0s autopkgtest [00:35:05]: starting date and time: 2025-10-20 00:35:05+0000 0s autopkgtest [00:35:05]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [00:35:05]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v14o9e_f/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:node-jquery --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- lxd -r lxd-armhf-10.145.243.227 lxd-armhf-10.145.243.227:autopkgtest/ubuntu/resolute/armhf 21s autopkgtest [00:35:26]: testbed dpkg architecture: armhf 23s autopkgtest [00:35:28]: testbed apt version: 3.1.6ubuntu2 27s autopkgtest [00:35:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [00:35:34]: testbed release detected to be: None 36s autopkgtest [00:35:41]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 38s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [83.3 kB] 39s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 39s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 39s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 39s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.8 kB] 39s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [396 kB] 39s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [47.8 kB] 39s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [95.2 kB] 39s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 39s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [265 kB] 39s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [5192 B] 39s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1400 kB] 40s Get:14 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.1 MB] 44s Get:15 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [307 kB] 44s Get:16 http://ftpmaster.internal/ubuntu resolute/restricted Sources [14.4 kB] 44s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1357 kB] 44s Get:18 http://ftpmaster.internal/ubuntu resolute/restricted armhf Packages [1672 B] 44s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.0 MB] 45s Get:20 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [182 kB] 47s Fetched 40.3 MB in 9s (4280 kB/s) 49s Reading package lists... 54s autopkgtest [00:35:59]: upgrading testbed (apt dist-upgrade and autopurge) 56s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 58s The following packages will be upgraded: 58s apparmor apt base-files binutils binutils-arm-linux-gnueabihf 58s binutils-common cloud-init cloud-init-base distro-info-data dpkg dpkg-dev 58s gcc-15-base gir1.2-girepository-2.0 libapparmor1 libapt-pkg7.0 libatomic1 58s libaudit-common libaudit1 libbinutils libcap-ng0 libctf-nobfd0 libctf0 58s libdpkg-perl libgcc-s1 libgirepository-1.0-1 libnewt0.52 libnftables1 58s libp11-kit0 libseccomp2 libsframe2 libstdc++6 lto-disabled-list nftables 58s python-apt-common python3-apt sudo-rs whiptail 58s 37 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 11.0 MB of archives. 58s After this operation, 433 kB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf base-files armhf 14ubuntu4 [75.4 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libatomic1 armhf 15.2.0-5ubuntu1 [7942 B] 59s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-base armhf 15.2.0-5ubuntu1 [58.1 kB] 59s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-s1 armhf 15.2.0-5ubuntu1 [40.6 kB] 59s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++6 armhf 15.2.0-5ubuntu1 [731 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libapt-pkg7.0 armhf 3.1.8ubuntu1 [1148 kB] 61s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg armhf 1.22.21ubuntu4 [1245 kB] 62s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libseccomp2 armhf 2.6.0-2ubuntu3 [53.5 kB] 62s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf apt armhf 3.1.8ubuntu1 [1404 kB] 63s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit-common all 1:4.0.5-1build2 [6596 B] 63s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libcap-ng0 armhf 0.8.5-4build3 [14.0 kB] 63s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit1 armhf 1:4.0.5-1build2 [51.7 kB] 63s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf distro-info-data all 0.68 [7378 B] 63s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libgirepository-1.0-1 armhf 1.86.0-6 [111 kB] 63s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-girepository-2.0 armhf 1.86.0-6 [25.3 kB] 63s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libapparmor1 armhf 5.0.0~alpha1-0ubuntu8.1 [52.9 kB] 63s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libnewt0.52 armhf 0.52.25-1ubuntu2 [39.9 kB] 63s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libp11-kit0 armhf 0.25.9-2 [265 kB] 63s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf python-apt-common all 3.0.0ubuntu2 [21.7 kB] 63s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf python3-apt armhf 3.0.0ubuntu2 [189 kB] 63s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf sudo-rs armhf 0.2.8-1ubuntu5.1 [548 kB] 63s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf whiptail armhf 0.52.25-1ubuntu2 [17.1 kB] 63s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf apparmor armhf 5.0.0~alpha1-0ubuntu8.1 [631 kB] 64s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf nftables armhf 1.1.5-2 [73.2 kB] 64s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libnftables1 armhf 1.1.5-2 [329 kB] 64s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libctf0 armhf 2.45-7ubuntu2 [75.7 kB] 64s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libctf-nobfd0 armhf 2.45-7ubuntu2 [79.1 kB] 64s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-arm-linux-gnueabihf armhf 2.45-7ubuntu2 [1022 kB] 65s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libbinutils armhf 2.45-7ubuntu2 [411 kB] 65s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf binutils armhf 2.45-7ubuntu2 [3240 B] 65s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-common armhf 2.45-7ubuntu2 [220 kB] 65s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libsframe2 armhf 2.45-7ubuntu2 [13.4 kB] 65s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init-base all 25.3-0ubuntu1 [625 kB] 66s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init all 25.3-0ubuntu1 [2106 B] 66s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg-dev all 1.22.21ubuntu4 [1088 kB] 66s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libdpkg-perl all 1.22.21ubuntu4 [280 kB] 66s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf lto-disabled-list all 71 [12.5 kB] 67s Preconfiguring packages ... 67s Fetched 11.0 MB in 8s (1325 kB/s) 67s (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.) 67s Preparing to unpack .../base-files_14ubuntu4_armhf.deb ... 67s Unpacking base-files (14ubuntu4) over (14ubuntu3) ... 67s Setting up base-files (14ubuntu4) ... 67s Installing new version of config file /etc/issue ... 67s Installing new version of config file /etc/issue.net ... 67s Installing new version of config file /etc/lsb-release ... 68s motd-news.service is a disabled or a static unit not running, not starting it. 68s (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.) 68s Preparing to unpack .../libatomic1_15.2.0-5ubuntu1_armhf.deb ... 68s Unpacking libatomic1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 68s Preparing to unpack .../gcc-15-base_15.2.0-5ubuntu1_armhf.deb ... 68s Unpacking gcc-15-base:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 69s Setting up gcc-15-base:armhf (15.2.0-5ubuntu1) ... 69s (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.) 69s Preparing to unpack .../libgcc-s1_15.2.0-5ubuntu1_armhf.deb ... 69s Unpacking libgcc-s1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 69s Setting up libgcc-s1:armhf (15.2.0-5ubuntu1) ... 69s (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.) 69s Preparing to unpack .../libstdc++6_15.2.0-5ubuntu1_armhf.deb ... 69s Unpacking libstdc++6:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 69s Setting up libstdc++6:armhf (15.2.0-5ubuntu1) ... 69s (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.) 69s Preparing to unpack .../libapt-pkg7.0_3.1.8ubuntu1_armhf.deb ... 69s Unpacking libapt-pkg7.0:armhf (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 69s Setting up libapt-pkg7.0:armhf (3.1.8ubuntu1) ... 69s (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.) 69s Preparing to unpack .../dpkg_1.22.21ubuntu4_armhf.deb ... 69s Unpacking dpkg (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 69s Setting up dpkg (1.22.21ubuntu4) ... 70s (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.) 70s Preparing to unpack .../libseccomp2_2.6.0-2ubuntu3_armhf.deb ... 70s Unpacking libseccomp2:armhf (2.6.0-2ubuntu3) over (2.6.0-2ubuntu2) ... 70s Setting up libseccomp2:armhf (2.6.0-2ubuntu3) ... 70s (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.) 70s Preparing to unpack .../apt_3.1.8ubuntu1_armhf.deb ... 70s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 70s Setting up apt (3.1.8ubuntu1) ... 71s (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.) 71s Preparing to unpack .../libaudit-common_1%3a4.0.5-1build2_all.deb ... 71s Unpacking libaudit-common (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 71s Setting up libaudit-common (1:4.0.5-1build2) ... 71s (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.) 71s Preparing to unpack .../libcap-ng0_0.8.5-4build3_armhf.deb ... 71s Unpacking libcap-ng0:armhf (0.8.5-4build3) over (0.8.5-4build2) ... 71s Setting up libcap-ng0:armhf (0.8.5-4build3) ... 71s (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.) 71s Preparing to unpack .../libaudit1_1%3a4.0.5-1build2_armhf.deb ... 71s Unpacking libaudit1:armhf (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 71s Setting up libaudit1:armhf (1:4.0.5-1build2) ... 71s (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.) 71s Preparing to unpack .../00-distro-info-data_0.68_all.deb ... 71s Unpacking distro-info-data (0.68) over (0.66) ... 71s Preparing to unpack .../01-libgirepository-1.0-1_1.86.0-6_armhf.deb ... 71s Unpacking libgirepository-1.0-1:armhf (1.86.0-6) over (1.84.0-1) ... 71s Preparing to unpack .../02-gir1.2-girepository-2.0_1.86.0-6_armhf.deb ... 71s Unpacking gir1.2-girepository-2.0:armhf (1.86.0-6) over (1.84.0-1) ... 71s Preparing to unpack .../03-libapparmor1_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 71s Unpacking libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 71s Preparing to unpack .../04-libnewt0.52_0.52.25-1ubuntu2_armhf.deb ... 71s Unpacking libnewt0.52:armhf (0.52.25-1ubuntu2) over (0.52.25-1ubuntu1) ... 71s Preparing to unpack .../05-libp11-kit0_0.25.9-2_armhf.deb ... 71s Unpacking libp11-kit0:armhf (0.25.9-2) over (0.25.5-3ubuntu1) ... 71s Preparing to unpack .../06-python-apt-common_3.0.0ubuntu2_all.deb ... 71s Unpacking python-apt-common (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 71s Preparing to unpack .../07-python3-apt_3.0.0ubuntu2_armhf.deb ... 