9.133e-07 755s sasa 1 1.112e+01 0.000e+00 0.000e+00 755s sav 1 0.000e+00 0.000e+00 0.000e+00 755s wca 1 5.827e-01 -2.767e-05 -2.767e-05 755s 755s 755s Solvent Accessible Surface Area (SASA) for each atom: 755s SASA for atom 0: 1.153275282828E+02 755s SASA for atom 1: 1.153114143344E+02 755s 755s Total solvent accessible surface area: 230.639 A^2 755s 755s Surface tension*area energies (gamma * SASA) for each atom: 755s Surface tension*area energy for atom 0: 8.303582036361E-02 755s Surface tension*area energy for atom 1: 8.302421832080E-02 755s 755s Total surface tension energy: 0.16606 kJ/mol 755s 755s Total solvent accessible volume: 0 A^3 755s 755s Total pressure*volume energy: 0 kJ/mol 755s 755s WCA dispersion Energies for each atom: 755s WCA energy for atom 0: -6.909718359932E+00 755s WCA energy for atom 1: -6.909422551724E+00 755s 755s Total WCA energy: -13.8191 kJ/mol 755s 755s Total non-polar energy = -1.365308087297E+01 kJ/mol 755s ---------------------------------------- 755s PRINT STATEMENTS 755s 755s print energy 1 (solv) - 2 (ref) end 755s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 755s Global net ELEC energy = -1.125191605614E+03 kJ/mol 755s print force 1 (solv) - 2 (ref) end 755s Printing per-atom forces (kJ/mol/A). 755s Legend: 755s tot n -- Total force for atom n 755s qf n -- Fixed charge force for atom n 755s db n -- Dielectric boundary force for atom n 755s ib n -- Ionic boundary force for atom n 755s tot all -- Total force for system 755s qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 755s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 755s db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 755s tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 755s qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 755s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 755s db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 755s tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 755s tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 755s 755s print APOL energy 1 (asolv) end 755s Global net APOL energy = -1.365308087297E+01 kJ/mol 755s 755s print APOL force 1 (asolv) end 755s Printing per atom forces (kJ/mol/A) 755s Legend: 755s tot n -- Total force for atom n 755s sasa n -- SASA force for atom n 755s sav n -- SAV force for atom n 755s wca n -- WCA force for atom n 755s tot all -- Total force for system 755s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 755s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 755s wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 755s tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 755s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 755s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 755s wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 755s tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 755s tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 755s ---------------------------------------- 755s CLEANING UP AND SHUTTING DOWN... 755s Destroying force arrays. 755s No energy arrays to destroy. 755s Destroying multigrid structures. 755s Destroying finite element structures. 755s Destroying 1 molecules 755s Final memory usage: 60.711 MB total, 62.228 MB high water 755s 755s 755s Thanks for using APBS! 755s 755s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 755s *** PASSED *** 755s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 755s *** PASSED *** 755s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 755s *** PASSED *** 755s Elapsed time: 8.731925 seconds 755s -------------------------------------------------------------------------------- 755s Total elapsed time: 8.731925 seconds 755s Test results have been logged 755s -------------------------------------------------------------------------------- 755s -------------------------------------------------------------------------------- 755s Testing input file apbs-mol-vdw.in 755s 786s Checking for intermediate energies in input file ion-pmf.out 786s EXPECTED COMPUTED: 4 786s EXPECTED EXPECTED: 4 786s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] 786s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 786s COMPUTED RESULT 7839.535983197 786s COMPUTED RESULT 8964.727588811 786s COMPUTED RESULT -1125.191605614 786s COMPUTED RESULT -13.65308087297 786s Running tests for pka-lig section 786s BINARY: /usr/bin/apbs 786s INPUT: apbs-mol-vdw.in 786s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 786s asc_getToken: Error occurred (bailing out). 786s Vio_scanf: Format problem with input. 786s 786s 786s ---------------------------------------------------------------------- 786s APBS -- Adaptive Poisson-Boltzmann Solver 786s Version APBS 3.4.1 786s 786s Nathan A. Baker (nathan.baker@pnnl.gov) 786s Pacific Northwest National Laboratory 786s 786s Additional contributing authors listed in the code documentation. 786s 786s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 786s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 786s Northwest Division for the U.S. Department of Energy. 786s 786s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 786s Portions Copyright (c) 2002-2020, Nathan A. Baker. 786s Portions Copyright (c) 1999-2002, The Regents of the University of California. 786s Portions Copyright (c) 1995, Michael Holst. 786s All rights reserved. 786s 786s Redistribution and use in source and binary forms, with or without 786s modification, are permitted provided that the following conditions are met: 786s 786s * Redistributions of source code must retain the above copyright notice, this 786s list of conditions and the following disclaimer. 786s 786s * Redistributions in binary form must reproduce the above copyright notice, 786s this list of conditions and the following disclaimer in the documentation 786s and/or other materials provided with the distribution. 786s 786s * Neither the name of the developer nor the names of its contributors may be 786s used to endorse or promote products derived from this software without 786s specific prior written permission. 786s 786s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 786s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 786s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 786s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 786s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 786s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 786s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 786s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 786s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 786s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 786s ---------------------------------------------------------------------- 786s APBS uses FETK (the Finite Element ToolKit) to solve the 786s Poisson-Boltzmann equation numerically. FETK is a portable collection 786s of finite element modeling class libraries developed by the Michael Holst 786s research group and written in an object-oriented form of C. FEtk is 786s designed to solve general coupled systems of nonlinear partial differential 786s equations using adaptive finite element methods, inexact Newton methods, 786s and algebraic multilevel methods. More information about FEtk may be found 786s at . 786s ---------------------------------------------------------------------- 786s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 786s Aqua is a modified form of the Holst group PMG library 786s which has been modified by Patrice Koehl 786s for improved efficiency and 786s memory usage when solving the Poisson-Boltzmann equation. 786s ---------------------------------------------------------------------- 786s Please cite your use of APBS as: 786s 786s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 786s nanosystems: application to microtubules and the ribosome. Proc. 786s Natl. Acad. Sci. USA 98, 10037-10041 2001. 786s 786s 786s This executable compiled on Jan 3 2025 at 11:01:42 786s 786s Parsing input file apbs-mol-vdw.in... 786s rank 0 size 1... 786s Parsed input file. 786s Got paths for 3 molecules 786s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 786s asc_getToken: Error occurred (bailing out). 786s Vio_scanf: Format problem with input. 786s 47 atoms 786s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 786s Net charge 1.11e-16 e 786s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 786s asc_getToken: Error occurred (bailing out). 786s Vio_scanf: Format problem with input. 786s 3423 atoms 786s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 786s Net charge 1.00e+00 e 786s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 786s 3470 atoms 786s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 786s Net charge 1.00e+00 e 786s Preparing to run 6 PBE calculations. 786s ---------------------------------------- 786s CALCULATION #1 (lig-coarse): MULTIGRID 786s Setting up problem... 786s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 786s Debye length: 0 A 786s Current memory usage: 203.811 MB total, 203.811 MB high water 786s Using linear spline charge discretization. 786s Grid dimensions: 97 x 97 x 97 786s Grid spacings: 0.729 x 0.729 x 0.729 786s Grid lengths: 70.000 x 70.000 x 70.000 786s Grid center: (28.969, -32.507, 27.022) 786s Multigrid levels: 4 786s Molecule ID: 1 786s Linearized traditional PBE 786s Single Debye-Huckel sphere boundary conditions 786s 2 ion species (0.000 M ionic strength): 786s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 786s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 786s Solute dielectric: 2.000 786s Solvent dielectric: 78.000 786s Using "molecular" surface definition; no smoothing 786s Solvent probe radius: 0.000 A 786s Temperature: 298.150 K 786s Electrostatic energies will be calculated 786s Total electrostatic energy = 2.224988750664E+03 kJ/mol 786s Calculating forces... 786s ---------------------------------------- 786s CALCULATION #2 (lig-fine): MULTIGRID 786s Setting up problem... 786s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 786s Debye length: 0 A 786s Current memory usage: 203.811 MB total, 405.040 MB high water 786s Using linear spline charge discretization. 786s Grid dimensions: 97 x 97 x 97 786s Grid spacings: 0.250 x 0.250 x 0.250 786s Grid lengths: 24.000 x 24.000 x 24.000 786s Grid center: (24.822, -33.153, 21.545) 786s Multigrid levels: 4 786s Molecule ID: 1 786s Linearized traditional PBE 786s Boundary conditions from focusing 786s 2 ion species (0.000 M ionic strength): 786s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 786s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 786s Solute dielectric: 2.000 786s Solvent dielectric: 78.000 786s Using "molecular" surface definition; no smoothing 786s Solvent probe radius: 0.000 A 786s Temperature: 298.150 K 786s Electrostatic energies will be calculated 786s Total electrostatic energy = 1.049695084686E+04 kJ/mol 786s Calculating forces... 786s ---------------------------------------- 786s CALCULATION #3 (pka-coarse): MULTIGRID 786s Setting up problem... 786s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 786s Debye length: 0 A 786s Current memory usage: 270.381 MB total, 405.040 MB high water 786s Using linear spline charge discretization. 786s Grid dimensions: 97 x 97 x 97 786s Grid spacings: 0.729 x 0.729 x 0.729 786s Grid lengths: 70.000 x 70.000 x 70.000 786s Grid center: (28.969, -32.507, 27.022) 786s Multigrid levels: 4 786s Molecule ID: 2 786s Linearized traditional PBE 786s Single Debye-Huckel sphere boundary conditions 786s 2 ion species (0.000 M ionic strength): 786s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 786s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 786s Solute dielectric: 2.000 786s Solvent dielectric: 78.000 786s Using "molecular" surface definition; no smoothing 786s Solvent probe radius: 0.000 A 786s Temperature: 298.150 K 786s Electrostatic energies will be calculated 786s Total electrostatic energy = 1.818450789522E+05 kJ/mol 786s Calculating forces... 786s [focusFillBound()]: WARNING: 786s Unusually large potential values 786s detected on the focusing boundary! 786s Convergence not guaranteed for NPBE/NRPBE calculations! 786s 786s ---------------------------------------- 786s CALCULATION #4 (pka-fine): MULTIGRID 786s Setting up problem... 786s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 786s Debye length: 0 A 786s Current memory usage: 270.381 MB total, 491.899 MB high water 786s Using linear spline charge discretization. 786s Grid dimensions: 97 x 97 x 97 786s Grid spacings: 0.250 x 0.250 x 0.250 786s Grid lengths: 24.000 x 24.000 x 24.000 786s Grid center: (24.8Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 786s *** PASSED *** 786s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 786s *** PASSED *** 786s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 786s *** PASSED *** 786s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 786s *** PASSED *** 786s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 786s *** PASSED *** 786s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 786s *** PASSED *** 786s Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) 786s *** PASSED *** 786s Elapsed time: 31.291506 seconds 786s -------------------------------------------------------------------------------- 786s -------------------------------------------------------------------------------- 786s Testing input file apbs-smol-vdw.in 786s 786s 22, -33.153, 21.545) 786s Multigrid levels: 4 786s Molecule ID: 2 786s Linearized traditional PBE 786s Boundary conditions from focusing 786s 2 ion species (0.000 M ionic strength): 786s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 786s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 786s Solute dielectric: 2.000 786s Solvent dielectric: 78.000 786s Using "molecular" surface definition; no smoothing 786s Solvent probe radius: 0.000 A 786s Temperature: 298.150 K 786s Electrostatic energies will be calculated 786s Total electrostatic energy = 3.008254338259E+05 kJ/mol 786s Calculating forces... 786s ---------------------------------------- 786s CALCULATION #5 (complex-coarse): MULTIGRID 786s Setting up problem... 786s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 786s Debye length: 0 A 786s Current memory usage: 271.059 MB total, 491.899 MB high water 786s Using linear spline charge discretization. 