72s Unpacking python3-apt (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 72s Preparing to unpack .../08-sudo-rs_0.2.8-1ubuntu5.1_armhf.deb ... 72s Unpacking sudo-rs (0.2.8-1ubuntu5.1) over (0.2.8-1ubuntu5) ... 72s Preparing to unpack .../09-whiptail_0.52.25-1ubuntu2_armhf.deb ... 72s Unpacking whiptail (0.52.25-1ubuntu2) over (0.52.25-1ubuntu1) ... 72s Preparing to unpack .../10-apparmor_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 73s Unpacking apparmor (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 74s Preparing to unpack .../11-nftables_1.1.5-2_armhf.deb ... 74s Unpacking nftables (1.1.5-2) over (1.1.5-1) ... 74s Preparing to unpack .../12-libnftables1_1.1.5-2_armhf.deb ... 74s Unpacking libnftables1:armhf (1.1.5-2) over (1.1.5-1) ... 74s Preparing to unpack .../13-libctf0_2.45-7ubuntu2_armhf.deb ... 74s Unpacking libctf0:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 74s Preparing to unpack .../14-libctf-nobfd0_2.45-7ubuntu2_armhf.deb ... 74s Unpacking libctf-nobfd0:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 74s Preparing to unpack .../15-binutils-arm-linux-gnueabihf_2.45-7ubuntu2_armhf.deb ... 74s Unpacking binutils-arm-linux-gnueabihf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 74s Preparing to unpack .../16-libbinutils_2.45-7ubuntu2_armhf.deb ... 74s Unpacking libbinutils:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 75s Preparing to unpack .../17-binutils_2.45-7ubuntu2_armhf.deb ... 75s Unpacking binutils (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 75s Preparing to unpack .../18-binutils-common_2.45-7ubuntu2_armhf.deb ... 75s Unpacking binutils-common:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 75s Preparing to unpack .../19-libsframe2_2.45-7ubuntu2_armhf.deb ... 75s Unpacking libsframe2:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 75s Preparing to unpack .../20-cloud-init-base_25.3-0ubuntu1_all.deb ... 75s Unpacking cloud-init-base (25.3-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 75s Preparing to unpack .../21-cloud-init_25.3-0ubuntu1_all.deb ... 75s Unpacking cloud-init (25.3-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 75s Preparing to unpack .../22-dpkg-dev_1.22.21ubuntu4_all.deb ... 75s Unpacking dpkg-dev (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 76s Preparing to unpack .../23-libdpkg-perl_1.22.21ubuntu4_all.deb ... 76s Unpacking libdpkg-perl (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 76s Preparing to unpack .../24-lto-disabled-list_71_all.deb ... 76s Unpacking lto-disabled-list (71) over (69) ... 76s Setting up lto-disabled-list (71) ... 76s Setting up libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) ... 76s Setting up libnewt0.52:armhf (0.52.25-1ubuntu2) ... 76s Setting up libnftables1:armhf (1.1.5-2) ... 76s Setting up nftables (1.1.5-2) ... 76s Setting up distro-info-data (0.68) ... 76s Setting up libsframe2:armhf (2.45-7ubuntu2) ... 76s Setting up binutils-common:armhf (2.45-7ubuntu2) ... 76s Setting up libctf-nobfd0:armhf (2.45-7ubuntu2) ... 76s Setting up cloud-init-base (25.3-0ubuntu1) ... 78s Setting up apparmor (5.0.0~alpha1-0ubuntu8.1) ... 78s Installing new version of config file /etc/apparmor.d/fusermount3 ... 79s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 79s 79s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 79s 79s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 79s 80s Reloading AppArmor profiles 80s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "bwrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "bfdd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "babeld". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "bgpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "alsamixer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "dnstracer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "eigrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "fabricd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "dig". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "hostname". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "iotop-c". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "fusermount3". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "isisd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ldpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "gs". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "john". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Unable to replace "linux-boot-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "compressor". /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "locale". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lsblk". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lsusb". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "mosquitto". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "irssi". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Unable to replace "mbsync". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "nhrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "nslookup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "nc.openbsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "notify-send". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ospf6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ospfd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "os-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "pathd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "pbrd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "pim6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "pimd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ripngd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "qpdf". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ripd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "openvpn". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "proftpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ssh-keyscan". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "staticd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "systemd-detect-virt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "tinyproxy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "mx-extract". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "rygel". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "/usr/sbin/chronyd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "wg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "vrrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "who". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "cmds". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "tnftp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "dumpcap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "tshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "wg-quick". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "znc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 80s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 80s 81s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 81s 81s Error: At least one profile failed to load 81s Setting up libp11-kit0:armhf (0.25.9-2) ... 81s Setting up libatomic1:armhf (15.2.0-5ubuntu1) ... 81s Setting up libdpkg-perl (1.22.21ubuntu4) ... 81s Setting up whiptail (0.52.25-1ubuntu2) ... 81s Setting up python-apt-common (3.0.0ubuntu2) ... 81s Setting up libgirepository-1.0-1:armhf (1.86.0-6) ... 81s Setting up libbinutils:armhf (2.45-7ubuntu2) ... 81s Setting up sudo-rs (0.2.8-1ubuntu5.1) ... 81s Setting up libctf0:armhf (2.45-7ubuntu2) ... 81s Setting up cloud-init (25.3-0ubuntu1) ... 81s Setting up python3-apt (3.0.0ubuntu2) ... 81s Setting up gir1.2-girepository-2.0:armhf (1.86.0-6) ... 81s Setting up binutils-arm-linux-gnueabihf (2.45-7ubuntu2) ... 81s Setting up binutils (2.45-7ubuntu2) ... 81s Setting up dpkg-dev (1.22.21ubuntu4) ... 81s Processing triggers for procps (2:4.0.4-8ubuntu3) ... 81s Processing triggers for install-info (7.1.1-1ubuntu1) ... 81s Processing triggers for libc-bin (2.42-0ubuntu3) ... 81s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 81s Processing triggers for systemd (257.9-0ubuntu2) ... 81s Processing triggers for man-db (2.13.1-1) ... 83s Processing triggers for plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu1) ... 86s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Solving dependencies... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [00:36:35]: rebooting testbed after setup commands that affected boot 131s autopkgtest [00:37:16]: 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 155s autopkgtest [00:37:40]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 212s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 212s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 212s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 213s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 213s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 213s gpgv: Can't check signature: No public key 213s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 215s autopkgtest [00:38:40]: testing package apbs version 3.4.1-6build2 221s autopkgtest [00:38:46]: build not needed 227s autopkgtest [00:38:52]: test test-apbs: preparing testbed 229s Reading package lists... 230s Building dependency tree... 230s Reading state information... 230s Solving dependencies... 231s The following NEW packages will be installed: 231s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax libamd3 231s libapbs-dev libapbs3t64 libarpack2t64 libblas3 libcamd3 libccolamd3 231s libcholmod5 libcolamd3 libfetk-dev libfetk1.9t64 libgfortran5 libgomp1 231s libhwloc15 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore 231s liblapack3 libmaloc-dev libmaloc1 libmpich12 libpython3.13 libspqr4 231s libsuitesparseconfig7 libsuperlu7 libumfpack6 python3-apbslib 231s sphinx-rtd-theme-common 231s 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. 231s Need to get 30.8 MB of archives. 231s After this operation, 116 MB of additional disk space will be used. 231s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-lato all 2.015-1 [2781 kB] 232s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf apbs-data all 3.4.1-6build2 [1769 kB] 232s Get:3 http://ftpmaster.internal/ubuntu resolute/universe armhf libmaloc1 armhf 1.5-2 [79.8 kB] 233s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-6build1 [133 kB] 233s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf libsuperlu7 armhf 7.0.1+dfsg1-2 [157 kB] 233s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-5ubuntu1 [129 kB] 233s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libsuitesparseconfig7 armhf 1:7.10.1+dfsg-1 [20.9 kB] 233s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf libamd3 armhf 1:7.10.1+dfsg-1 [37.7 kB] 233s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libcamd3 armhf 1:7.10.1+dfsg-1 [34.3 kB] 233s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libccolamd3 armhf 1:7.10.1+dfsg-1 [36.0 kB] 233s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libcolamd3 armhf 1:7.10.1+dfsg-1 [28.0 kB] 233s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-5ubuntu1 [334 kB] 233s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-6build1 [2091 kB] 233s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf libcholmod5 armhf 1:7.10.1+dfsg-1 [681 kB] 233s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf libumfpack6 armhf 1:7.10.1+dfsg-1 [296 kB] 233s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf libfetk1.9t64 armhf 3.4.1-6build2 [538 kB] 233s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf libapbs3t64 armhf 3.4.1-6build2 [257 kB] 233s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 233s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 234s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf libarpack2t64 armhf 3.9.1-6 [88.7 kB] 234s Get:21 http://ftpmaster.internal/ubuntu resolute/universe armhf libhwloc15 armhf 2.12.2-1 [149 kB] 234s Get:22 http://ftpmaster.internal/ubuntu resolute/universe armhf libmpich12 armhf 4.3.0+really4.2.1-1build1 [1688 kB] 234s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf libspqr4 armhf 1:7.10.1+dfsg-1 [138 kB] 234s Get:24 http://ftpmaster.internal/ubuntu resolute/universe armhf apbs armhf 3.4.1-6build2 [75.0 kB] 234s Get:25 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 234s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 234s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 234s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 234s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 234s Get:30 http://ftpmaster.internal/ubuntu resolute/universe armhf apbs-doc all 3.4.1-6build2 [5850 kB] 235s Get:31 http://ftpmaster.internal/ubuntu resolute/universe armhf libapbs-dev armhf 3.4.1-6build2 [99.5 kB] 235s Get:32 http://ftpmaster.internal/ubuntu resolute/universe armhf libmaloc-dev armhf 1.5-2 [918 kB] 235s Get:33 http://ftpmaster.internal/ubuntu resolute/universe armhf libfetk-dev armhf 3.4.1-6build2 [144 kB] 235s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13 armhf 3.13.7-1 [2123 kB] 235s Get:35 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-apbslib armhf 3.4.1-6build2 [222 kB] 236s Fetched 30.8 MB in 4s (7627 kB/s) 236s Selecting previously unselected package fonts-lato. 236s (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 ... 61085 files and directories currently installed.) 236s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 236s Unpacking fonts-lato (2.015-1) ... 236s Selecting previously unselected package apbs-data. 236s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 236s Unpacking apbs-data (3.4.1-6build2) ... 236s Selecting previously unselected package libmaloc1:armhf. 236s Preparing to unpack .../02-libmaloc1_1.5-2_armhf.deb ... 236s Unpacking libmaloc1:armhf (1.5-2) ... 236s Selecting previously unselected package libblas3:armhf. 236s Preparing to unpack .../03-libblas3_3.12.1-6build1_armhf.deb ... 236s Unpacking libblas3:armhf (3.12.1-6build1) ... 236s Selecting previously unselected package libsuperlu7:armhf. 236s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_armhf.deb ... 236s Unpacking libsuperlu7:armhf (7.0.1+dfsg1-2) ... 236s Selecting previously unselected package libgomp1:armhf. 236s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_armhf.deb ... 236s Unpacking libgomp1:armhf (15.2.0-5ubuntu1) ... 236s Selecting previously unselected package libsuitesparseconfig7:armhf. 236s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_armhf.deb ... 236s Unpacking libsuitesparseconfig7:armhf (1:7.10.1+dfsg-1) ... 236s Selecting previously unselected package libamd3:armhf. 236s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_armhf.deb ... 236s Unpacking libamd3:armhf (1:7.10.1+dfsg-1) ... 236s Selecting previously unselected package libcamd3:armhf. 236s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_armhf.deb ... 236s Unpacking libcamd3:armhf (1:7.10.1+dfsg-1) ... 237s Selecting previously unselected package libccolamd3:armhf. 237s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_armhf.deb ... 237s Unpacking libccolamd3:armhf (1:7.10.1+dfsg-1) ... 237s Selecting previously unselected package libcolamd3:armhf. 237s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_armhf.deb ... 237s Unpacking libcolamd3:armhf (1:7.10.1+dfsg-1) ... 237s Selecting previously unselected package libgfortran5:armhf. 237s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_armhf.deb ... 237s Unpacking libgfortran5:armhf (15.2.0-5ubuntu1) ... 237s Selecting previously unselected package liblapack3:armhf. 237s Preparing to unpack .../12-liblapack3_3.12.1-6build1_armhf.deb ... 237s Unpacking liblapack3:armhf (3.12.1-6build1) ... 237s Selecting previously unselected package libcholmod5:armhf. 237s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_armhf.deb ... 237s Unpacking libcholmod5:armhf (1:7.10.1+dfsg-1) ... 237s Selecting previously unselected package libumfpack6:armhf. 237s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_armhf.deb ... 237s Unpacking libumfpack6:armhf (1:7.10.1+dfsg-1) ... 237s Selecting previously unselected package libfetk1.9t64:armhf. 237s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_armhf.deb ... 237s Unpacking libfetk1.9t64:armhf (3.4.1-6build2) ... 237s Selecting previously unselected package libapbs3t64:armhf. 237s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_armhf.deb ... 237s Unpacking libapbs3t64:armhf (3.4.1-6build2) ... 237s Selecting previously unselected package fonts-mathjax. 237s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 237s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 237s Selecting previously unselected package libjs-mathjax. 237s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 237s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 238s Selecting previously unselected package libarpack2t64:armhf. 238s Preparing to unpack .../19-libarpack2t64_3.9.1-6_armhf.deb ... 238s Unpacking libarpack2t64:armhf (3.9.1-6) ... 238s Selecting previously unselected package libhwloc15:armhf. 238s Preparing to unpack .../20-libhwloc15_2.12.2-1_armhf.deb ... 238s Unpacking libhwloc15:armhf (2.12.2-1) ... 239s Selecting previously unselected package libmpich12:armhf. 239s Preparing to unpack .../21-libmpich12_4.3.0+really4.2.1-1build1_armhf.deb ... 239s Unpacking libmpich12:armhf (4.3.0+really4.2.1-1build1) ... 239s Selecting previously unselected package libspqr4:armhf. 239s Preparing to unpack .../22-libspqr4_1%3a7.10.1+dfsg-1_armhf.deb ... 239s Unpacking libspqr4:armhf (1:7.10.1+dfsg-1) ... 239s Selecting previously unselected package apbs. 239s Preparing to unpack .../23-apbs_3.4.1-6build2_armhf.deb ... 239s Unpacking apbs (3.4.1-6build2) ... 239s Selecting previously unselected package libjs-jquery. 239s Preparing to unpack .../24-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 239s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 239s Selecting previously unselected package libjs-underscore. 239s Preparing to unpack .../25-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 239s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 239s Selecting previously unselected package libjs-sphinxdoc. 239s Preparing to unpack .../26-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 239s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 239s Selecting previously unselected package fonts-font-awesome. 239s Preparing to unpack .../27-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 239s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 239s Selecting previously unselected package sphinx-rtd-theme-common. 239s Preparing to unpack .../28-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 239s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 239s Selecting previously unselected package apbs-doc. 239s Preparing to unpack .../29-apbs-doc_3.4.1-6build2_all.deb ... 239s Unpacking apbs-doc (3.4.1-6build2) ... 239s Selecting previously unselected package libapbs-dev:armhf. 239s Preparing to unpack .../30-libapbs-dev_3.4.1-6build2_armhf.deb ... 239s Unpacking libapbs-dev:armhf (3.4.1-6build2) ... 239s Selecting previously unselected package libmaloc-dev. 239s Preparing to unpack .../31-libmaloc-dev_1.5-2_armhf.deb ... 239s Unpacking libmaloc-dev (1.5-2) ... 239s Selecting previously unselected package libfetk-dev:armhf. 239s Preparing to unpack .../32-libfetk-dev_3.4.1-6build2_armhf.deb ... 239s Unpacking libfetk-dev:armhf (3.4.1-6build2) ... 239s Selecting previously unselected package libpython3.13:armhf. 239s Preparing to unpack .../33-libpython3.13_3.13.7-1_armhf.deb ... 239s Unpacking libpython3.13:armhf (3.13.7-1) ... 239s Selecting previously unselected package python3-apbslib. 239s Preparing to unpack .../34-python3-apbslib_3.4.1-6build2_armhf.deb ... 239s Unpacking python3-apbslib (3.4.1-6build2) ... 239s Setting up libpython3.13:armhf (3.13.7-1) ... 239s Setting up libmaloc1:armhf (1.5-2) ... 239s Setting up fonts-lato (2.015-1) ... 239s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 239s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 239s Setting up apbs-data (3.4.1-6build2) ... 239s Setting up libgomp1:armhf (15.2.0-5ubuntu1) ... 239s Setting up libblas3:armhf (3.12.1-6build1) ... 240s 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 240s Setting up libhwloc15:armhf (2.12.2-1) ... 240s Setting up libgfortran5:armhf (15.2.0-5ubuntu1) ... 240s Setting up libmpich12:armhf (4.3.0+really4.2.1-1build1) ... 240s Setting up libsuitesparseconfig7:armhf (1:7.10.1+dfsg-1) ... 240s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 240s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 240s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 240s Setting up libmaloc-dev (1.5-2) ... 240s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 240s Setting up liblapack3:armhf (3.12.1-6build1) ... 240s 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 240s Setting up libarpack2t64:armhf (3.9.1-6) ... 240s Setting up libamd3:armhf (1:7.10.1+dfsg-1) ... 240s Setting up libcolamd3:armhf (1:7.10.1+dfsg-1) ... 240s Setting up libcamd3:armhf (1:7.10.1+dfsg-1) ... 240s Setting up libsuperlu7:armhf (7.0.1+dfsg1-2) ... 240s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 240s Setting up libccolamd3:armhf (1:7.10.1+dfsg-1) ... 240s Setting up libcholmod5:armhf (1:7.10.1+dfsg-1) ... 240s Setting up libspqr4:armhf (1:7.10.1+dfsg-1) ... 240s Setting up apbs-doc (3.4.1-6build2) ... 