786s Grid dimensions: 97 x 97 x 97 786s Grid spacings: 0.729 x 0.729 x 0.729 786s Grid lengths: 70.000 x 70.000 x 70.000 786s Grid center: (28.969, -32.507, 27.022) 786s Multigrid levels: 4 786s Molecule ID: 3 786s Linearized traditional PBE 786s Single Debye-Huckel sphere boundary conditions 786s 2 ion species (0.000 M ionic strength): 786s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 786s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 786s Solute dielectric: 2.000 786s Solvent dielectric: 78.000 786s Using "molecular" surface definition; no smoothing 786s Solvent probe radius: 0.000 A 786s Temperature: 298.150 K 786s Electrostatic energies will be calculated 786s Total electrostatic energy = 1.840918409896E+05 kJ/mol 786s Calculating forces... 786s [focusFillBound()]: WARNING: 786s Unusually large potential values 786s detected on the focusing boundary! 786s Convergence not guaranteed for NPBE/NRPBE calculations! 786s 786s ---------------------------------------- 786s CALCULATION #6 (complex-fine): MULTIGRID 786s Setting up problem... 786s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 786s Debye length: 0 A 786s Current memory usage: 271.059 MB total, 492.811 MB high water 786s Using linear spline charge discretization. 786s Grid dimensions: 97 x 97 x 97 786s Grid spacings: 0.250 x 0.250 x 0.250 786s Grid lengths: 24.000 x 24.000 x 24.000 786s Grid center: (24.822, -33.153, 21.545) 786s Multigrid levels: 4 786s Molecule ID: 3 786s Linearized traditional PBE 786s Boundary conditions from focusing 786s 2 ion species (0.000 M ionic strength): 786s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 786s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 786s Solute dielectric: 2.000 786s Solvent dielectric: 78.000 786s Using "molecular" surface definition; no smoothing 786s Solvent probe radius: 0.000 A 786s Temperature: 298.150 K 786s Electrostatic energies will be calculated 786s Total electrostatic energy = 3.113304681884E+05 kJ/mol 786s Calculating forces... 786s ---------------------------------------- 786s PRINT STATEMENTS 786s 786s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 786s Local net energy (PE 0) = 8.083515648730E+00 kJ/mol 786s Global net ELEC energy = 8.083515648730E+00 kJ/mol 786s ---------------------------------------- 786s CLEANING UP AND SHUTTING DOWN... 786s Destroying force arrays. 786s No energy arrays to destroy. 786s Destroying multigrid structures. 786s Destroying finite element structures. 786s Destroying 3 molecules 786s Final memory usage: 0.001 MB total, 492.811 MB high water 786s 786s 786s Thanks for using APBS! 786s 809s Checking for intermediate energies in input file apbs-mol-vdw.out 809s EXPECTED COMPUTED: 7 809s EXPECTED EXPECTED: 7 809s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] 809s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 809s COMPUTED RESULT 2224.988750664 809s COMPUTED RESULT 10496.95084686 809s COMPUTED RESULT 181845.0789522 809s COMPUTED RESULT 300825.4338259 809s COMPUTED RESULT 184091.8409896 809s COMPUTED RESULT 311330.4681884 809s COMPUTED RESULT 8.08351564873 809s BINARY: /usr/bin/apbs 809s INPUT: apbs-smol-vdw.in 809s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 809s asc_getToken: Error occurred (bailing out). 809s Vio_scanf: Format problem with input. 809s 809s 809s ---------------------------------------------------------------------- 809s APBS -- Adaptive Poisson-Boltzmann Solver 809s Version APBS 3.4.1 809s 809s Nathan A. Baker (nathan.baker@pnnl.gov) 809s Pacific Northwest National Laboratory 809s 809s Additional contributing authors listed in the code documentation. 809s 809s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 809s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 809s Northwest Division for the U.S. Department of Energy. 809s 809s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 809s Portions Copyright (c) 2002-2020, Nathan A. Baker. 809s Portions Copyright (c) 1999-2002, The Regents of the University of California. 809s Portions Copyright (c) 1995, Michael Holst. 809s All rights reserved. 809s 809s Redistribution and use in source and binary forms, with or without 809s modification, are permitted provided that the following conditions are met: 809s 809s * Redistributions of source code must retain the above copyright notice, this 809s list of conditions and the following disclaimer. 809s 809s * Redistributions in binary form must reproduce the above copyright notice, 809s this list of conditions and the following disclaimer in the documentation 809s and/or other materials provided with the distribution. 809s 809s * Neither the name of the developer nor the names of its contributors may be 809s used to endorse or promote products derived from this software without 809s specific prior written permission. 809s 809s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 809s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 809s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 809s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 809s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 809s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 809s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 809s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 809s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 809s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 809s ---------------------------------------------------------------------- 809s APBS uses FETK (the Finite Element ToolKit) to solve the 809s Poisson-Boltzmann equation numerically. FETK is a portable collection 809s of finite element modeling class libraries developed by the Michael Holst 809s research group and written in an object-oriented form of C. FEtk is 809s designed to solve general coupled systems of nonlinear partial differential 809s equations using adaptive finite element methods, inexact Newton methods, 809s and algebraic multilevel methods. More information about FEtk may be found 809s at . 809s ---------------------------------------------------------------------- 809s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 809s Aqua is a modified form of the Holst group PMG library 809s which has been modified by Patrice Koehl 809s for improved efficiency and 809s memory usage when solving the Poisson-Boltzmann equation. 809s ---------------------------------------------------------------------- 809s Please cite your use of APBS as: 809s 809s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 809s nanosystems: application to microtubules and the ribosome. Proc. 809s Natl. Acad. Sci. USA 98, 10037-10041 2001. 809s 809s 809s This executable compiled on Jan 3 2025 at 11:01:42 809s 809s Parsing input file apbs-smol-vdw.in... 809s rank 0 size 1... 809s Parsed input file. 809s Got paths for 3 molecules 809s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 809s asc_getToken: Error occurred (bailing out). 809s Vio_scanf: Format problem with input. 809s 47 atoms 809s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 809s Net charge 1.11e-16 e 809s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 809s asc_getToken: Error occurred (bailing out). 809s Vio_scanf: Format problem with input. 809s 3423 atoms 809s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 809s Net charge 1.00e+00 e 809s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 809s 3470 atoms 809s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 809s Net charge 1.00e+00 e 809s Preparing to run 6 PBE calculations. 809s ---------------------------------------- 809s CALCULATION #1 (lig-coarse): MULTIGRID 809s Setting up problem... 809s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 809s Debye length: 0 A 809s Current memory usage: 203.811 MB total, 203.811 MB high water 809s Using linear spline charge discretization. 809s Grid dimensions: 97 x 97 x 97 809s Grid spacings: 0.729 x 0.729 x 0.729 809s Grid lengths: 70.000 x 70.000 x 70.000 809s Grid center: (28.969, -32.507, 27.022) 809s Multigrid levels: 4 809s Molecule ID: 1 809s Linearized traditional PBE 809s Single Debye-Huckel sphere boundary conditions 809s 2 ion species (0.000 M ionic strength): 809s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 809s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 809s Solute dielectric: 2.000 809s Solvent dielectric: 78.000 809s Using "molecular" surface definition;harmonic average smoothing 809s Solvent probe radius: 0.000 A 809s Temperature: 298.150 K 809s Electrostatic energies will be calculated 809s Total electrostatic energy = 2.226793167046E+03 kJ/mol 809s Calculating forces... 809s ---------------------------------------- 809s CALCULATION #2 (lig-fine): MULTIGRID 809s Setting up problem... 809s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 809s Debye length: 0 A 809s Current memory usage: 203.811 MB total, 405.040 MB high water 809s Using linear spline charge discretization. 809s Grid dimensions: 97 x 97 x 97 809s Grid spacings: 0.250 x 0.250 x 0.250 809s Grid lengths: 24.000 x 24.000 x 24.000 809s Grid center: (24.822, -33.153, 21.545) 809s Multigrid levels: 4 809s Molecule ID: 1 809s Linearized traditional PBE 809s Boundary conditions from focusing 809s 2 ion species (0.000 M ionic strength): 809s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 809s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 809s Solute dielectric: 2.000 809s Solvent dielectric: 78.000 809s Using "molecular" surface definition;harmonic average smoothing 809s Solvent probe radius: 0.000 A 809s Temperature: 298.150 K 809s Electrostatic energies will be calculated 809s Total electrostatic energy = 1.050504485887E+04 kJ/mol 809s Calculating forces... 809s ---------------------------------------- 809s CALCULATION #3 (pka-coarse): MULTIGRID 809s Setting up problem... 809s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 809s Debye length: 0 A 809s Current memory usage: 270.381 MB total, 405.040 MB high water 809s Using linear spline charge discretization. 809s Grid dimensions: 97 x 97 x 97 809s Grid spacings: 0.729 x 0.729 x 0.729 809s Grid lengths: 70.000 x 70.000 x 70.000 809s Grid center: (28.969, -32.507, 27.022) 809s Multigrid levels: 4 809s Molecule ID: 2 809s Linearized traditional PBE 809s Single Debye-Huckel sphere boundary conditions 809s 2 ion species (0.000 M ionic strength): 809s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 809s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 809s Solute dielectric: 2.000 809s Solvent dielectric: 78.000 809s Using "molecular" surface definition;harmonic average smoothing 809s Solvent probe radius: 0.000 A 809s Temperature: 298.150 K 809s Electrostatic energies will be calculated 809s Total electrostatic energy = 1.827976621645E+05 kJ/mol 809s Calculating forces... 809s [focusFillBound()]: WARNING: 809s Unusually large potential values 809s detected on the focusing boundary! 809s Convergence not guaranteed for NPBE/NRPBE calculations! 809s 809s ---------------------------------------- 809s CALCULATION #4 (pka-fine): MULTIGRID 809s Setting up problem... 809s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 809s Debye length: 0 A 809s Current memory usage: 270.381 MB total, 491.899 MB high water 809s Using linear spline charge discretization. 809s Grid dimensions: 97 x 97 x 97 809s Grid spacings: 0.250 x 0.250 x 0.250 809s Grid lengths: 24.000 x 24.000 x 24.000 809s Grid center: (24.822, -33.153, 21.545) 809s Multigrid levels: 4 809s Molecule ID: 2 809s Linearized traditional PBE 809s Boundary conditions from focusing 809s 2 ion species (0.000 M ionic strength): 809s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 809s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 809s Solute dielectric: 2.000 809s Solvent dielectric: 78.000 809s Using "molecular" surface definition;harmonic average smoothing 809s Solvent probe radius: 0.000 A 809s Temperature: 298.150 K 809s Electrostatic energies will be calculated 809s Total electrostatic energy = 3.017228546773E+05 kJ/mol 809s Calculating forces... 809s ---------------------------------------- 809s CALCULATION #5 (complex-coarse): MULTIGRID 809s Setting up problem... 809s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 809s Debye length: 0 A 809s Current memory usage: 271.059 MB total, 491.899 MB high water 809s Using linear spline charge discretization. 809s Grid dimensions: 97 x 97 x 97 809s Grid spacings: 0.729 x 0.729 x 0.729 809s Grid lengths: 70.000 x 70.000 x 70.000 809s Grid center: (28.969, -32.507, 27.022) 809s Multigrid levels: 4 809s Molecule ID: 3 809s Linearized traditional PBE 809s Single Debye-Huckel sphere boundary conditions 809s 2 ion species (0.000 M ionic strength): 809s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 809s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 809s Solute dielectric: 2.000 809s Solvent dielectric: 78.000 809s Using "molecular" surface definition;harmonic average smoothing 809s Solvent probe radius: 0.000 A 809s Temperature: 298.150 K 809s Electrostatic energies will be calculated 809s Total electrostatic energy = 1.850819075387E+05 kJ/mol 809s Calculating forces... 809s [focusFillBound()]: WARNING: 809s Unusually large potential values 809s detected on the focusing boundary! 809s Convergence not guaranteed for NPBE/NRPBE calculations! 809s 809s ---------------------------------------- 809s CALCULATION #6 (complex-fine): MULTIGRID 809s Setting up problem... 809s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 809s Debye length: 0 A 809s Current memory usage: 271.059 MB total, 492.811 MB high water 809s Using linear spline charge discretization. 809s Grid dimensions: 97 x 97 x 97 809s Grid spacings: 0.250 x 0.250 x 0.250 809s Grid lengths: 24.000 x 24.000 x 24.000 809s Grid center: (24.822, -33.153, 21.545) 809s Multigrid levels: 4 809s Molecule ID: 3 809s Linearized traditional PBE 809s Boundary conditions from focusing 809s 2 ion species (0.000 M ionic strength): 809s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 809s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 809s Solute dielectric: 2.000 809s Solvent dielectric: 78.000 809s Using "molecular" surface definition;harmonic average smoothing 809s Solvent probe radius: 0.000 A 809s Temperature: 298.150 K 809s Electrostatic energies will be calculated 809s Total electrostatic energy = 3.122488625388E+05 kJ/mol 809s Calculating forces... 