240s Setting up libumfpack6:armhf (1:7.10.1+dfsg-1) ... 240s Setting up libfetk1.9t64:armhf (3.4.1-6build2) ... 240s Setting up libapbs3t64:armhf (3.4.1-6build2) ... 240s Setting up libfetk-dev:armhf (3.4.1-6build2) ... 240s Setting up libapbs-dev:armhf (3.4.1-6build2) ... 240s Setting up apbs (3.4.1-6build2) ... 240s Setting up python3-apbslib (3.4.1-6build2) ... 240s Processing triggers for man-db (2.13.1-1) ... 240s Processing triggers for libc-bin (2.42-0ubuntu3) ... 261s autopkgtest [00:39:26]: test test-apbs: [----------------------- 263s TESTING WITH BINARY_NAME:apbs 263s START_DIR:/tmp/autopkgtest.cbSb6j/autopkgtest_tmp/build 263s -------------------------------------------------------------------------------- 263s Testing forces from apbs-forces.in 263s 263s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001146 seconds 263s -------------------------------------------------------------------------------- 263s -------------------------------------------------------------------------------- 263s Testing input file apbs-mol-auto.in 263s 268s CHECKING:/usr/local/sbin/apbs 268s CHECKING:/usr/local/bin/apbs 268s CHECKING:/usr/sbin/apbs 268s CHECKING:/usr/bin/apbs 268s NOTE: Using apbs binary:/usr/bin/apbs 268s Testing all sections 268s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 268s ================================================================================ 268s Running tests for born section 268s BINARY: /usr/bin/apbs 268s INPUT: apbs-mol-auto.in 268s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 268s asc_getToken: Error occurred (bailing out). 268s Vio_scanf: Format problem with input. 268s 268s 268s ---------------------------------------------------------------------- 268s APBS -- Adaptive Poisson-Boltzmann Solver 268s Version APBS 3.4.1 268s 268s Nathan A. Baker (nathan.baker@pnnl.gov) 268s Pacific Northwest National Laboratory 268s 268s Additional contributing authors listed in the code documentation. 268s 268s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 268s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 268s Northwest Division for the U.S. Department of Energy. 268s 268s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 268s Portions Copyright (c) 2002-2020, Nathan A. Baker. 268s Portions Copyright (c) 1999-2002, The Regents of the University of California. 268s Portions Copyright (c) 1995, Michael Holst. 268s All rights reserved. 268s 268s Redistribution and use in source and binary forms, with or without 268s modification, are permitted provided that the following conditions are met: 268s 268s * Redistributions of source code must retain the above copyright notice, this 268s list of conditions and the following disclaimer. 268s 268s * Redistributions in binary form must reproduce the above copyright notice, 268s this list of conditions and the following disclaimer in the documentation 268s and/or other materials provided with the distribution. 268s 268s * Neither the name of the developer nor the names of its contributors may be 268s used to endorse or promote products derived from this software without 268s specific prior written permission. 268s 268s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 268s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 268s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 268s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 268s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 268s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 268s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 268s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 268s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 268s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 268s ---------------------------------------------------------------------- 268s APBS uses FETK (the Finite Element ToolKit) to solve the 268s Poisson-Boltzmann equation numerically. FETK is a portable collection 268s of finite element modeling class libraries developed by the Michael Holst 268s research group and written in an object-oriented form of C. FEtk is 268s designed to solve general coupled systems of nonlinear partial differential 268s equations using adaptive finite element methods, inexact Newton methods, 268s and algebraic multilevel methods. More information about FEtk may be found 268s at . 268s ---------------------------------------------------------------------- 268s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 268s Aqua is a modified form of the Holst group PMG library 268s which has been modified by Patrice Koehl 268s for improved efficiency and 268s memory usage when solving the Poisson-Boltzmann equation. 268s ---------------------------------------------------------------------- 268s Please cite your use of APBS as: 268s 268s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 268s nanosystems: application to microtubules and the ribosome. Proc. 268s Natl. Acad. Sci. USA 98, 10037-10041 2001. 268s 268s 268s This executable compiled on Jan 3 2025 at 11:01:42 268s 268s Parsing input file apbs-mol-auto.in... 268s rank 0 size 1... 268s Parsed input file. 268s Got paths for 1 molecules 268s Reading PQR-format atom data from ion.pqr. 268s 1 atoms 268s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 268s Net charge 1.00e+00 e 268s Preparing to run 6 PBE calculations. 268s ---------------------------------------- 268s CALCULATION #1 (solvated): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 268s Debye length: 0 A 268s Current memory usage: 61.262 MB total, 61.262 MB high water 268s Using cubic spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.781 x 0.781 x 0.781 268s Grid lengths: 50.000 x 50.000 x 50.000 268s Grid center: (0.000, 0.000, 0.000) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 0 ion species (0.000 M ionic strength): 268s Solute dielectric: 1.000 268s Solvent dielectric: 78.540 268s Using "molecular" surface definition; no smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 9.607073836227E+02 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #2 (solvated): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 268s Debye length: 0 A 268s Current memory usage: 61.262 MB total, 122.067 MB high water 268s Using cubic spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.383 x 0.383 x 0.383 268s Grid lengths: 24.495 x 24.495 x 24.495 268s Grid center: (0.000, 0.000, 0.000) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 0 ion species (0.000 M ionic strength): 268s Solute dielectric: 1.000 268s Solvent dielectric: 78.540 268s Using "molecular" surface definition; no smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 2.200266567971E+03 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #3 (solvated): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 268s Debye length: 0 A 268s Current memory usage: 61.262 MB total, 122.067 MB high water 268s Using cubic spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.188 x 0.188 x 0.188 268s Grid lengths: 12.000 x 12.000 x 12.000 268s Grid center: (0.000, 0.000, 0.000) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 0 ion species (0.000 M ionic strength): 268s Solute dielectric: 1.000 268s Solvent dielectric: 78.540 268s Using "molecular" surface definition; no smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Potential to be written to potential.dx.gz 268s Total electrostatic energy = 4.732245131587E+03 kJ/mol 268s Calculating forces... 268s Writing potential to potential-PE0.dx.gz 268s ---------------------------------------- 268s CALCULATION #4 (reference): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 268s Debye length: 0 A 268s Current memory usage: 61.189 MB total, 122.067 MB high water 268s Using cubic spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.781 x 0.781 x 0.781 268s Grid lengths: 50.000 x 50.000 x 50.000 268s Grid center: (0.000, 0.000, 0.000) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 0 ion species (0.000 M ionic strength): 268s Solute dielectric: 1.000 268s Solvent dielectric: 1.000 268s Using "molecular" surface definition; no smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.190871482831E+03 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #5 (reference): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 268s Debye length: 0 A 268s Current memory usage: 61.189 MB total, 122.067 MB high water 268s Using cubic spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.383 x 0.383 x 0.383 268s Grid lengths: 24.495 x 24.495 x 24.495 268s Grid center: (0.000, 0.000, 0.000) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 0 ion species (0.000 M ionic strength): 268s Solute dielectric: 1.000 268s Solvent dielectric: 1.000 268s Using "molecular" surface definition; no smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 2.430874049735E+03 kJ/mol 268s Calculating forces... 268s [focusFillBound()]: WARNING: 268s Unusually large potential values 268s detected on the focusing boundary! 268s Convergence not guaranteed for NPBE/NRPBE calculations! 268s 268s ---------------------------------------- 268s CALCULATION #6 (reference): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 268s Debye length: 0 A 268s Current memory usage: 61.189 MB total, 122.067 MB high water 268s Using cubic spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.188 x 0.188 x 0.188 268s Grid lengths: 12.000 x 12.000 x 12.000 268s Grid center: (0.000, 0.000, 0.000) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 0 ion species (0.000 M ionic strength): 268s Solute dielectric: 1.000 268s Solvent dielectric: 1.000 268s Using "molecular" surface definition; no smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 4.962018684215E+03 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s PRINT STATEMENTS 268s 268s print energy 1 (solvated) - 2 (reference) end 268s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 268s Global net ELEC energy = -2.297735526282E+02 kJ/mol 268s ---------------------------------------- 268s CLEANING UP AND SHUTTING DOWN... 268s Destroying force arrays. 268s No energy arrays to destroy. 268s Destroying multigrid structures. 268s Destroying finite element structures. 