809s ---------------------------------------- 809s PRINT STATEMENTS 809s 809s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 809s Local net energy (PE 0) = 2.096300255723E+01 kJ/mol 809s Global net ELEC energy = 2.096300255723E+01 kJ/mol 809s ---------------------------------------- 809s CLEANING UP AND SHUTTING DOWN... 809s Destroying force arrays. 809s No energy arrays to destroy. 809s Destroying multigrid structures. 809s Destroying finite element structures. 809s Destroying 3 molecules 809s Final memory usage: 0.001 MB total, 492.811 MB high water 809s 809s 809s Thanks for using APBS! 809s 809s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 809s *** PASSED *** 809s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 809s *** PASSED *** 809s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 809s *** PASSED *** 809s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 809s *** PASSED *** 809s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 809s *** PASSED *** 809s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 809s *** PASSED *** 809s Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01) 809s *** PASSED *** 809s Elapsed time: 23.042236 seconds 809s -------------------------------------------------------------------------------- 809s -------------------------------------------------------------------------------- 809s Testing input file apbs-mol-surf.in 809s 834s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 834s *** PASSED *** 834s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 834s *** PASSED *** 834s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 834s *** PASSED *** 834s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 834s *** PASSED *** 834s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 834s *** PASSED *** 834s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 834s *** PASSED *** 834s Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) 834s *** PASSED *** 834s Elapsed time: 24.323496 seconds 834s -------------------------------------------------------------------------------- 834s -------------------------------------------------------------------------------- 834s Testing input file apbs-smol-surf.in 834s 834s Checking for intermediate energies in input file apbs-smol-vdw.out 834s EXPECTED COMPUTED: 7 834s EXPECTED EXPECTED: 7 834s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] 834s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 834s COMPUTED RESULT 2226.793167046 834s COMPUTED RESULT 10505.04485887 834s COMPUTED RESULT 182797.6621645 834s COMPUTED RESULT 301722.8546773 834s COMPUTED RESULT 185081.9075387 834s COMPUTED RESULT 312248.8625388 834s COMPUTED RESULT 20.96300255723 834s BINARY: /usr/bin/apbs 834s INPUT: apbs-mol-surf.in 834s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 834s asc_getToken: Error occurred (bailing out). 834s Vio_scanf: Format problem with input. 834s 834s 834s ---------------------------------------------------------------------- 834s APBS -- Adaptive Poisson-Boltzmann Solver 834s Version APBS 3.4.1 834s 834s Nathan A. Baker (nathan.baker@pnnl.gov) 834s Pacific Northwest National Laboratory 834s 834s Additional contributing authors listed in the code documentation. 834s 834s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 834s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 834s Northwest Division for the U.S. Department of Energy. 834s 834s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 834s Portions Copyright (c) 2002-2020, Nathan A. Baker. 834s Portions Copyright (c) 1999-2002, The Regents of the University of California. 834s Portions Copyright (c) 1995, Michael Holst. 834s All rights reserved. 834s 834s Redistribution and use in source and binary forms, with or without 834s modification, are permitted provided that the following conditions are met: 834s 834s * Redistributions of source code must retain the above copyright notice, this 834s list of conditions and the following disclaimer. 834s 834s * Redistributions in binary form must reproduce the above copyright notice, 834s this list of conditions and the following disclaimer in the documentation 834s and/or other materials provided with the distribution. 834s 834s * Neither the name of the developer nor the names of its contributors may be 834s used to endorse or promote products derived from this software without 834s specific prior written permission. 834s 834s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 834s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 834s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 834s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 834s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 834s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 834s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 834s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 834s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 834s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 834s ---------------------------------------------------------------------- 834s APBS uses FETK (the Finite Element ToolKit) to solve the 834s Poisson-Boltzmann equation numerically. FETK is a portable collection 834s of finite element modeling class libraries developed by the Michael Holst 834s research group and written in an object-oriented form of C. FEtk is 834s designed to solve general coupled systems of nonlinear partial differential 834s equations using adaptive finite element methods, inexact Newton methods, 834s and algebraic multilevel methods. More information about FEtk may be found 834s at . 834s ---------------------------------------------------------------------- 834s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 834s Aqua is a modified form of the Holst group PMG library 834s which has been modified by Patrice Koehl 834s for improved efficiency and 834s memory usage when solving the Poisson-Boltzmann equation. 834s ---------------------------------------------------------------------- 834s Please cite your use of APBS as: 834s 834s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 834s nanosystems: application to microtubules and the ribosome. Proc. 834s Natl. Acad. Sci. USA 98, 10037-10041 2001. 834s 834s 834s This executable compiled on Jan 3 2025 at 11:01:42 834s 834s Parsing input file apbs-mol-surf.in... 834s rank 0 size 1... 834s Parsed input file. 834s Got paths for 3 molecules 834s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 834s asc_getToken: Error occurred (bailing out). 834s Vio_scanf: Format problem with input. 834s 47 atoms 834s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 834s Net charge 1.11e-16 e 834s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 834s asc_getToken: Error occurred (bailing out). 834s Vio_scanf: Format problem with input. 834s 3423 atoms 834s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 834s Net charge 1.00e+00 e 834s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 834s 3470 atoms 834s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 834s Net charge 1.00e+00 e 834s Preparing to run 6 PBE calculations. 834s ---------------------------------------- 834s CALCULATION #1 (lig-coarse): MULTIGRID 834s Setting up problem... 834s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 834s Debye length: 0 A 834s Current memory usage: 203.396 MB total, 203.396 MB high water 834s Using linear spline charge discretization. 834s Grid dimensions: 97 x 97 x 97 834s Grid spacings: 0.729 x 0.729 x 0.729 834s Grid lengths: 70.000 x 70.000 x 70.000 834s Grid center: (28.969, -32.507, 27.022) 834s Multigrid levels: 4 834s Molecule ID: 1 834s Linearized traditional PBE 834s Single Debye-Huckel sphere boundary conditions 834s 2 ion species (0.000 M ionic strength): 834s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 834s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 834s Solute dielectric: 2.000 834s Solvent dielectric: 78.000 834s Using "molecular" surface definition; no smoothing 834s Solvent probe radius: 1.400 A 834s Temperature: 298.150 K 834s Electrostatic energies will be calculated 834s Total electrostatic energy = 2.244350164274E+03 kJ/mol 834s Calculating forces... 834s ---------------------------------------- 834s CALCULATION #2 (lig-fine): MULTIGRID 834s Setting up problem... 834s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 834s Debye length: 0 A 834s Current memory usage: 203.396 MB total, 404.625 MB high water 834s Using linear spline charge discretization. 834s Grid dimensions: 97 x 97 x 97 834s Grid spacings: 0.250 x 0.250 x 0.250 834s Grid lengths: 24.000 x 24.000 x 24.000 834s Grid center: (24.822, -33.153, 21.545) 834s Multigrid levels: 4 834s Molecule ID: 1 834s Linearized traditional PBE 834s Boundary conditions from focusing 834s 2 ion species (0.000 M ionic strength): 834s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 834s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 834s Solute dielectric: 2.000 834s Solvent dielectric: 78.000 834s Using "molecular" surface definition; no smoothing 834s Solvent probe radius: 1.400 A 834s Temperature: 298.150 K 834s Electrostatic energies will be calculated 834s Total electrostatic energy = 1.052149475373E+04 kJ/mol 834s Calculating forces... 834s ---------------------------------------- 834s CALCULATION #3 (pka-coarse): MULTIGRID 834s Setting up problem... 834s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 834s Debye length: 0 A 834s Current memory usage: 230.750 MB total, 404.625 MB high water 834s Using linear spline charge discretization. 834s Grid dimensions: 97 x 97 x 97 834s Grid spacings: 0.729 x 0.729 x 0.729 834s Grid lengths: 70.000 x 70.000 x 70.000 834s Grid center: (28.969, -32.507, 27.022) 834s Multigrid levels: 4 834s Molecule ID: 2 834s Linearized traditional PBE 834s Single Debye-Huckel sphere boundary conditions 834s 2 ion species (0.000 M ionic strength): 834s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 834s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 834s Solute dielectric: 2.000 834s Solvent dielectric: 78.000 834s Using "molecular" surface definition; no smoothing 834s Solvent probe radius: 1.400 A 834s Temperature: 298.150 K 834s Electrostatic energies will be calculated 834s Total electrostatic energy = 1.862615690066E+05 kJ/mol 834s Calculating forces... 834s [focusFillBound()]: WARNING: 834s Unusually large potential values 834s detected on the focusing boundary! 834s Convergence not guaranteed for NPBE/NRPBE calculations! 834s 834s ---------------------------------------- 834s CALCULATION #4 (pka-fine): MULTIGRID 834s Setting up problem... 834s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 834s Debye length: 0 A 834s Current memory usage: 230.750 MB total, 452.268 MB high water 834s Using linear spline charge discretization. 834s Grid dimensions: 97 x 97 x 97 834s Grid spacings: 0.250 x 0.250 x 0.250 834s Grid lengths: 24.000 x 24.000 x 24.000 834s Grid center: (24.822, -33.153, 21.545) 834s Multigrid levels: 4 834s Molecule ID: 2 834s Linearized traditional PBE 834s Boundary conditions from focusing 834s 2 ion species (0.000 M ionic strength): 834s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 834s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 834s Solute dielectric: 2.000 834s Solvent dielectric: 78.000 834s Using "molecular" surface definition; no smoothing 834s Solvent probe radius: 1.400 A 834s Temperature: 298.150 K 834s Electrostatic energies will be calculated 834s Total electrostatic energy = 3.051810884053E+05 kJ/mol 834s Calculating forces... 834s ---------------------------------------- 834s CALCULATION #5 (complex-coarse): MULTIGRID 834s Setting up problem... 834s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 834s Debye length: 0 A 834s Current memory usage: 230.854 MB total, 452.268 MB high water 834s Using linear spline charge discretization. 834s Grid dimensions: 97 x 97 x 97 834s Grid spacings: 0.729 x 0.729 x 0.729 834s Grid lengths: 70.000 x 70.000 x 70.000 834s Grid center: (28.969, -32.507, 27.022) 834s Multigrid levels: 4 834s Molecule ID: 3 834s Linearized traditional PBE 834s Single Debye-Huckel sphere boundary conditions 834s 2 ion species (0.000 M ionic strength): 834s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 834s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 834s Solute dielectric: 2.000 834s Solvent dielectric: 78.000 834s Using "molecular" surface definition; no smoothing 834s Solvent probe radius: 1.400 A 834s Temperature: 298.150 K 834s Electrostatic energies will be calculated 834s Total electrostatic energy = 1.886625455219E+05 kJ/mol 834s Calculating forces... 834s [focusFillBound()]: WARNING: 834s Unusually large potential values 834s detected on the focusing boundary! 834s Convergence not guaranteed for NPBE/NRPBE calculations! 834s 834s ---------------------------------------- 834s CALCULATION #6 (complex-fine): MULTIGRID 834s Setting up problem... 834s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 834s Debye length: 0 A 834s Current memory usage: 230.854 MB total, 452.606 MB high water 834s Using linear spline charge discretization. 834s Grid dimensions: 97 x 97 x 97 834s Grid spacings: 0.250 x 0.250 x 0.250 834s Grid lengths: 24.000 x 24.000 x 24.000 834s Grid center: (24.822, -33.153, 21.545) 834s Multigrid levels: 4 834s Molecule ID: 3 834s Linearized traditional PBE 834s Boundary conditions from focusing 834s 2 ion species (0.000 M ionic strength): 834s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 834s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 834s Solute dielectric: 2.000 834s Solvent dielectric: 78.000 834s Using "molecular" surface definition; no smoothing 834s Solvent probe radius: 1.400 A 834s Temperature: 298.150 K 834s Electrostatic energies will be calculated 834s Total electrostatic energy = 3.158218439277E+05 kJ/mol 834s Calculating forces... 834s ---------------------------------------- 834s PRINT STATEMENTS 834s 834s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 834s Local net energy (PE 0) = 1.192607686581E+02 kJ/mol 834s Global net ELEC energy = 1.192607686581E+02 kJ/mol 834s ---------------------------------------- 834s CLEANING UP AND SHUTTING DOWN... 834s Destroying force arrays. 