268s Destroying 1 molecules 268s Final memory usage: 0.001 MB total, 122.067 MB high water 268s 268s 268s Thanks for using APBS! 268s 268s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 268s *** PASSED *** 268s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 268s *** PASSED *** 268s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 268s *** PASSED *** 268s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 268s *** PASSED *** 268s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 268s *** PASSED *** 268s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 268s *** PASSED *** 268s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 268s *** PASSED *** 268s Elapsed time: 5.271942 seconds 268s -------------------------------------------------------------------------------- 268s -------------------------------------------------------------------------------- 268s Testing input file apbs-smol-auto.in 268s 273s Checking for intermediate energies in input file apbs-mol-auto.out 273s EXPECTED COMPUTED: 7 273s EXPECTED EXPECTED: 7 273s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 273s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 273s COMPUTED RESULT 960.7073836227 273s COMPUTED RESULT 2200.266567971 273s COMPUTED RESULT 4732.245131587 273s COMPUTED RESULT 1190.871482831 273s COMPUTED RESULT 2430.874049735 273s COMPUTED RESULT 4962.018684215 273s COMPUTED RESULT -229.7735526282 273s BINARY: /usr/bin/apbs 273s INPUT: apbs-smol-auto.in 273s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 273s asc_getToken: Error occurred (bailing out). 273s Vio_scanf: Format problem with input. 273s 273s 273s ---------------------------------------------------------------------- 273s APBS -- Adaptive Poisson-Boltzmann Solver 273s Version APBS 3.4.1 273s 273s Nathan A. Baker (nathan.baker@pnnl.gov) 273s Pacific Northwest National Laboratory 273s 273s Additional contributing authors listed in the code documentation. 273s 273s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 273s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 273s Northwest Division for the U.S. Department of Energy. 273s 273s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 273s Portions Copyright (c) 2002-2020, Nathan A. Baker. 273s Portions Copyright (c) 1999-2002, The Regents of the University of California. 273s Portions Copyright (c) 1995, Michael Holst. 273s All rights reserved. 273s 273s Redistribution and use in source and binary forms, with or without 273s modification, are permitted provided that the following conditions are met: 273s 273s * Redistributions of source code must retain the above copyright notice, this 273s list of conditions and the following disclaimer. 273s 273s * Redistributions in binary form must reproduce the above copyright notice, 273s this list of conditions and the following disclaimer in the documentation 273s and/or other materials provided with the distribution. 273s 273s * Neither the name of the developer nor the names of its contributors may be 273s used to endorse or promote products derived from this software without 273s specific prior written permission. 273s 273s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 273s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 273s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 273s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 273s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 273s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 273s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 273s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 273s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 273s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 273s ---------------------------------------------------------------------- 273s APBS uses FETK (the Finite Element ToolKit) to solve the 273s Poisson-Boltzmann equation numerically. FETK is a portable collection 273s of finite element modeling class libraries developed by the Michael Holst 273s research group and written in an object-oriented form of C. FEtk is 273s designed to solve general coupled systems of nonlinear partial differential 273s equations using adaptive finite element methods, inexact Newton methods, 273s and algebraic multilevel methods. More information about FEtk may be found 273s at . 273s ---------------------------------------------------------------------- 273s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 273s Aqua is a modified form of the Holst group PMG library 273s which has been modified by Patrice Koehl 273s for improved efficiency and 273s memory usage when solving the Poisson-Boltzmann equation. 273s ---------------------------------------------------------------------- 273s Please cite your use of APBS as: 273s 273s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 273s nanosystems: application to microtubules and the ribosome. Proc. 273s Natl. Acad. Sci. USA 98, 10037-10041 2001. 273s 273s 273s This executable compiled on Jan 3 2025 at 11:01:42 273s 273s Parsing input file apbs-smol-auto.in... 273s rank 0 size 1... 273s Parsed input file. 273s Got paths for 1 molecules 273s Reading PQR-format atom data from ion.pqr. 273s 1 atoms 273s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 273s Net charge 1.00e+00 e 273s Preparing to run 6 PBE calculations. 273s ---------------------------------------- 273s CALCULATION #1 (solvated): MULTIGRID 273s Setting up problem... 273s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 273s Debye length: 0 A 273s Current memory usage: 61.262 MB total, 61.262 MB high water 273s Using cubic spline charge discretization. 273s Grid dimensions: 65 x 65 x 65 273s Grid spacings: 0.781 x 0.781 x 0.781 273s Grid lengths: 50.000 x 50.000 x 50.000 273s Grid center: (0.000, 0.000, 0.000) 273s Multigrid levels: 5 273s Molecule ID: 1 273s Linearized traditional PBE 273s Multiple Debye-Huckel sphere boundary conditions 273s 0 ion species (0.000 M ionic strength): 273s Solute dielectric: 1.000 273s Solvent dielectric: 78.540 273s Using "molecular" surface definition;harmonic average smoothing 273s Solvent probe radius: 1.400 A 273s Temperature: 298.150 K 273s Electrostatic energies will be calculated 273s Total electrostatic energy = 9.532928767450E+02 kJ/mol 273s Calculating forces... 273s ---------------------------------------- 273s CALCULATION #2 (solvated): MULTIGRID 273s Setting up problem... 273s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 273s Debye length: 0 A 273s Current memory usage: 61.262 MB total, 122.067 MB high water 273s Using cubic spline charge discretization. 273s Grid dimensions: 65 x 65 x 65 273s Grid spacings: 0.383 x 0.383 x 0.383 273s Grid lengths: 24.495 x 24.495 x 24.495 273s Grid center: (0.000, 0.000, 0.000) 273s Multigrid levels: 5 273s Molecule ID: 1 273s Linearized traditional PBE 273s Boundary conditions from focusing 273s 0 ion species (0.000 M ionic strength): 273s Solute dielectric: 1.000 273s Solvent dielectric: 78.540 273s Using "molecular" surface definition;harmonic average smoothing 273s Solvent probe radius: 1.400 A 273s Temperature: 298.150 K 273s Electrostatic energies will be calculated 273s Total electrostatic energy = 2.201243880085E+03 kJ/mol 273s Calculating forces... 273s ---------------------------------------- 273s CALCULATION #3 (solvated): MULTIGRID 273s Setting up problem... 273s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 273s Debye length: 0 A 273s Current memory usage: 61.262 MB total, 122.067 MB high water 273s Using cubic spline charge discretization. 273s Grid dimensions: 65 x 65 x 65 273s Grid spacings: 0.188 x 0.188 x 0.188 273s Grid lengths: 12.000 x 12.000 x 12.000 273s Grid center: (0.000, 0.000, 0.000) 273s Multigrid levels: 5 273s Molecule ID: 1 273s Linearized traditional PBE 273s Boundary conditions from focusing 273s 0 ion species (0.000 M ionic strength): 273s Solute dielectric: 1.000 273s Solvent dielectric: 78.540 273s Using "molecular" surface definition;harmonic average smoothing 273s Solvent probe radius: 1.400 A 273s Temperature: 298.150 K 273s Electrostatic energies will be calculated 273s Total electrostatic energy = 4.733006258977E+03 kJ/mol 273s Calculating forces... 273s ---------------------------------------- 273s CALCULATION #4 (reference): MULTIGRID 273s Setting up problem... 273s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 273s Debye length: 0 A 273s Current memory usage: 61.189 MB total, 122.067 MB high water 273s Using cubic spline charge discretization. 273s Grid dimensions: 65 x 65 x 65 273s Grid spacings: 0.781 x 0.781 x 0.781 273s Grid lengths: 50.000 x 50.000 x 50.000 273s Grid center: (0.000, 0.000, 0.000) 273s Multigrid levels: 5 273s Molecule ID: 1 273s Linearized traditional PBE 273s Multiple Debye-Huckel sphere boundary conditions 273s 0 ion species (0.000 M ionic strength): 273s Solute dielectric: 1.000 273s Solvent dielectric: 1.000 273s Using "molecular" surface definition;harmonic average smoothing 273s Solvent probe radius: 1.400 A 273s Temperature: 298.150 K 273s Electrostatic energies will be calculated 273s Total electrostatic energy = 1.190871482831E+03 kJ/mol 273s Calculating forces... 273s ---------------------------------------- 273s CALCULATION #5 (reference): MULTIGRID 273s Setting up problem... 273s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 273s Debye length: 0 A 273s Current memory usage: 61.189 MB total, 122.067 MB high water 273s Using cubic spline charge discretization. 273s Grid dimensions: 65 x 65 x 65 273s Grid spacings: 0.383 x 0.383 x 0.383 273s Grid lengths: 24.495 x 24.495 x 24.495 273s Grid center: (0.000, 0.000, 0.000) 273s Multigrid levels: 5 273s Molecule ID: 1 273s Linearized traditional PBE 273s Boundary conditions from focusing 273s 0 ion species (0.000 M ionic strength): 273s Solute dielectric: 1.000 273s Solvent dielectric: 1.000 273s Using "molecular" surface definition;harmonic average smoothing 273s Solvent probe radius: 1.400 A 273s Temperature: 298.150 K 273s Electrostatic energies will be calculated 273s Total electrostatic energy = 2.430874049735E+03 kJ/mol 273s Calculating forces... 273s [focusFillBound()]: WARNING: 273s Unusually large potential values 273s detected on the focusing boundary! 273s Convergence not guaranteed for NPBE/NRPBE calculations! 273s 273s ---------------------------------------- 273s CALCULATION #6 (reference): MULTIGRID 273s Setting up problem... 273s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 273s Debye length: 0 A 273s Current memory usage: 61.189 MB total, 122.067 MB high water 273s Using cubic spline charge discretization. 273s Grid dimensions: 65 x 65 x 65 273s Grid spacings: 0.188 x 0.188 x 0.188 273s Grid lengths: 12.000 x 12.000 x 12.000 273s Grid center: (0.000, 0.000, 0.000) 273s Multigrid levels: 5 273s Molecule ID: 1 273s Linearized traditional PBE 273s Boundary conditions from focusing 273s 0 ion species (0.000 M ionic strength): 273s Solute dielectric: 1.000 273s Solvent dielectric: 1.000 273s Using "molecular" surface definition;harmonic average smoothing 273s Solvent probe radius: 1.400 A 273s Temperature: 298.150 K 273s Electrostatic energies will be calculated 273s Total electrostatic energy = 4.962018684215E+03 kJ/mol 273s Calculating forces... 273s ---------------------------------------- 273s PRINT STATEMENTS 273s 273s print energy 1 (solvated) - 2 (reference) end 273s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 273s Global net ELEC energy = -2.290124252387E+02 kJ/mol 273s ---------------------------------------- 273s CLEANING UP AND SHUTTING DOWN... 273s Destroying force arrays. 273s No energy arrays to destroy. 273s Destroying multigrid structures. 273s Destroying finite element structures. 273s Destroying 1 molecules 273s Final memory usage: 0.001 MB total, 122.067 MB high water 273s 273s 273s Thanks for using APBS! 273s 273s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 273s *** PASSED *** 273s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 273s *** PASSED *** 273s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 273s *** PASSED *** 273s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 273s *** PASSED *** 273s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 273s *** PASSED *** 273s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 273s *** PASSED *** 273s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 273s *** PASSED *** 273s Elapsed time: 4.896339 seconds 273s -------------------------------------------------------------------------------- 273s -------------------------------------------------------------------------------- 273s Testing input file apbs-mol-parallel.in 273s 273s Splitting the input file into 4 separate files using the inputgen utility 273s 279s Checking for intermediate energies in input file apbs-smol-auto.out 279s EXPECTED COMPUTED: 7 279s EXPECTED EXPECTED: 7 279s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 279s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 279s COMPUTED RESULT 953.292876745 279s COMPUTED RESULT 2201.243880085 279s COMPUTED RESULT 4733.006258977 279s COMPUTED RESULT 1190.871482831 279s COMPUTED RESULT 2430.874049735 279s COMPUTED RESULT 4962.018684215 279s COMPUTED RESULT -229.0124252387 279s BINARY: /usr/bin/apbs 279s INPUT: apbs-mol-parallel-PE0.in 279s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 279s asc_getToken: Error occurred (bailing out). 279s Vio_scanf: Format problem with input. 279s 279s 279s ---------------------------------------------------------------------- 279s APBS -- Adaptive Poisson-Boltzmann Solver 279s Version APBS 3.4.1 279s 279s Nathan A. Baker (nathan.baker@pnnl.gov) 279s Pacific Northwest National Laboratory 279s 279s Additional contributing authors listed in the code documentation. 279s 279s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 279s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 279s Northwest Division for the U.S. Department of Energy. 279s 279s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 279s Portions Copyright (c) 2002-2020, Nathan A. Baker. 279s Portions Copyright (c) 1999-2002, The Regents of the University of California. 279s Portions Copyright (c) 1995, Michael Holst. 279s All rights reserved. 279s 279s Redistribution and use in source and binary forms, with or without 279s modification, are permitted provided that the following conditions are met: 279s 279s * Redistributions of source code must retain the above copyright notice, this 279s list of conditions and the following disclaimer. 279s 279s * Redistributions in binary form must reproduce the above copyright notice, 279s this list of conditions and the following disclaimer in the documentation 279s and/or other materials provided with the distribution. 279s 279s * Neither the name of the developer nor the names of its contributors may be 279s used to endorse or promote products derived from this software without 279s specific prior written permission. 279s 279s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 279s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 279s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 279s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 279s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 279s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 279s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 279s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 279s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 279s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 279s ---------------------------------------------------------------------- 279s APBS uses FETK (the Finite Element ToolKit) to solve the 279s Poisson-Boltzmann equation numerically. FETK is a portable collection 279s of finite element modeling class libraries developed by the Michael Holst 279s research group and written in an object-oriented form of C. FEtk is 279s designed to solve general coupled systems of nonlinear partial differential 279s equations using adaptive finite element methods, inexact Newton methods, 279s and algebraic multilevel methods. More information about FEtk may be found 279s at . 279s ---------------------------------------------------------------------- 279s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 279s Aqua is a modified form of the Holst group PMG library 279s which has been modified by Patrice Koehl 279s for improved efficiency and 279s memory usage when solving the Poisson-Boltzmann equation. 279s ---------------------------------------------------------------------- 279s Please cite your use of APBS as: 279s 279s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 279s nanosystems: application to microtubules and the ribosome. Proc. 279s Natl. Acad. Sci. USA 98, 10037-10041 2001. 279s 279s 279s This executable compiled on Jan 3 2025 at 11:01:42 279s 279s Parsing input file apbs-mol-parallel-PE0.in... 279s rank 0 size 1... 279s Parsed input file. 279s Got paths for 1 molecules 279s Reading PQR-format atom data from ion.pqr. 279s 1 atoms 279s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 279s Net charge 1.00e+00 e 279s Preparing to run 6 PBE calculations. 279s ---------------------------------------- 279s CALCULATION #1 (solvated): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 279s Debye length: 0 A 279s Current memory usage: 61.262 MB total, 61.262 MB high water 279s Using cubic spline charge discretization. 279s Partition overlap fraction = 0.1 279s Processor array = 2 x 2 x 1 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.781 x 0.781 x 0.781 279s Grid lengths: 50.000 x 50.000 x 50.000 279s Grid center: (0.000, 0.000, 0.000) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 0 ion species (0.000 M ionic strength): 279s Solute dielectric: 1.000 279s Solvent dielectric: 78.540 279s Using "molecular" surface definition; no smoothing 279s Solvent probe radius: 1.400 A 279s Temperature: 298.150 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 2.401768459022E+02 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #2 (solvated): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 279s Debye length: 0 A 279s Current memory usage: 61.262 MB total, 122.067 MB high water 279s Using cubic spline charge discretization. 279s Partition overlap fraction = 0.1 279s Processor array = 2 x 2 x 1 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.296 x 0.296 x 0.383 279s Grid lengths: 18.944 x 18.944 x 24.495 279s Grid center: (-2.411, -2.411, 0.000) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 0 ion species (0.000 M ionic strength): 279s Solute dielectric: 1.000 279s Solvent dielectric: 78.540 279s Using "molecular" surface definition; no smoothing 279s Solvent probe radius: 1.400 A 279s Temperature: 298.150 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 8.142935592471E+02 kJ/mol 279s Calculating forces... 279s [focusFillBound()]: WARNING: 279s Unusually large potential values 279s detected on the focusing boundary! 279s Convergence not guaranteed for NPBE/NRPBE calculations! 279s 279s ---------------------------------------- 279s CALCULATION #3 (solvated): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 279s Debye length: 0 A 279s Current memory usage: 61.262 MB total, 122.067 MB high water 279s Using cubic spline charge discretization. 279s Partition overlap fraction = 0.1 279s Processor array = 2 x 2 x 1 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.112 x 0.112 x 0.188 279s Grid lengths: 7.178 x 7.178 x 12.000 279s Grid center: (-2.411, -2.411, 0.000) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 0 ion species (0.000 M ionic strength): 279s Solute dielectric: 1.000 279s Solvent dielectric: 78.540 279s Using "molecular" surface definition; no smoothing 279s Solvent probe radius: 1.400 A 279s Temperature: 298.150 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 1.485255308186E+03 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #4 (reference): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 279s Debye length: 0 A 279s Current memory usage: 61.189 MB total, 122.067 MB high water 279s Using cubic spline charge discretization. 279s Partition overlap fraction = 0.1 279s Processor array = 2 x 2 x 1 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.781 x 0.781 x 0.781 279s Grid lengths: 50.000 x 50.000 x 50.000 279s Grid center: (0.000, 0.000, 0.000) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 0 ion species (0.000 M ionic strength): 279s Solute dielectric: 1.000 279s Solvent dielectric: 1.000 279s Using "molecular" surface definition; no smoothing 279s Solvent probe radius: 1.400 A 279s Temperature: 298.150 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 2.977178707009E+02 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #5 (reference): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 279s Debye length: 0 A 279s Current memory usage: 61.189 MB total, 122.067 MB high water 279s Using cubic spline charge discretization. 279s Partition overlap fraction = 0.1 279s Processor array = 2 x 2 x 1 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.296 x 0.296 x 0.383 279s Grid lengths: 18.944 x 18.944 x 24.495 279s Grid center: (-2.411, -2.411, 0.000) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 0 ion species (0.000 M ionic strength): 279s Solute dielectric: 1.000 279s Solvent dielectric: 1.000 279s Using "molecular" surface definition; no smoothing 279s Solvent probe radius: 1.400 A 279s Temperature: 298.150 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 8.799304557588E+02 kJ/mol 279s Calculating forces... 279s [focusFillBound()]: WARNING: 279s Unusually large potential values 279s detected on the focusing boundary! 279s Convergence not guaranteed for NPBE/NRPBE calculations! 279s 279s ---------------------------------------- 279s CALCULATION #6 (reference): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 279s Debye length: 0 A 279s Current memory usage: 61.189 MB total, 122.067 MB high water 279s Using cubic spline charge discretization. 