834s No energy arrays to destroy. 834s Destroying multigrid structures. 834s Destroying finite element structures. 834s Destroying 3 molecules 834s Final memory usage: 0.001 MB total, 452.606 MB high water 834s 834s 834s Thanks for using APBS! 834s 853s Checking for intermediate energies in input file apbs-mol-surf.out 853s EXPECTED COMPUTED: 7 853s EXPECTED EXPECTED: 7 853s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] 853s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 853s COMPUTED RESULT 2244.350164274 853s COMPUTED RESULT 10521.49475373 853s COMPUTED RESULT 186261.5690066 853s COMPUTED RESULT 305181.0884053 853s COMPUTED RESULT 188662.5455219 853s COMPUTED RESULT 315821.8439277 853s COMPUTED RESULT 119.2607686581 853s BINARY: /usr/bin/apbs 853s INPUT: apbs-smol-surf.in 853s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 853s asc_getToken: Error occurred (bailing out). 853s Vio_scanf: Format problem with input. 853s 853s 853s ---------------------------------------------------------------------- 853s APBS -- Adaptive Poisson-Boltzmann Solver 853s Version APBS 3.4.1 853s 853s Nathan A. Baker (nathan.baker@pnnl.gov) 853s Pacific Northwest National Laboratory 853s 853s Additional contributing authors listed in the code documentation. 853s 853s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 853s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 853s Northwest Division for the U.S. Department of Energy. 853s 853s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 853s Portions Copyright (c) 2002-2020, Nathan A. Baker. 853s Portions Copyright (c) 1999-2002, The Regents of the University of California. 853s Portions Copyright (c) 1995, Michael Holst. 853s All rights reserved. 853s 853s Redistribution and use in source and binary forms, with or without 853s modification, are permitted provided that the following conditions are met: 853s 853s * Redistributions of source code must retain the above copyright notice, this 853s list of conditions and the following disclaimer. 853s 853s * Redistributions in binary form must reproduce the above copyright notice, 853s this list of conditions and the following disclaimer in the documentation 853s and/or other materials provided with the distribution. 853s 853s * Neither the name of the developer nor the names of its contributors may be 853s used to endorse or promote products derived from this software without 853s specific prior written permission. 853s 853s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 853s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 853s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 853s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 853s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 853s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 853s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 853s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 853s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 853s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 853s ---------------------------------------------------------------------- 853s APBS uses FETK (the Finite Element ToolKit) to solve the 853s Poisson-Boltzmann equation numerically. FETK is a portable collection 853s of finite element modeling class libraries developed by the Michael Holst 853s research group and written in an object-oriented form of C. FEtk is 853s designed to solve general coupled systems of nonlinear partial differential 853s equations using adaptive finite element methods, inexact Newton methods, 853s and algebraic multilevel methods. More information about FEtk may be found 853s at . 853s ---------------------------------------------------------------------- 853s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 853s Aqua is a modified form of the Holst group PMG library 853s which has been modified by Patrice Koehl 853s for improved efficiency and 853s memory usage when solving the Poisson-Boltzmann equation. 853s ---------------------------------------------------------------------- 853s Please cite your use of APBS as: 853s 853s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 853s nanosystems: application to microtubules and the ribosome. Proc. 853s Natl. Acad. Sci. USA 98, 10037-10041 2001. 853s 853s 853s This executable compiled on Jan 3 2025 at 11:01:42 853s 853s Parsing input file apbs-smol-surf.in... 853s rank 0 size 1... 853s Parsed input file. 853s Got paths for 3 molecules 853s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 853s asc_getToken: Error occurred (bailing out). 853s Vio_scanf: Format problem with input. 853s 47 atoms 853s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 853s Net charge 1.11e-16 e 853s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 853s asc_getToken: Error occurred (bailing out). 853s Vio_scanf: Format problem with input. 853s 3423 atoms 853s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 853s Net charge 1.00e+00 e 853s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 853s 3470 atoms 853s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 853s Net charge 1.00e+00 e 853s Preparing to run 6 PBE calculations. 853s ---------------------------------------- 853s CALCULATION #1 (lig-coarse): MULTIGRID 853s Setting up problem... 853s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 853s Debye length: 0 A 853s Current memory usage: 203.396 MB total, 203.396 MB high water 853s Using linear spline charge discretization. 853s Grid dimensions: 97 x 97 x 97 853s Grid spacings: 0.729 x 0.729 x 0.729 853s Grid lengths: 70.000 x 70.000 x 70.000 853s Grid center: (28.969, -32.507, 27.022) 853s Multigrid levels: 4 853s Molecule ID: 1 853s Linearized traditional PBE 853s Single Debye-Huckel sphere boundary conditions 853s 2 ion species (0.000 M ionic strength): 853s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 853s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 853s Solute dielectric: 2.000 853s Solvent dielectric: 78.000 853s Using "molecular" surface definition;harmonic average smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 2.251466789420E+03 kJ/mol 853s Calculating forces... 853s ---------------------------------------- 853s CALCULATION #2 (lig-fine): MULTIGRID 853s Setting up problem... 853s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 853s Debye length: 0 A 853s Current memory usage: 203.396 MB total, 404.625 MB high water 853s Using linear spline charge discretization. 853s Grid dimensions: 97 x 97 x 97 853s Grid spacings: 0.250 x 0.250 x 0.250 853s Grid lengths: 24.000 x 24.000 x 24.000 853s Grid center: (24.822, -33.153, 21.545) 853s Multigrid levels: 4 853s Molecule ID: 1 853s Linearized traditional PBE 853s Boundary conditions from focusing 853s 2 ion species (0.000 M ionic strength): 853s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 853s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 853s Solute dielectric: 2.000 853s Solvent dielectric: 78.000 853s Using "molecular" surface definition;harmonic average smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 1.052814502873E+04 kJ/mol 853s Calculating forces... 853s ---------------------------------------- 853s CALCULATION #3 (pka-coarse): MULTIGRID 853s Setting up problem... 853s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 853s Debye length: 0 A 853s Current memory usage: 230.750 MB total, 404.625 MB high water 853s Using linear spline charge discretization. 853s Grid dimensions: 97 x 97 x 97 853s Grid spacings: 0.729 x 0.729 x 0.729 853s Grid lengths: 70.000 x 70.000 x 70.000 853s Grid center: (28.969, -32.507, 27.022) 853s Multigrid levels: 4 853s Molecule ID: 2 853s Linearized traditional PBE 853s Single Debye-Huckel sphere boundary conditions 853s 2 ion species (0.000 M ionic strength): 853s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 853s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 853s Solute dielectric: 2.000 853s Solvent dielectric: 78.000 853s Using "molecular" surface definition;harmonic average smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 1.864071689626E+05 kJ/mol 853s Calculating forces... 853s [focusFillBound()]: WARNING: 853s Unusually large potential values 853s detected on the focusing boundary! 853s Convergence not guaranteed for NPBE/NRPBE calculations! 853s 853s ---------------------------------------- 853s CALCULATION #4 (pka-fine): MULTIGRID 853s Setting up problem... 853s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 853s Debye length: 0 A 853s Current memory usage: 230.750 MB total, 452.268 MB high water 853s Using linear spline charge discretization. 853s Grid dimensions: 97 x 97 x 97 853s Grid spacings: 0.250 x 0.250 x 0.250 853s Grid lengths: 24.000 x 24.000 x 24.000 853s Grid center: (24.822, -33.153, 21.545) 853s Multigrid levels: 4 853s Molecule ID: 2 853s Linearized traditional PBE 853s Boundary conditions from focusing 853s 2 ion species (0.000 M ionic strength): 853s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 853s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 853s Solute dielectric: 2.000 853s Solvent dielectric: 78.000 853s Using "molecular" surface definition;harmonic average smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 3.053319953673E+05 kJ/mol 853s Calculating forces... 853s ---------------------------------------- 853s CALCULATION #5 (complex-coarse): MULTIGRID 853s Setting up problem... 853s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 853s Debye length: 0 A 853s Current memory usage: 230.854 MB total, 452.268 MB high water 853s Using linear spline charge discretization. 853s Grid dimensions: 97 x 97 x 97 853s Grid spacings: 0.729 x 0.729 x 0.729 853s Grid lengths: 70.000 x 70.000 x 70.000 853s Grid center: (28.969, -32.507, 27.022) 853s Multigrid levels: 4 853s Molecule ID: 3 853s Linearized traditional PBE 853s Single Debye-Huckel sphere boundary conditions 853s 2 ion species (0.000 M ionic strength): 853s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 853s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 853s Solute dielectric: 2.000 853s Solvent dielectric: 78.000 853s Using "molecular" surface definition;harmonic average smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 1.888027142979E+05 kJ/mol 853s Calculating forces... 853s [focusFillBound()]: WARNING: 853s Unusually large potential values 853s detected on the focusing boundary! 853s Convergence not guaranteed for NPBE/NRPBE calculations! 853s 853s ---------------------------------------- 853s CALCULATION #6 (complex-fine): MULTIGRID 853s Setting up problem... 853s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 853s Debye length: 0 A 853s Current memory usage: 230.854 MB total, 452.606 MB high water 853s Using linear spline charge discretization. 853s Grid dimensions: 97 x 97 x 97 853s Grid spacings: 0.250 x 0.250 x 0.250 853s Grid lengths: 24.000 x 24.000 x 24.000 853s Grid center: (24.822, -33.153, 21.545) 853s Multigrid levels: 4 853s Molecule ID: 3 853s Linearized traditional PBE 853s Boundary conditions from focusing 853s 2 ion species (0.000 M ionic strength): 853s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 853s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 853s Solute dielectric: 2.000 853s Solvent dielectric: 78.000 853s Using "molecular" surface definition;harmonic average smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 3.159690177241E+05 kJ/mol 853s Calculating forces... 853s ---------------------------------------- 853s PRINT STATEMENTS 853s 853s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 853s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 853s Global net ELEC energy = 1.088773280806E+02 kJ/mol 853s ---------------------------------------- 853s CLEANING UP AND SHUTTING DOWN... 853s Destroying force arrays. 853s No energy arrays to destroy. 853s Destroying multigrid structures. 853s Destroying finite element structures. 853s Destroying 3 molecules 853s Final memory usage: 0.001 MB total, 452.606 MB high water 853s 853s 853s Thanks for using APBS! 853s 853s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 853s *** PASSED *** 853s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 853s *** PASSED *** 853s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 853s *** PASSED *** 853s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 853s *** PASSED *** 853s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 853s *** PASSED *** 853s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 853s *** PASSED *** 853s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 853s *** PASSED *** 853s Elapsed time: 19.752828 seconds 853s -------------------------------------------------------------------------------- 853s Total elapsed time: 98.410066 seconds 853s Test results have been logged 853s -------------------------------------------------------------------------------- 853s -------------------------------------------------------------------------------- 853s Testing input file complex-0_1.in 853s 855s Checking for intermediate energies in input file apbs-smol-surf.out 855s EXPECTED COMPUTED: 7 855s EXPECTED EXPECTED: 7 855s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 855s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 855s COMPUTED RESULT 2251.46678942 855s COMPUTED RESULT 10528.14502873 855s COMPUTED RESULT 186407.1689626 855s COMPUTED RESULT 305331.9953673 855s COMPUTED RESULT 188802.7142979 855s COMPUTED RESULT 315969.0177241 855s COMPUTED RESULT 108.8773280806 855s Running tests for point-pmf section 855s BINARY: /usr/bin/apbs 855s INPUT: complex-0_1.in 855s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 855s asc_getToken: Error occurred (bailing out). 855s Vio_scanf: Format problem with input. 855s 855s 855s ---------------------------------------------------------------------- 855s APBS -- Adaptive Poisson-Boltzmann Solver 855s Version APBS 3.4.1 855s 855s Nathan A. Baker (nathan.baker@pnnl.gov) 855s Pacific Northwest National Laboratory 855s 855s Additional contributing authors listed in the code documentation. 855s 855s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 855s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 855s Northwest Division for the U.S. Department of Energy. 855s 855s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 855s Portions Copyright (c) 2002-2020, Nathan A. Baker. 855s Portions Copyright (c) 1999-2002, The Regents of the University of California. 855s Portions Copyright (c) 1995, Michael Holst. 855s All rights reserved. 855s 855s Redistribution and use in source and binary forms, with or without 855s modification, are permitted provided that the following conditions are met: 855s 855s * Redistributions of source code must retain the above copyright notice, this 855s list of conditions and the following disclaimer. 855s 855s * Redistributions in binary form must reproduce the above copyright notice, 855s this list of conditions and the following disclaimer in the documentation 855s and/or other materials provided with the distribution. 855s 855s * Neither the name of the developer nor the names of its contributors may be 855s used to endorse or promote products derived from this software without 855s specific prior written permission. 855s 855s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 855s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 855s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 855s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 855s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 855s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 855s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 855s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 855s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 855s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 855s ---------------------------------------------------------------------- 855s APBS uses FETK (the Finite Element ToolKit) to solve the 855s Poisson-Boltzmann equation numerically. FETK is a portable collection 855s of finite element modeling class libraries developed by the Michael Holst 855s research group and written in an object-oriented form of C. FEtk is 855s designed to solve general coupled systems of nonlinear partial differential 855s equations using adaptive finite element methods, inexact Newton methods, 855s and algebraic multilevel methods. More information about FEtk may be found 855s at . 855s ---------------------------------------------------------------------- 855s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 855s Aqua is a modified form of the Holst group PMG library 855s which has been modified by Patrice Koehl 855s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 855s *** PASSED *** 855s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 855s *** PASSED *** 855s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 855s *** PASSED *** 855s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 855s *** PASSED *** 855s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 855s *** PASSED *** 855s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 855s *** PASSED *** 855s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 855s *** PASSED *** 855s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 855s *** PASSED *** 855s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 855s *** PASSED *** 855s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 855s *** PASSED *** 855s Elapsed time: 2.015701 seconds 855s -------------------------------------------------------------------------------- 855s -------------------------------------------------------------------------------- 855s Testing input file complex-0_2.in 855s 855s for improved efficiency and 855s memory usage when solving the Poisson-Boltzmann equation. 855s ---------------------------------------------------------------------- 855s Please cite your use of APBS as: 855s 855s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 855s nanosystems: application to microtubules and the ribosome. Proc. 855s Natl. Acad. Sci. USA 98, 10037-10041 2001. 855s 855s 855s This executable compiled on Jan 3 2025 at 11:01:42 855s 855s Parsing input file complex-0_1.in... 855s rank 0 size 1... 855s Parsed input file. 855s Got paths for 3 molecules 855s Reading PQR-format atom data from mol0.pqr. 855s asc_getToken: Error occurred (bailing out). 855s Vio_scanf: Format problem with input. 855s 1 atoms 855s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 855s Net charge 1.00e+00 e 855s Reading PQR-format atom data from mol1.pqr. 855s asc_getToken: Error occurred (bailing out). 855s Vio_scanf: Format problem with input. 855s 1 atoms 855s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 855s Net charge 1.00e+00 e 855s Reading PQR-format atom data from complex-0_1.pqr. 855s 2 atoms 855s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 855s Net charge 2.00e+00 e 855s Preparing to run 3 PBE calculations. 855s ---------------------------------------- 855s CALCULATION #1 (point1): MULTIGRID 855s Setting up problem... 855s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 855s Debye length: 0 A 855s Current memory usage: 61.059 MB total, 61.059 MB high water 855s Using linear spline charge discretization. 855s Grid dimensions: 65 x 65 x 65 855s Grid spacings: 0.210 x 0.210 x 0.210 855s Grid lengths: 13.440 x 13.440 x 13.440 855s Grid center: (0.000, 0.000, 0.000) 855s Multigrid levels: 5 855s Molecule ID: 1 855s Linearized traditional PBE 855s Multiple Debye-Huckel sphere boundary conditions 855s 0 ion species (0.000 M ionic strength): 855s Solute dielectric: 78.540 855s Solvent dielectric: 78.540 855s Using spline-based surface definition;window = 0.300 855s Temperature: 298.150 K 855s Electrostatic energies will be calculated 855s Total electrostatic energy = 9.776035707281E+01 kJ/mol 855s Fixed charge energy = 97.7604 kJ/mol 855s Mobile charge energy = 0 kJ/mol 855s Dielectric energy = 96.5336 kJ/mol 855s Per-atom energies: 855s Atom 0: 9.776035707281E+01 kJ/mol 855s Calculating forces... 855s ---------------------------------------- 855s CALCULATION #2 (point2): MULTIGRID 855s Setting up problem... 855s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 855s Debye length: 0 A 855s Current memory usage: 61.059 MB total, 61.066 MB high water 855s Using linear spline charge discretization. 855s Grid dimensions: 65 x 65 x 65 855s Grid spacings: 0.210 x 0.210 x 0.210 855s Grid lengths: 13.440 x 13.440 x 13.440 855s Grid center: (0.000, 0.000, 0.000) 855s Multigrid levels: 5 855s Molecule ID: 2 855s Linearized traditional PBE 855s Multiple Debye-Huckel sphere boundary conditions 855s 0 ion species (0.000 M ionic strength): 855s Solute dielectric: 78.540 855s Solvent dielectric: 78.540 855s Using spline-based surface definition;window = 0.300 855s Temperature: 298.150 K 855s Electrostatic energies will be calculated 855s Total electrostatic energy = 8.975920687031E+01 kJ/mol 855s Fixed charge energy = 89.7592 kJ/mol 855s Mobile charge energy = 0 kJ/mol 855s Dielectric energy = 88.6151 kJ/mol 855s Per-atom energies: 855s Atom 0: 8.975920687031E+01 kJ/mol 855s Calculating forces... 855s ---------------------------------------- 855s CALCULATION #3 (complex): MULTIGRID 855s Setting up problem... 855s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 855s Debye length: 0 A 855s Current memory usage: 61.059 MB total, 61.066 MB high water 855s Using linear spline charge discretization. 855s Grid dimensions: 65 x 65 x 65 855s Grid spacings: 0.210 x 0.210 x 0.210 855s Grid lengths: 13.440 x 13.440 x 13.440 855s Grid center: (0.000, 0.000, 0.000) 855s Multigrid levels: 5 855s Molecule ID: 3 855s Linearized traditional PBE 855s Multiple Debye-Huckel sphere boundary conditions 855s 0 ion species (0.000 M ionic strength): 855s Solute dielectric: 78.540 855s Solvent dielectric: 78.540 855s Using spline-based surface definition;window = 0.300 855s Temperature: 298.150 K 855s Electrostatic energies will be calculated 855s Total electrostatic energy = 2.058277719334E+02 kJ/mol 855s Fixed charge energy = 205.828 kJ/mol 855s Mobile charge energy = 0 kJ/mol 855s Dielectric energy = 201.106 kJ/mol 855s Per-atom energies: 855s Atom 0: 1.069144350786E+02 kJ/mol 855s Atom 1: 9.891333685475E+01 kJ/mol 855s Calculating forces... 855s ---------------------------------------- 855s PRINT STATEMENTS 855s 855s print energy 3 (complex) - 1 (point1) - 2 (point2) end 855s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 855s Global net ELEC energy = 1.830820799027E+01 kJ/mol 855s ---------------------------------------- 855s CLEANING UP AND SHUTTING DOWN... 855s Destroying force arrays. 855s No energy arrays to destroy. 855s Destroying multigrid structures. 855s Destroying finite element structures. 855s Destroying 3 molecules 855s Final memory usage: 0.001 MB total, 61.066 MB high water 855s 855s 855s Thanks for using APBS! 855s 858s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 858s *** PASSED *** 858s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 858s *** PASSED *** 858s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 858s *** PASSED *** 858s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 858s *** PASSED *** 858s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 858s *** PASSED *** 858s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 858s *** PASSED *** 858s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 858s *** PASSED *** 858s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 858s *** PASSED *** 858s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 858s *** PASSED *** 858s Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) 858s *** PASSED *** 858s Elapsed time: 2.770028 seconds 858s -------------------------------------------------------------------------------- 858s -------------------------------------------------------------------------------- 858s Testing input file complex-0_3.in 858s 858s Checking for intermediate energies in input file complex-0_1.out 858s EXPECTED COMPUTED: 13 858s EXPECTED EXPECTED: 13 858s 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] 858s 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'] 858s COMPUTED RESULT 97.76035707281 858s COMPUTED RESULT 89.75920687031 858s COMPUTED RESULT 205.8277719334 858s COMPUTED RESULT 0.0 858s COMPUTED RESULT 0.0 858s COMPUTED RESULT 0.0 858s COMPUTED RESULT 97.7604 858s COMPUTED RESULT 89.7592 858s COMPUTED RESULT 205.828 858s COMPUTED RESULT 96.5336 858s COMPUTED RESULT 88.6151 858s COMPUTED RESULT 201.106 858s COMPUTED RESULT 18.30820799027 858s BINARY: /usr/bin/apbs 858s INPUT: complex-0_2.in 858s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 858s asc_getToken: Error occurred (bailing out). 858s Vio_scanf: Format problem with input. 858s 858s 858s ---------------------------------------------------------------------- 858s APBS -- Adaptive Poisson-Boltzmann Solver 858s Version APBS 3.4.1 858s 858s Nathan A. Baker (nathan.baker@pnnl.gov) 858s Pacific Northwest National Laboratory 858s 858s Additional contributing authors listed in the code documentation. 858s 858s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 858s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 858s Northwest Division for the U.S. Department of Energy. 858s 858s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 858s Portions Copyright (c) 2002-2020, Nathan A. Baker. 858s Portions Copyright (c) 1999-2002, The Regents of the University of California. 858s Portions Copyright (c) 1995, Michael Holst. 858s All rights reserved. 858s 858s Redistribution and use in source and binary forms, with or without 858s modification, are permitted provided that the following conditions are met: 858s 858s * Redistributions of source code must retain the above copyright notice, this 858s list of conditions and the following disclaimer. 858s 858s * Redistributions in binary form must reproduce the above copyright notice, 858s this list of conditions and the following disclaimer in the documentation 858s and/or other materials provided with the distribution. 858s 858s * Neither the name of the developer nor the names of its contributors may be 858s used to endorse or promote products derived from this software without 858s specific prior written permission. 858s 858s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 858s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 858s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 858s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 858s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 858s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 858s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 858s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 858s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 858s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 858s ---------------------------------------------------------------------- 858s APBS uses FETK (the Finite Element ToolKit) to solve the 858s Poisson-Boltzmann equation numerically. FETK is a portable collection 858s of finite element modeling class libraries developed by the Michael Holst 858s research group and written in an object-oriented form of C. FEtk is 858s designed to solve general coupled systems of nonlinear partial differential 858s equations using adaptive finite element methods, inexact Newton methods, 858s and algebraic multilevel methods. More information about FEtk may be found 858s at . 858s ---------------------------------------------------------------------- 858s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 858s Aqua is a modified form of the Holst group PMG library 858s which has been modified by Patrice Koehl 858s for improved efficiency and 858s memory usage when solving the Poisson-Boltzmann equation. 858s ---------------------------------------------------------------------- 858s Please cite your use of APBS as: 858s 858s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 858s nanosystems: application to microtubules and the ribosome. Proc. 858s Natl. Acad. Sci. USA 98, 10037-10041 2001. 858s 858s 858s This executable compiled on Jan 3 2025 at 11:01:42 858s 858s Parsing input file complex-0_2.in... 858s rank 0 size 1... 858s Parsed input file. 858s Got paths for 3 molecules 858s Reading PQR-format atom data from mol0.pqr. 858s asc_getToken: Error occurred (bailing out). 858s Vio_scanf: Format problem with input. 858s 1 atoms 858s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 858s Net charge 1.00e+00 e 858s Reading PQR-format atom data from mol2.pqr. 858s asc_getToken: Error occurred (bailing out). 