279s Partition overlap fraction = 0.1 279s Processor array = 2 x 2 x 1 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.112 x 0.112 x 0.188 279s Grid lengths: 7.178 x 7.178 x 12.000 279s Grid center: (-2.411, -2.411, 0.000) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 0 ion species (0.000 M ionic strength): 279s Solute dielectric: 1.000 279s Solvent dielectric: 1.000 279s Using "molecular" surface definition; no smoothing 279s Solvent probe radius: 1.400 A 279s Temperature: 298.150 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 1.542873949131E+03 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s PRINT STATEMENTS 279s 279s print energy 1 (solvated) - 2 (reference) end 279s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 279s Global net ELEC energy = -5.761864094552E+01 kJ/mol 279s ---------------------------------------- 279s CLEANING UP AND SHUTTING DOWN... 279s Destroying force arrays. 279s No energy arrays to destroy. 279s Destroying multigrid structures. 279s Destroying finite element structures. 279s Destroying 1 molecules 279s Final memory usage: 0.001 MB total, 122.067 MB high water 279s 279s 279s Thanks for using APBS! 279s 279s 2.401768459022e+02 279s 8.142935592471e+02 279s 1.485255308186e+03 279s 2.977178707009e+02 279s 8.799304557588e+02 279s 1.542873949131e+03 279s -5.761864094552e+01 279s 284s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 284s BINARY: /usr/bin/apbs 284s INPUT: apbs-mol-parallel-PE1.in 284s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 284s asc_getToken: Error occurred (bailing out). 284s Vio_scanf: Format problem with input. 284s 284s 284s ---------------------------------------------------------------------- 284s APBS -- Adaptive Poisson-Boltzmann Solver 284s Version APBS 3.4.1 284s 284s Nathan A. Baker (nathan.baker@pnnl.gov) 284s Pacific Northwest National Laboratory 284s 284s Additional contributing authors listed in the code documentation. 284s 284s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 284s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 284s Northwest Division for the U.S. Department of Energy. 284s 284s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 284s Portions Copyright (c) 2002-2020, Nathan A. Baker. 284s Portions Copyright (c) 1999-2002, The Regents of the University of California. 284s Portions Copyright (c) 1995, Michael Holst. 284s All rights reserved. 284s 284s Redistribution and use in source and binary forms, with or without 284s modification, are permitted provided that the following conditions are met: 284s 284s * Redistributions of source code must retain the above copyright notice, this 284s list of conditions and the following disclaimer. 284s 284s * Redistributions in binary form must reproduce the above copyright notice, 284s this list of conditions and the following disclaimer in the documentation 284s and/or other materials provided with the distribution. 284s 284s * Neither the name of the developer nor the names of its contributors may be 284s used to endorse or promote products derived from this software without 284s specific prior written permission. 284s 284s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 284s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 284s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 284s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 284s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 284s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 284s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 284s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 284s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 284s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 284s ---------------------------------------------------------------------- 284s APBS uses FETK (the Finite Element ToolKit) to solve the 284s Poisson-Boltzmann equation numerically. FETK is a portable collection 284s of finite element modeling class libraries developed by the Michael Holst 284s research group and written in an object-oriented form of C. FEtk is 284s designed to solve general coupled systems of nonlinear partial differential 284s equations using adaptive finite element methods, inexact Newton methods, 284s and algebraic multilevel methods. More information about FEtk may be found 284s at . 284s ---------------------------------------------------------------------- 284s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 284s Aqua is a modified form of the Holst group PMG library 284s which has been modified by Patrice Koehl 284s for improved efficiency and 284s memory usage when solving the Poisson-Boltzmann equation. 284s ---------------------------------------------------------------------- 284s Please cite your use of APBS as: 284s 284s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 284s nanosystems: application to microtubules and the ribosome. Proc. 284s Natl. Acad. Sci. USA 98, 10037-10041 2001. 284s 284s 284s This executable compiled on Jan 3 2025 at 11:01:42 284s 284s Parsing input file apbs-mol-parallel-PE1.in... 284s rank 0 size 1... 284s Parsed input file. 284s Got paths for 1 molecules 284s Reading PQR-format atom data from ion.pqr. 284s 1 atoms 284s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 284s Net charge 1.00e+00 e 284s Preparing to run 6 PBE calculations. 284s ---------------------------------------- 284s CALCULATION #1 (solvated): MULTIGRID 284s Setting up problem... 284s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 284s Debye length: 0 A 284s Current memory usage: 61.262 MB total, 61.262 MB high water 284s Using cubic spline charge discretization. 284s Partition overlap fraction = 0.1 284s Processor array = 2 x 2 x 1 284s Grid dimensions: 65 x 65 x 65 284s Grid spacings: 0.781 x 0.781 x 0.781 284s Grid lengths: 50.000 x 50.000 x 50.000 284s Grid center: (0.000, 0.000, 0.000) 284s Multigrid levels: 5 284s Molecule ID: 1 284s Linearized traditional PBE 284s Multiple Debye-Huckel sphere boundary conditions 284s 0 ion species (0.000 M ionic strength): 284s Solute dielectric: 1.000 284s Solvent dielectric: 78.540 284s Using "molecular" surface definition; no smoothing 284s Solvent probe radius: 1.400 A 284s Temperature: 298.150 K 284s Electrostatic energies will be calculated 284s Total electrostatic energy = 2.401768459022E+02 kJ/mol 284s Calculating forces... 284s ---------------------------------------- 284s CALCULATION #2 (solvated): MULTIGRID 284s Setting up problem... 284s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 284s Debye length: 0 A 284s Current memory usage: 61.262 MB total, 122.067 MB high water 284s Using cubic spline charge discretization. 284s Partition overlap fraction = 0.1 284s Processor array = 2 x 2 x 1 284s Grid dimensions: 65 x 65 x 65 284s Grid spacings: 0.296 x 0.296 x 0.383 284s Grid lengths: 18.944 x 18.944 x 24.495 284s Grid center: (2.411, -2.411, 0.000) 284s Multigrid levels: 5 284s Molecule ID: 1 284s Linearized traditional PBE 284s Boundary conditions from focusing 284s 0 ion species (0.000 M ionic strength): 284s Solute dielectric: 1.000 284s Solvent dielectric: 78.540 284s Using "molecular" surface definition; no smoothing 284s Solvent probe radius: 1.400 A 284s Temperature: 298.150 K 284s Electrostatic energies will be calculated 284s Total electrostatic energy = 8.142778312125E+02 kJ/mol 284s Calculating forces... 284s [focusFillBound()]: WARNING: 284s Unusually large potential values 284s detected on the focusing boundary! 284s Convergence not guaranteed for NPBE/NRPBE calculations! 284s 284s ---------------------------------------- 284s CALCULATION #3 (solvated): MULTIGRID 284s Setting up problem... 284s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 284s Debye length: 0 A 284s Current memory usage: 61.262 MB total, 122.067 MB high water 284s Using cubic spline charge discretization. 284s Partition overlap fraction = 0.1 284s Processor array = 2 x 2 x 1 284s Grid dimensions: 65 x 65 x 65 284s Grid spacings: 0.112 x 0.112 x 0.188 284s Grid lengths: 7.178 x 7.178 x 12.000 284s Grid center: (2.411, -2.411, 0.000) 284s Multigrid levels: 5 284s Molecule ID: 1 284s Linearized traditional PBE 284s Boundary conditions from focusing 284s 0 ion species (0.000 M ionic strength): 284s Solute dielectric: 1.000 284s Solvent dielectric: 78.540 284s Using "molecular" surface definition; no smoothing 284s Solvent probe radius: 1.400 A 284s Temperature: 298.150 K 284s Electrostatic energies will be calculated 284s Total electrostatic energy = 1.485246667424E+03 kJ/mol 284s Calculating forces... 284s ---------------------------------------- 284s CALCULATION #4 (reference): MULTIGRID 284s Setting up problem... 284s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 284s Debye length: 0 A 284s Current memory usage: 61.189 MB total, 122.067 MB high water 284s Using cubic spline charge discretization. 284s Partition overlap fraction = 0.1 284s Processor array = 2 x 2 x 1 284s Grid dimensions: 65 x 65 x 65 284s Grid spacings: 0.781 x 0.781 x 0.781 284s Grid lengths: 50.000 x 50.000 x 50.000 284s Grid center: (0.000, 0.000, 0.000) 284s Multigrid levels: 5 284s Molecule ID: 1 284s Linearized traditional PBE 284s Multiple Debye-Huckel sphere boundary conditions 284s 0 ion species (0.000 M ionic strength): 284s Solute dielectric: 1.000 284s Solvent dielectric: 1.000 284s Using "molecular" surface definition; no smoothing 284s Solvent probe radius: 1.400 A 284s Temperature: 298.150 K 284s Electrostatic energies will be calculated 284s Total electrostatic energy = 2.977178707009E+02 kJ/mol 284s Calculating forces... 284s ---------------------------------------- 284s CALCULATION #5 (reference): MULTIGRID 284s Setting up problem... 284s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 284s Debye length: 0 A 284s Current memory usage: 61.189 MB total, 122.067 MB high water 284s Using cubic spline charge discretization. 284s Partition overlap fraction = 0.1 284s Processor array = 2 x 2 x 1 284s Grid dimensions: 65 x 65 x 65 284s Grid spacings: 0.296 x 0.296 x 0.383 284s Grid lengths: 18.944 x 18.944 x 24.495 284s Grid center: (2.411, -2.411, 0.000) 284s Multigrid levels: 5 284s Molecule ID: 1 284s Linearized traditional PBE 284s Boundary conditions from focusing 284s 0 ion species (0.000 M ionic strength): 284s Solute dielectric: 1.000 284s Solvent dielectric: 1.000 284s Using "molecular" surface definition; no smoothing 284s Solvent probe radius: 1.400 A 284s Temperature: 298.150 K 284s Electrostatic energies will be calculated 284s Total electrostatic energy = 8.799304557588E+02 kJ/mol 284s Calculating forces... 284s [focusFillBound()]: WARNING: 284s Unusually large potential values 284s detected on the focusing boundary! 284s Convergence not guaranteed for NPBE/NRPBE calculations! 284s 284s ---------------------------------------- 284s CALCULATION #6 (reference): MULTIGRID 284s Setting up problem... 