858s Vio_scanf: Format problem with input. 858s 1 atoms 858s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 858s Net charge 1.00e+00 e 858s Reading PQR-format atom data from complex-0_2.pqr. 858s 2 atoms 858s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 858s Net charge 2.00e+00 e 858s Preparing to run 3 PBE calculations. 858s ---------------------------------------- 858s CALCULATION #1 (point1): MULTIGRID 858s Setting up problem... 858s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 858s Debye length: 0 A 858s Current memory usage: 61.059 MB total, 61.059 MB high water 858s Using linear spline charge discretization. 858s Grid dimensions: 65 x 65 x 65 858s Grid spacings: 0.210 x 0.210 x 0.210 858s Grid lengths: 13.440 x 13.440 x 13.440 858s Grid center: (0.000, 0.000, 0.000) 858s Multigrid levels: 5 858s Molecule ID: 1 858s Linearized traditional PBE 858s Multiple Debye-Huckel sphere boundary conditions 858s 0 ion species (0.000 M ionic strength): 858s Solute dielectric: 78.540 858s Solvent dielectric: 78.540 858s Using spline-based surface definition;window = 0.300 858s Temperature: 298.150 K 858s Electrostatic energies will be calculated 858s Total electrostatic energy = 9.776035707281E+01 kJ/mol 858s Fixed charge energy = 97.7604 kJ/mol 858s Mobile charge energy = 0 kJ/mol 858s Dielectric energy = 96.5336 kJ/mol 858s Per-atom energies: 858s Atom 0: 9.776035707281E+01 kJ/mol 858s Calculating forces... 858s ---------------------------------------- 858s CALCULATION #2 (point2): MULTIGRID 858s Setting up problem... 858s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 858s Debye length: 0 A 858s Current memory usage: 61.059 MB total, 61.066 MB high water 858s Using linear spline charge discretization. 858s Grid dimensions: 65 x 65 x 65 858s Grid spacings: 0.210 x 0.210 x 0.210 858s Grid lengths: 13.440 x 13.440 x 13.440 858s Grid center: (0.000, 0.000, 0.000) 858s Multigrid levels: 5 858s Molecule ID: 2 858s Linearized traditional PBE 858s Multiple Debye-Huckel sphere boundary conditions 858s 0 ion species (0.000 M ionic strength): 858s Solute dielectric: 78.540 858s Solvent dielectric: 78.540 858s Using spline-based surface definition;window = 0.300 858s Temperature: 298.150 K 858s Electrostatic energies will be calculated 858s Total electrostatic energy = 1.017611498797E+02 kJ/mol 858s Fixed charge energy = 101.761 kJ/mol 858s Mobile charge energy = 0 kJ/mol 858s Dielectric energy = 100.656 kJ/mol 858s Per-atom energies: 858s Atom 0: 1.017611498797E+02 kJ/mol 858s Calculating forces... 858s ---------------------------------------- 858s CALCULATION #3 (complex): MULTIGRID 858s Setting up problem... 858s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 858s Debye length: 0 A 858s Current memory usage: 61.059 MB total, 61.066 MB high water 858s Using linear spline charge discretization. 858s Grid dimensions: 65 x 65 x 65 858s Grid spacings: 0.210 x 0.210 x 0.210 858s Grid lengths: 13.440 x 13.440 x 13.440 858s Grid center: (0.000, 0.000, 0.000) 858s Multigrid levels: 5 858s Molecule ID: 3 858s Linearized traditional PBE 858s Multiple Debye-Huckel sphere boundary conditions 858s 0 ion species (0.000 M ionic strength): 858s Solute dielectric: 78.540 858s Solvent dielectric: 78.540 858s Using spline-based surface definition;window = 0.300 858s Temperature: 298.150 K 858s Electrostatic energies will be calculated 858s Total electrostatic energy = 2.084282010393E+02 kJ/mol 858s Fixed charge energy = 208.428 kJ/mol 858s Mobile charge energy = 0 kJ/mol 858s Dielectric energy = 203.83 kJ/mol 858s Per-atom energies: 858s Atom 0: 1.022136878480E+02 kJ/mol 858s Atom 1: 1.062145131913E+02 kJ/mol 858s Calculating forces... 858s ---------------------------------------- 858s PRINT STATEMENTS 858s 858s print energy 3 (complex) - 1 (point1) - 2 (point2) end 858s Local net energy (PE 0) = 8.906694086750E+00 kJ/mol 858s Global net ELEC energy = 8.906694086750E+00 kJ/mol 858s ---------------------------------------- 858s CLEANING UP AND SHUTTING DOWN... 858s Destroying force arrays. 858s No energy arrays to destroy. 858s Destroying multigrid structures. 858s Destroying finite element structures. 858s Destroying 3 molecules 858s Final memory usage: 0.001 MB total, 61.066 MB high water 858s 858s 858s Thanks for using APBS! 858s 861s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 861s *** PASSED *** 861s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 861s *** PASSED *** 861s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 861s *** PASSED *** 861s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 861s *** PASSED *** 861s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 861s *** PASSED *** 861s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 861s *** PASSED *** 861s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 861s *** PASSED *** 861s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 861s *** PASSED *** 861s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 861s *** PASSED *** 861s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 861s *** PASSED *** 861s Elapsed time: 2.452717 seconds 861s -------------------------------------------------------------------------------- 861s -------------------------------------------------------------------------------- 861s Testing input file complex-0_4.in 861s 861s Checking for intermediate energies in input file complex-0_2.out 861s EXPECTED COMPUTED: 13 861s EXPECTED EXPECTED: 13 861s 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] 861s 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'] 861s COMPUTED RESULT 97.76035707281 861s COMPUTED RESULT 101.7611498797 861s COMPUTED RESULT 208.4282010393 861s COMPUTED RESULT 0.0 861s COMPUTED RESULT 0.0 861s COMPUTED RESULT 0.0 861s COMPUTED RESULT 97.7604 861s COMPUTED RESULT 101.761 861s COMPUTED RESULT 208.428 861s COMPUTED RESULT 96.5336 861s COMPUTED RESULT 100.656 861s COMPUTED RESULT 203.83 861s COMPUTED RESULT 8.90669408675 861s BINARY: /usr/bin/apbs 861s INPUT: complex-0_3.in 861s COMMAND: ['/usr/bin/apbs', 'complex-0_3.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 . 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 861s which has been modified by Patrice Koehl 861s 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 Jan 3 2025 at 11:01:42 861s 861s Parsing input file complex-0_3.in... 861s rank 0 size 1... 861s Parsed input file. 861s Got paths for 3 molecules 861s Reading PQR-format atom data from mol0.pqr. 861s asc_getToken: Error occurred (bailing out). 861s Vio_scanf: Format problem with input. 861s 1 atoms 861s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 861s Net charge 1.00e+00 e 861s Reading PQR-format atom data from mol3.pqr. 861s asc_getToken: Error occurred (bailing out). 861s Vio_scanf: Format problem with input. 861s 1 atoms 861s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 861s Net charge 1.00e+00 e 861s Reading PQR-format atom data from complex-0_3.pqr. 861s 2 atoms 861s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 861s Net charge 2.00e+00 e 861s Preparing to run 3 PBE calculations. 861s ---------------------------------------- 861s CALCULATION #1 (point1): 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: 61.059 MB total, 61.059 MB high water 861s Using linear spline charge discretization. 861s Grid dimensions: 65 x 65 x 65 861s Grid spacings: 0.210 x 0.210 x 0.210 861s Grid lengths: 13.440 x 13.440 x 13.440 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: 78.540 861s Solvent dielectric: 78.540 861s Using spline-based surface definition;window = 0.300 861s Temperature: 298.150 K 861s Electrostatic energies will be calculated 861s Total electrostatic energy = 9.776035707281E+01 kJ/mol 861s Fixed charge energy = 97.7604 kJ/mol 861s Mobile charge energy = 0 kJ/mol 861s Dielectric energy = 96.5336 kJ/mol 861s Per-atom energies: 861s Atom 0: 9.776035707281E+01 kJ/mol 861s Calculating forces... 861s ---------------------------------------- 861s CALCULATION #2 (point2): 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: 61.059 MB total, 61.066 MB high water 861s Using linear spline charge discretization. 861s Grid dimensions: 65 x 65 x 65 861s Grid spacings: 0.210 x 0.210 x 0.210 861s Grid lengths: 13.440 x 13.440 x 13.440 861s Grid center: (0.000, 0.000, 0.000) 861s Multigrid levels: 5 861s Molecule ID: 2 861s Linearized traditional PBE 861s Multiple Debye-Huckel sphere boundary conditions 861s 0 ion species (0.000 M ionic strength): 861s Solute dielectric: 78.540 861s Solvent dielectric: 78.540 861s Using spline-based surface definition;window = 0.300 861s Temperature: 298.150 K 861s Electrostatic energies will be calculated 861s Total electrostatic energy = 1.337661883222E+02 kJ/mol 861s Fixed charge energy = 133.766 kJ/mol 861s Mobile charge energy = 0 kJ/mol 861s Dielectric energy = 132.672 kJ/mol 861s Per-atom energies: 861s Atom 0: 1.337661883222E+02 kJ/mol 861s Calculating forces... 861s ---------------------------------------- 861s CALCULATION #3 (complex): 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: 61.059 MB total, 61.066 MB high water 861s Using linear spline charge discretization. 861s Grid dimensions: 65 x 65 x 65 861s Grid spacings: 0.210 x 0.210 x 0.210 861s Grid lengths: 13.440 x 13.440 x 13.440 861s Grid center: (0.000, 0.000, 0.000) 861s Multigrid levels: 5 861s Molecule ID: 3 861s Linearized traditional PBE 861s Multiple Debye-Huckel sphere boundary conditions 861s 0 ion species (0.000 M ionic strength): 861s Solute dielectric: 78.540 861s Solvent dielectric: 78.540 861s Using spline-based surface definition;window = 0.300 861s Temperature: 298.150 K 861s Electrostatic energies will be calculated 861s Total electrostatic energy = 2.374361452120E+02 kJ/mol 861s Fixed charge energy = 237.436 kJ/mol 861s Mobile charge energy = 0 kJ/mol 861s Dielectric energy = 232.924 kJ/mol 861s Per-atom energies: 861s Atom 0: 1.007151570480E+02 kJ/mol 861s Atom 1: 1.367209881640E+02 kJ/mol 861s Calculating forces... 861s ---------------------------------------- 861s PRINT STATEMENTS 861s 861s print energy 3 (complex) - 1 (point1) - 2 (point2) end 861s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 861s Global net ELEC energy = 5.909599816984E+00 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 3 molecules 861s Final memory usage: 0.001 MB total, 61.066 MB high water 861s 861s 861s Thanks for using APBS! 861s 863s Checking for intermediate energies in input file complex-0_3.out 863s EXPECTED COMPUTED: 13 863s EXPECTED EXPECTED: 13 863s 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] 863s 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'] 863s COMPUTED RESULT 97.76035707281 863s COMPUTED RESULT 133.7661883222 863s COMPUTED RESULT 237.436145212 863s COMPUTED RESULT 0.0 863s COMPUTED RESULT 0.0 863s COMPUTED RESULT 0.0 863s COMPUTED RESULT 97.7604 863s COMPUTED RESULT 133.766 863s COMPUTED RESULT 237.436 863s COMPUTED RESULT 96.5336 863s COMPUTED RESULT 132.672 863s COMPUTED RESULT 232.924 863s COMPUTED RESULT 5.909599816984 863s BINARY: /usr/bin/apbs 863s INPUT: complex-0_4.in 863s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 863s asc_getToken: Error occurred (bailing out). 863s Vio_scanf: Format problem with input. 863s 863s 863s ---------------------------------------------------------------------- 863s APBS -- Adaptive Poisson-Boltzmann Solver 863s Version APBS 3.4.1 863s 863s Nathan A. Baker (nathan.baker@pnnl.gov) 863s Pacific Northwest National Laboratory 863s 863s Additional contributing authors listed in the code documentation. 863s 863s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 863s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 863s Northwest Division for the U.S. Department of Energy. 863s 863s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 863s Portions Copyright (c) 2002-2020, Nathan A. Baker. 863s Portions Copyright (c) 1999-2002, The Regents of the University of California. 863s Portions Copyright (c) 1995, Michael Holst. 863s All rights reserved. 863s 863s Redistribution and use in source and binary forms, with or without 863s modification, are permitted provided that the following conditions are met: 863s 863s * Redistributions of source code must retain the above copyright notice, this 863s list of conditions and the following disclaimer. 863s 863s * Redistributions in binary form must reproduce the above copyright notice, 863s this list of conditions and the following disclaimer in the documentation 863s and/or other materials provided with the distribution. 863s 863s * Neither the name of the developer nor the names of its contributors may be 863s used to endorse or promote products derived from this software without 863s specific prior written permission. 863s 863s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 863s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 863s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 863s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 863s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 863s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 863s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 863s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 863s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 863s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 863s ---------------------------------------------------------------------- 863s APBS uses FETK (the Finite Element ToolKit) to solve the 863s Poisson-Boltzmann equation numerically. FETK is a portable collection 863s of finite element modeling class libraries developed by the Michael Holst 863s research group and written in an object-oriented form of C. FEtk is 863s designed to solve general coupled systems of nonlinear partial differential 863s equations using adaptive finite element methods, inexact Newton methods, 863s and algebraic multilevel methods. More information about FEtk may be found 863s at . 863s ---------------------------------------------------------------------- 863s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 863s Aqua is a modified form of the Holst group PMG library 863s which has been modified by Patrice Koehl 863s for improved efficiency and 863s memory usage when solving the Poisson-Boltzmann equation. 863s ---------------------------------------------------------------------- 863s Please cite your use of APBS as: 863s 863s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 863s nanosystems: application to microtubules and the ribosome. Proc. 863s Natl. Acad. Sci. USA 98, 10037-10041 2001. 863s 863s 863s This executable compiled on Jan 3 2025 at 11:01:42 863s 863s Parsing input file complex-0_4.in... 863s rank 0 size 1... 863s Parsed input file. 863s Got paths for 3 molecules 863s Reading PQR-format atom data from mol0.pqr. 863s asc_getToken: Error occurred (bailing out). 863s Vio_scanf: Format problem with input. 863s 1 atoms 863s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 863s Net charge 1.00e+00 e 863s Reading PQR-format atom data from mol4.pqr. 863s asc_getToken: Error occurred (bailing out). 863s Vio_scanf: Format problem with input. 863s 1 atoms 863s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 863s Net charge 1.00e+00 e 863s Reading PQR-format atom data from complex-0_4.pqr. 863s 2 atoms 863s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 863s Net charge 2.00e+00 e 863s Preparing to run 3 PBE calculations. 863s ---------------------------------------- 863s CALCULATION #1 (point1): MULTIGRID 863s Setting up problem... 863s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 863s Debye length: 0 A 863s Current memory usage: 61.059 MB total, 61.059 MB high water 863s Using linear spline charge discretization. 863s Grid dimensions: 65 x 65 x 65 863s Grid spacings: 0.210 x 0.210 x 0.210 863s Grid lengths: 13.440 x 13.440 x 13.440 863s Grid center: (0.000, 0.000, 0.000) 863s Multigrid levels: 5 863s Molecule ID: 1 863s Linearized traditional PBE 863s Multiple Debye-Huckel sphere boundary conditions 863s 0 ion species (0.000 M ionic strength): 863s Solute dielectric: 78.540 863s Solvent dielectric: 78.540 863s Using spline-based surface definition;window = 0.300 863s Temperature: 298.150 K 863s Electrostatic energies will be calculated 863s Total electrostatic energy = 9.776035707281E+01 kJ/mol 863s Fixed charge energy = 97.7604 kJ/mol 863s Mobile charge energy = 0 kJ/mol 863s Dielectric energy = 96.5336 kJ/mol 863s Per-atom energies: 863s Atom 0: 9.776035707281E+01 kJ/mol 863s Calculating forces... 863s ---------------------------------------- 863s CALCULATION #2 (point2): MULTIGRID 863s Setting up problem... 863s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 863s Debye length: 0 A 863s Current memory usage: 61.059 MB total, 61.066 MB high water 863s Using linear spline charge discretization. 863s Grid dimensions: 65 x 65 x 65 863s Grid spacings: 0.210 x 0.210 x 0.210 863s Grid lengths: 13.440 x 13.440 x 13.440 863s Grid center: (0.000, 0.000, 0.000) 863s Multigrid levels: 5 863s Molecule ID: 2 863s Linearized traditional PBE 863s Multiple Debye-Huckel sphere boundary conditions 863s 0 ion species (0.000 M ionic strength): 863s Solute dielectric: 78.540 863s Solvent dielectric: 78.540 863s Using spline-based surface definition;window = 0.300 863s Temperature: 298.150 K 863s Electrostatic energies will be calculated 863s Total electrostatic energy = 1.017611498797E+02 kJ/mol 863s Fixed charge energy = 101.761 kJ/mol 863s Mobile charge energy = 0 kJ/mol 863s Dielectric energy = 100.654 kJ/mol 863s Per-atom energies: 863s Atom 0: 1.017611498797E+02 kJ/mol 863s Calculating forces... 863s ---------------------------------------- 863s CALCULATION #3 (complex): MULTIGRID 863s Setting up problem... 863s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 863s Debye length: 0 A 863s Current memory usage: 61.059 MB total, 61.066 MB high water 863s Using linear spline charge discretization. 863s Grid dimensions: 65 x 65 x 65 863s Grid spacings: 0.210 x 0.210 x 0.210 863s Grid lengths: 13.440 x 13.440 x 13.440 863s Grid center: (0.000, 0.000, 0.000) 863s Multigrid levels: 5 863s Molecule ID: 3 863s Linearized traditional PBE 863s Multiple Debye-Huckel sphere boundary conditions 863s 0 ion species (0.000 M ionic strength): 863s Solute dielectric: 78.540 863s Solvent dielectric: 78.540 863s Using spline-based surface definition;window = 0.300 863s Temperature: 298.150 K 863s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 863s Electrostatic energies will be calculated 863s Total electrostatic energy = 2.039516519000E+02 kJ/mol 863s Fixed charge energy = 203.952 kJ/mol 863s Mobile charge energy = 0 kJ/mol 863s Dielectric energy = 199.493 kJ/mol 863s Per-atom energies: 863s Atom 0: 9.997541697022E+01 kJ/mol 863s Atom 1: 1.039762349297E+02 kJ/mol 863s Calculating forces... 863s ---------------------------------------- 863s PRINT STATEMENTS 863s 863s print energy 3 (complex) - 1 (point1) - 2 (point2) end 863s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 863s Global net ELEC energy = 4.430144947418E+00 kJ/mol 863s ---------------------------------------- 863s CLEANING UP AND SHUTTING DOWN... 863s Destroying force arrays. 863s No energy arrays to destroy. 863s Destroying multigrid structures. 863s Destroying finite element structures. 863s Destroying 3 molecules 863s Final memory usage: 0.001 MB total, 61.066 MB high water 863s 863s 863s Thanks for using APBS! 863s 863s *** PASSED *** 863s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 863s *** PASSED *** 863s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 863s *** PASSED *** 863s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 863s *** PASSED *** 863s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 863s *** PASSED *** 863s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 863s *** PASSED *** 863s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 863s *** PASSED *** 863s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 863s *** PASSED *** 863s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 863s *** PASSED *** 863s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 863s *** PASSED *** 863s Elapsed time: 2.066848 seconds 863s -------------------------------------------------------------------------------- 863s Total elapsed time: 9.305294 seconds 863s Test results have been logged 863s -------------------------------------------------------------------------------- 863s -------------------------------------------------------------------------------- 863s Testing input file apbs-mol.in 863s 866s Checking for intermediate energies in input file complex-0_4.out 866s EXPECTED COMPUTED: 13 866s EXPECTED EXPECTED: 13 866s 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] 866s 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'] 866s COMPUTED RESULT 97.76035707281 866s COMPUTED RESULT 101.7611498797 866s COMPUTED RESULT 203.9516519 866s COMPUTED RESULT 0.0 866s COMPUTED RESULT 0.0 866s COMPUTED RESULT 0.0 866s COMPUTED RESULT 97.7604 866s COMPUTED RESULT 101.761 866s COMPUTED RESULT 203.952 866s COMPUTED RESULT 96.5336 866s COMPUTED RESULT 100.654 866s COMPUTED RESULT 199.493 866s COMPUTED RESULT 4.430144947418 866s Running tests for solv section 866s BINARY: /usr/bin/apbs 866s INPUT: apbs-mol.in 866s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 866s asc_getToken: Error occurred (bailing out). 866s Vio_scanf: Format problem with input. 866s 866s 866s ---------------------------------------------------------------------- 866s APBS -- Adaptive Poisson-Boltzmann Solver 866s Version APBS 3.4.1 866s 866s Nathan A. Baker (nathan.baker@pnnl.gov) 866s Pacific Northwest National Laboratory 866s 866s Additional contributing authors listed in the code documentation. 866s 866s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 866s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 866s Northwest Division for the U.S. Department of Energy. 866s 866s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 866s Portions Copyright (c) 2002-2020, Nathan A. Baker. 866s Portions Copyright (c) 1999-2002, The Regents of the University of California. 866s Portions Copyright (c) 1995, Michael Holst. 866s All rights reserved. 866s 866s Redistribution and use in source and binary forms, with or without 866s modification, are permitted provided that the following conditions are met: 866s 866s * Redistributions of source code must retain the above copyright notice, this 866s list of conditions and the following disclaimer. 866s 866s * Redistributions in binary form must reproduce the above copyright notice, 866s this list of conditions and the following disclaimer in the documentation 866s and/or other materials provided with the distribution. 866s 866s * Neither the name of the developer nor the names of its contributors may be 866s used to endorse or promote products derived from this software without 866s specific prior written permission. 866s 866s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 866s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 866s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 866s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 866s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 866s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 866s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 866s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 866s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 866s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 866s ---------------------------------------------------------------------- 866s APBS uses FETK (the Finite Element ToolKit) to solve the 866s Poisson-Boltzmann equation numerically. FETK is a portable collection 866s of finite element modeling class libraries developed by the Michael Holst 866s research group and written in an object-oriented form of C. FEtk is 866s designed to solve general coupled systems of nonlinear partial differential 866s equations using adaptive finite element methods, inexact Newton methods, 866s and algebraic multilevel methods. More information about FEtk may be found 866s at . 866s ---------------------------------------------------------------------- 866s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 866s Aqua is a modified form of the Holst group PMG library 866s which has been modified by Patrice Koehl 866s for improved efficiency and 866s memory usage when solving the Poisson-Boltzmann equation. 866s ---------------------------------------------------------------------- 866s Please cite your use of APBS as: 866s 866s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 866s nanosystems: application to microtubules and the ribosome. Proc. 866s Natl. Acad. Sci. USA 98, 10037-10041 2001. 866s 866s 866s This executable compiled on Jan 3 2025 at 11:01:42 866s 866s Parsing input file apbs-mol.in... 866s rank 0 size 1... 866s Parsed input file. 866s Got paths for 2 molecules 866s Reading PQR-format atom data from methanol.pqr. 866s asc_getToken: Error occurred (bailing out). 866s Vio_scanf: Format problem with input. 866s 3 atoms 866s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 866s Net charge 5.55e-17 e 866s Reading PQR-format atom data from methoxide.pqr. 866s 2 atoms 866s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 866s Net charge -1.00e+00 e 866s Preparing to run 4 PBE calculations. 866s ---------------------------------------- 866s CALCULATION #1 (methanol-solv): MULTIGRID 866s Setting up problem... 866s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 866s Debye length: 0 A 866s Current memory usage: 61.247 MB total, 61.247 MB high water 866s Using linear spline charge discretization. 866s Grid dimensions: 65 x 65 x 65 866s Grid spacings: 0.250 x 0.250 x 0.250 866s Grid lengths: 16.000 x 16.000 x 16.000 866s Grid center: (0.309, 0.000, -0.242) 866s Multigrid levels: 5 866s Molecule ID: 1 866s Linearized traditional PBE 866s Multiple Debye-Huckel sphere boundary conditions 866s 2 ion species (0.000 M ionic strength): 866s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 866s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 866s Solute dielectric: 2.000 866s Solvent dielectric: 78.000 866s Using "molecular" surface definition; no smoothing 866s Solvent probe radius: 0.000 A 866s Temperature: 300.000 K 866s Electrostatic energies will be calculated 866s Total electrostatic energy = 1.847663548071E+03 kJ/mol 866s Calculating forces... 866s ---------------------------------------- 866s CALCULATION #2 (methanol-ref): MULTIGRID 866s Setting up problem... 866s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 866s Debye length: 0 A 866s Current memory usage: 61.247 MB total, 61.316 MB high water 866s Using linear spline charge discretization. 866s Grid dimensions: 65 x 65 x 65 866s Grid spacings: 0.250 x 0.250 x 0.250 866s Grid lengths: 16.000 x 16.000 x 16.000 866s Grid center: (0.309, 0.000, -0.242) 866s Multigrid levels: 5 866s Molecule ID: 1 866s Linearized traditional PBE 866s Multiple Debye-Huckel sphere boundary conditions 866s 2 ion species (0.000 M ionic strength): 866s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 866s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 866s Solute dielectric: 2.000 866s Solvent dielectric: 1.000 866s Using "molecular" surface definition; no smoothing 866s Solvent probe radius: 0.000 A 866s Temperature: 300.000 K 866s Electrostatic energies will be calculated 866s Total electrostatic energy = 1.883912182952E+03 kJ/mol 866s Calculating forces... 866s ---------------------------------------- 866s CALCULATION #3 (methoxide-solv): MULTIGRID 866s Setting up problem... 866s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 866s Debye length: 0 A 866s Current memory usage: 61.243 MB total, 61.316 MB high water 866s Using linear spline charge discretization. 866s Grid dimensions: 65 x 65 x 65 866s Grid spacings: 0.250 x 0.250 x 0.250 866s Grid lengths: 16.000 x 16.000 x 16.000 866s Grid center: (0.000, 0.000, -0.128) 866s Multigrid levels: 5 866s Molecule ID: 2 866s Linearized traditional PBE 866s Multiple Debye-Huckel sphere boundary conditions 866s 2 ion species (0.000 M ionic strength): 866s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 866s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 866s Solute dielectric: 2.000 866s Solvent dielectric: 78.000 866s Using "molecular" surface definition; no smoothing 866s Solvent probe radius: 0.000 A 866s Temperature: 300.000 K 866s Electrostatic energies will be calculated 866s Total electrostatic energy =Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 866s *** PASSED *** 866s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 866s *** PASSED *** 866s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 866s *** PASSED *** 866s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 866s *** PASSED *** 866s Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) 866s *** PASSED *** 866s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 866s *** PASSED *** 866s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 866s *** PASSED *** 866s Elapsed time: 3.487696 seconds 866s -------------------------------------------------------------------------------- 866s -------------------------------------------------------------------------------- 866s Testing input file apbs-smol.in 866s 866s 2.732623683321E+03 kJ/mol 866s Calculating forces... 866s ---------------------------------------- 866s CALCULATION #4 (methoxide-ref): MULTIGRID 866s Setting up problem... 866s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 866s Debye length: 0 A 866s Current memory usage: 61.243 MB total, 61.316 MB high water 866s Using linear spline charge discretization. 866s Grid dimensions: 65 x 65 x 65 866s Grid spacings: 0.250 x 0.250 x 0.250 866s Grid lengths: 16.000 x 16.000 x 16.000 866s Grid center: (0.000, 0.000, -0.128) 866s Multigrid levels: 5 866s Molecule ID: 2 866s Linearized traditional PBE 866s Multiple Debye-Huckel sphere boundary conditions 866s 2 ion species (0.000 M ionic strength): 866s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 866s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 866s Solute dielectric: 2.000 866s Solvent dielectric: 1.000 866s Using "molecular" surface definition; no smoothing 866s Solvent probe radius: 0.000 A 866s Temperature: 300.000 K 866s Electrostatic energies will be calculated 866s Total electrostatic energy = 3.123035854133E+03 kJ/mol 866s Calculating forces... 866s ---------------------------------------- 866s PRINT STATEMENTS 866s 866s print energy 1 (methanol-solv) - 2 (methanol-ref) end 866s Local net energy (PE 0) = -3.624863488074E+01 kJ/mol 866s Global net ELEC energy = -3.624863488074E+01 kJ/mol 866s 866s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 866s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 866s Global net ELEC energy = -3.904121708125E+02 kJ/mol 866s 866s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 866s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 866s Global net ELEC energy = -3.541635359318E+02 kJ/mol 866s ---------------------------------------- 866s CLEANING UP AND SHUTTING DOWN... 866s Destroying force arrays. 866s No energy arrays to destroy. 866s Destroying multigrid structures. 866s Destroying finite element structures. 866s Destroying 2 molecules 866s Final memory usage: 0.001 MB total, 61.316 MB high water 866s 866s 866s Thanks for using APBS! 866s 870s Checking for intermediate energies in input file apbs-mol.out 870s EXPECTED COMPUTED: 7 870s EXPECTED EXPECTED: 7 870s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] 870s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 870s COMPUTED RESULT 1847.663548071 870s COMPUTED RESULT 1883.912182952 870s COMPUTED RESULT 2732.623683321 870s COMPUTED RESULT 3123.035854133 870s COMPUTED RESULT -36.24863488074 870s COMPUTED RESULT -390.4121708125 870s COMPUTED RESULT -354.1635359318 870s BINARY: /usr/bin/apbs 870s INPUT: apbs-smol.in 870s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 870s asc_getToken: Error occurred (bailing out). 870s Vio_scanf: Format problem with input. 870s 870s 870s ---------------------------------------------------------------------- 870s APBS -- Adaptive Poisson-Boltzmann Solver 870s Version APBS 3.4.1 870s 870s Nathan A. Baker (nathan.baker@pnnl.gov) 870s Pacific Northwest National Laboratory 870s 870s Additional contributing authors listed in the code documentation. 870s 870s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 870s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 870s Northwest Division for the U.S. Department of Energy. 870s 870s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 870s Portions Copyright (c) 2002-2020, Nathan A. Baker. 870s Portions Copyright (c) 1999-2002, The Regents of the University of California. 870s Portions Copyright (c) 1995, Michael Holst. 870s All rights reserved. 870s 870s Redistribution and use in source and binary forms, with or without 870s modification, are permitted provided that the following conditions are met: 870s 870s * Redistributions of source code must retain the above copyright notice, this 870s list of conditions and the following disclaimer. 870s 870s * Redistributions in binary form must reproduce the above copyright notice, 870s this list of conditions and the following disclaimer in the documentation 870s and/or other materials provided with the distribution. 870s 870s * Neither the name of the developer nor the names of its contributors may be 870s used to endorse or promote products derived from this software without 870s specific prior written permission. 870s 870s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 870s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 870s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 870s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 870s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 870s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 870s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 870s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 870s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 870s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 870s ---------------------------------------------------------------------- 870s APBS uses FETK (the Finite Element ToolKit) to solve the 870s Poisson-Boltzmann equation numerically. FETK is a portable collection 870s of finite element modeling class libraries developed by the Michael Holst 870s research group and written in an object-oriented form of C. FEtk is 870s designed to solve general coupled systems of nonlinear partial differential 870s equations using adaptive finite element methods, inexact Newton methods, 870s and algebraic multilevel methods. More information about FEtk may be found 870s at . 870s ---------------------------------------------------------------------- 870s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 870s Aqua is a modified form of the Holst group PMG library 870s which has been modified by Patrice Koehl 870s for improved efficiency and 870s memory usage when solving the Poisson-Boltzmann equation. 870s ---------------------------------------------------------------------- 870s Please cite your use of APBS as: 870s 870s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 870s nanosystems: application to microtubules and the ribosome. Proc. 870s Natl. Acad. Sci. USA 98, 10037-10041 2001. 870s 870s 870s This executable compiled on Jan 3 2025 at 11:01:42 870s 870s Parsing input file apbs-smol.in... 870s rank 0 size 1... 870s Parsed input file. 870s Got paths for 2 molecules 870s Reading PQR-format atom data from methanol.pqr. 870s asc_getToken: Error occurred (bailing out). 870s Vio_scanf: Format problem with input. 870s 3 atoms 870s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 870s Net charge 5.55e-17 e 870s Reading PQR-format atom data from methoxide.pqr. 870s 2 atoms 870s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 870s Net charge -1.00e+00 e 870s Preparing to run 4 PBE calculations. 870s ---------------------------------------- 870s CALCULATION #1 (methanol-solv): MULTIGRID 870s Setting up problem... 870s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 870s Debye length: 0 A 870s Current memory usage: 61.247 MB total, 61.247 MB high water 870s Using linear spline charge discretization. 870s Grid dimensions: 65 x 65 x 65 870s Grid spacings: 0.250 x 0.250 x 0.250 870s Grid lengths: 16.000 x 16.000 x 16.000 870s Grid center: (0.309, 0.000, -0.242) 870s Multigrid levels: 5 870s Molecule ID: 1 870s Linearized traditional PBE 870s Multiple Debye-Huckel sphere boundary conditions 870s 2 ion species (0.000 M ionic strength): 870s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 870s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 870s Solute dielectric: 2.000 870s Solvent dielectric: 78.000 870s Using "molecular" surface definition;harmonic average smoothing 870s Solvent probe radius: 0.000 A 870s Temperature: 300.000 K 870s Electrostatic energies will be calculated 870s Total electrostatic energy = 1.847860440020E+03 kJ/mol 870s Calculating forces... 870s ---------------------------------------- 870s CALCULATION #2 (methanol-ref): MULTIGRID 870s Setting up problem... 870s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 870s Debye length: 0 A 870s Current memory usage: 61.247 MB total, 61.316 MB high water 870s Using linear spline charge discretization. 870s Grid dimensions: 65 x 65 x 65 870s Grid spacings: 0.250 x 0.250 x 0.250 870s Grid lengths: 16.000 x 16.000 x 16.000 870s Grid center: (0.309, 0.000, -0.242) 870s Multigrid levels: 5 870s Molecule ID: 1 870s Linearized traditional PBE 870s Multiple Debye-Huckel sphere boundary conditions 870s 2 ion species (0.000 M ionic strength): 870s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 870s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 870s Solute dielectric: 2.000 870s Solvent dielectric: 1.000 870s Using "molecular" surface definition;harmonic average smoothing 870s Solvent probe radius: 0.000 A 870s Temperature: 300.000 K 870s Electrostatic energies will be calculated 870s Total electrostatic energy = 1.885436377745E+03 kJ/mol 870s Calculating forces... 870s ---------------------------------------- 870s CALCULATION #3 (methoxide-solv): MULTIGRID 870s Setting up problem... 870s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 870s Debye length: 0 A 870s Current memory usage: 61.243 MB total, 61.316 MB high water 870s Using linear spline charge discretization. 870s Grid dimensions: 65 x 65 x 65 870s Grid spacings: 0.250 x 0.250 x 0.250 870s Grid lengths: 16.000 x 16.000 x 16.000 870s Grid center: (0.000, 0.000, -0.128) 870s Multigrid levels: 5 870s Molecule ID: 2 870s Linearized traditional PBE 870s Multiple Debye-Huckel sphere boundary conditions 870s 2 ion species (0.000 M ionic strength): 870s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 870s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 870s Solute dielectric: 2.000 870s Solvent dielectric: 78.000 870s Using "molecular" surface definition;harmonic average smoothing 870s Solvent probe radius: 0.000 A 870s Temperature: 300.000 K 870s Electrostatic energies will be calculated 870s Total electrostatic energy = 2.734040568569E+03 kJ/mol 870s Calculating forces... 870s ---------------------------------------- 870s CALCULATION #4 (methoxide-ref): MULTIGRID 870s Setting up problem... 870s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 870s Debye length: 0 A 870s Current memory usage: 61.243 MB total, 61.316 MB high water 870s Using linear spline charge discretization. 870s Grid dimensions: 65 x 65 x 65 870s Grid spacings: 0.250 x 0.250 x 0.250 870s Grid lengths: 16.000 x 16.000 x 16.000 870s Grid center: (0.000, 0.000, -0.128) 870s Multigrid levels: 5 870s Molecule ID: 2 870s Linearized traditional PBE 870s Multiple Debye-Huckel sphere boundary conditions 870s 2 ion species (0.000 M ionic strength): 870s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 870s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 870s Solute dielectric: 2.000 870s Solvent dielectric: 1.000 870s Using "molecular" surface definition;harmonic average smoothing 870s Solvent probe radius: 0.000 A 870s Temperature: 300.000 K 870s Electrostatic energies will be calculated 870s Total electrostatic energy = 3.125279428954E+03 kJ/mol 870s Calculating forces... 870s ---------------------------------------- 870s PRINT STATEMENTS 870s 870s print energy 1 (methanol-solv) - 2 (methanol-ref) end 870s Local net energy (PE 0) = -3.757593772493E+01 kJ/mol 870s Global net ELEC energy = -3.757593772493E+01 kJ/mol 870s 870s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 870s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 870s Global net ELEC energy = -3.912388603848E+02 kJ/mol 870s 870s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 870s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 870s Global net ELEC energy = -3.536629226599E+02 kJ/mol 870s ---------------------------------------- 870s CLEANING UP AND SHUTTING DOWN... 870s Destroying force arrays. 870s No energy arrays to destroy. 870s Destroying multigrid structures. 870s Destroying finite element structures. 870s Destroying 2 molecules 870s Final memory usage: 0.001 MB total, 61.316 MB high water 870s 870s 870s Thanks for using APBS! 870s 870s Checking for intermediate energies in input file apbs-smol.out 870s EXPECTED COMPUTED: 7 870s EXPECTED EXPECTED: 7 870s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] 870s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 870s COMPUTED RESULT 1847.86044002 870s COMPUTED RESULT 1885.436377745 870s COMPUTED RESULT 2734.040568569 870s COMPUTED RESULT 3125.279428954 870s COMPUTED RESULT -37.57593772493 870s COMPUTED RESULT -391.2388603848 870s COMPUTED RESULT -353.6629226599 870s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 870s *** PASSED *** 870s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 870s *** PASSED *** 870s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 870s *** PASSED *** 870s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 870s *** PASSED *** 870s Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) 870s *** PASSED *** 870s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 870s *** PASSED *** 870s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 870s *** PASSED *** 870s Elapsed time: 3.326992 seconds 870s -------------------------------------------------------------------------------- 870s Total elapsed time: 6.814688 seconds 870s Test results have been logged 870s -------------------------------------------------------------------------------- 870s autopkgtest [15:27:29]: test test-apbs: -----------------------] 874s autopkgtest [15:27:33]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 874s test-apbs PASS 878s autopkgtest [15:27:37]: @@@@@@@@@@@@@@@@@@@@ summary 878s test-apbs PASS