284s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 284s Debye length: 0 A 284s Current memory usage: 61.189 MB total, 122.067 MB high water 284s Using cubic spline charge discretization. 284s Partition overlap fraction = 0.1 284s Processor array = 2 x 2 x 1 284s Grid dimensions: 65 x 65 x 65 284s Grid spacings: 0.112 x 0.112 x 0.188 284s Grid lengths: 7.178 x 7.178 x 12.000 284s Grid center: (2.411, -2.411, 0.000) 284s Multigrid levels: 5 284s Molecule ID: 1 284s Linearized traditional PBE 284s Boundary conditions from focusing 284s 0 ion species (0.000 M ionic strength): 284s Solute dielectric: 1.000 284s Solvent dielectric: 1.000 284s Using "molecular" surface definition; no smoothing 284s Solvent probe radius: 1.400 A 284s Temperature: 298.150 K 284s Electrostatic energies will be calculated 284s Total electrostatic energy = 1.542873949131E+03 kJ/mol 284s Calculating forces... 284s ---------------------------------------- 284s PRINT STATEMENTS 284s 284s print energy 1 (solvated) - 2 (reference) end 284s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 284s Global net ELEC energy = -5.762728170718E+01 kJ/mol 284s ---------------------------------------- 284s CLEANING UP AND SHUTTING DOWN... 284s Destroying force arrays. 284s No energy arrays to destroy. 284s Destroying multigrid structures. 284s Destroying finite element structures. 284s Destroying 1 molecules 284s Final memory usage: 0.001 MB total, 122.067 MB high water 284s 284s 284s Thanks for using APBS! 284s 284s Processor 1 results: 284s 2.401768459022e+02 284s 8.142778312125e+02 284s 1.485246667424e+03 284s 2.977178707009e+02 284s 8.799304557588e+02 284s 1.542873949131e+03 284s -5.762728170718e+01 284s 290s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 290s BINARY: /usr/bin/apbs 290s INPUT: apbs-mol-parallel-PE2.in 290s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 290s asc_getToken: Error occurred (bailing out). 290s Vio_scanf: Format problem with input. 290s 290s 290s ---------------------------------------------------------------------- 290s APBS -- Adaptive Poisson-Boltzmann Solver 290s Version APBS 3.4.1 290s 290s Nathan A. Baker (nathan.baker@pnnl.gov) 290s Pacific Northwest National Laboratory 290s 290s Additional contributing authors listed in the code documentation. 290s 290s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 290s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 290s Northwest Division for the U.S. Department of Energy. 290s 290s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 290s Portions Copyright (c) 2002-2020, Nathan A. Baker. 290s Portions Copyright (c) 1999-2002, The Regents of the University of California. 290s Portions Copyright (c) 1995, Michael Holst. 290s All rights reserved. 290s 290s Redistribution and use in source and binary forms, with or without 290s modification, are permitted provided that the following conditions are met: 290s 290s * Redistributions of source code must retain the above copyright notice, this 290s list of conditions and the following disclaimer. 290s 290s * Redistributions in binary form must reproduce the above copyright notice, 290s this list of conditions and the following disclaimer in the documentation 290s and/or other materials provided with the distribution. 290s 290s * Neither the name of the developer nor the names of its contributors may be 290s used to endorse or promote products derived from this software without 290s specific prior written permission. 290s 290s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 290s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 290s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 290s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 290s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 290s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 290s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 290s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 290s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 290s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 290s ---------------------------------------------------------------------- 290s APBS uses FETK (the Finite Element ToolKit) to solve the 290s Poisson-Boltzmann equation numerically. FETK is a portable collection 290s of finite element modeling class libraries developed by the Michael Holst 290s research group and written in an object-oriented form of C. FEtk is 290s designed to solve general coupled systems of nonlinear partial differential 290s equations using adaptive finite element methods, inexact Newton methods, 290s and algebraic multilevel methods. More information about FEtk may be found 290s at . 290s ---------------------------------------------------------------------- 290s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 290s Aqua is a modified form of the Holst group PMG library 290s which has been modified by Patrice Koehl 290s for improved efficiency and 290s memory usage when solving the Poisson-Boltzmann equation. 290s ---------------------------------------------------------------------- 290s Please cite your use of APBS as: 290s 290s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 290s nanosystems: application to microtubules and the ribosome. Proc. 290s Natl. Acad. Sci. USA 98, 10037-10041 2001. 290s 290s 290s This executable compiled on Jan 3 2025 at 11:01:42 290s 290s Parsing input file apbs-mol-parallel-PE2.in... 290s rank 0 size 1... 290s Parsed input file. 290s Got paths for 1 molecules 290s Reading PQR-format atom data from ion.pqr. 290s 1 atoms 290s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 290s Net charge 1.00e+00 e 290s Preparing to run 6 PBE calculations. 290s ---------------------------------------- 290s CALCULATION #1 (solvated): MULTIGRID 290s Setting up problem... 290s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 290s Debye length: 0 A 290s Current memory usage: 61.262 MB total, 61.262 MB high water 290s Using cubic spline charge discretization. 290s Partition overlap fraction = 0.1 290s Processor array = 2 x 2 x 1 290s Grid dimensions: 65 x 65 x 65 290s Grid spacings: 0.781 x 0.781 x 0.781 290s Grid lengths: 50.000 x 50.000 x 50.000 290s Grid center: (0.000, 0.000, 0.000) 290s Multigrid levels: 5 290s Molecule ID: 1 290s Linearized traditional PBE 290s Multiple Debye-Huckel sphere boundary conditions 290s 0 ion species (0.000 M ionic strength): 290s Solute dielectric: 1.000 290s Solvent dielectric: 78.540 290s Using "molecular" surface definition; no smoothing 290s Solvent probe radius: 1.400 A 290s Temperature: 298.150 K 290s Electrostatic energies will be calculated 290s Total electrostatic energy = 2.401768459091E+02 kJ/mol 290s Calculating forces... 290s ---------------------------------------- 290s CALCULATION #2 (solvated): MULTIGRID 290s Setting up problem... 290s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 290s Debye length: 0 A 290s Current memory usage: 61.262 MB total, 122.067 MB high water 290s Using cubic spline charge discretization. 290s Partition overlap fraction = 0.1 290s Processor array = 2 x 2 x 1 290s Grid dimensions: 65 x 65 x 65 290s Grid spacings: 0.296 x 0.296 x 0.383 290s Grid lengths: 18.944 x 18.944 x 24.495 290s Grid center: (-2.411, 2.411, 0.000) 290s Multigrid levels: 5 290s Molecule ID: 1 290s Linearized traditional PBE 290s Boundary conditions from focusing 290s 0 ion species (0.000 M ionic strength): 290s Solute dielectric: 1.000 290s Solvent dielectric: 78.540 290s Using "molecular" surface definition; no smoothing 290s Solvent probe radius: 1.400 A 290s Temperature: 298.150 K 290s Electrostatic energies will be calculated 290s Total electrostatic energy = 8.142935605696E+02 kJ/mol 290s Calculating forces... 290s [focusFillBound()]: WARNING: 290s Unusually large potential values 290s detected on the focusing boundary! 290s Convergence not guaranteed for NPBE/NRPBE calculations! 290s 290s ---------------------------------------- 290s CALCULATION #3 (solvated): MULTIGRID 290s Setting up problem... 290s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 290s Debye length: 0 A 290s Current memory usage: 61.262 MB total, 122.067 MB high water 290s Using cubic spline charge discretization. 290s Partition overlap fraction = 0.1 290s Processor array = 2 x 2 x 1 290s Grid dimensions: 65 x 65 x 65 290s Grid spacings: 0.112 x 0.112 x 0.188 290s Grid lengths: 7.178 x 7.178 x 12.000 290s Grid center: (-2.411, 2.411, 0.000) 290s Multigrid levels: 5 290s Molecule ID: 1 290s Linearized traditional PBE 290s Boundary conditions from focusing 290s 0 ion species (0.000 M ionic strength): 290s Solute dielectric: 1.000 290s Solvent dielectric: 78.540 290s Using "molecular" surface definition; no smoothing 290s Solvent probe radius: 1.400 A 290s Temperature: 298.150 K 290s Electrostatic energies will be calculated 290s Total electrostatic energy = 1.485255306569E+03 kJ/mol 290s Calculating forces... 290s ---------------------------------------- 290s CALCULATION #4 (reference): MULTIGRID 290s Setting up problem... 290s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 290s Debye length: 0 A 290s Current memory usage: 61.189 MB total, 122.067 MB high water 290s Using cubic spline charge discretization. 290s Partition overlap fraction = 0.1 290s Processor array = 2 x 2 x 1 290s Grid dimensions: 65 x 65 x 65 290s Grid spacings: 0.781 x 0.781 x 0.781 290s Grid lengths: 50.000 x 50.000 x 50.000 290s Grid center: (0.000, 0.000, 0.000) 290s Multigrid levels: 5 290s Molecule ID: 1 290s Linearized traditional PBE 290s Multiple Debye-Huckel sphere boundary conditions 290s 0 ion species (0.000 M ionic strength): 290s Solute dielectric: 1.000 290s Solvent dielectric: 1.000 290s Using "molecular" surface definition; no smoothing 290s Solvent probe radius: 1.400 A 290s Temperature: 298.150 K 290s Electrostatic energies will be calculated 290s Total electrostatic energy = 2.977178707146E+02 kJ/mol 290s Calculating forces... 290s ---------------------------------------- 290s CALCULATION #5 (reference): MULTIGRID 290s Setting up problem... 290s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 290s Debye length: 0 A 290s Current memory usage: 61.189 MB total, 122.067 MB high water 290s Using cubic spline charge discretization. 290s Partition overlap fraction = 0.1 290s Processor array = 2 x 2 x 1 290s Grid dimensions: 65 x 65 x 65 290s Grid spacings: 0.296 x 0.296 x 0.383 290s Grid lengths: 18.944 x 18.944 x 24.495 290s Grid center: (-2.411, 2.411, 0.000) 290s Multigrid levels: 5 290s Molecule ID: 1 290s Linearized traditional PBE 290s Boundary conditions from focusing 290s 0 ion species (0.000 M ionic strength): 290s Solute dielectric: 1.000 290s Solvent dielectric: 1.000 290s Using "molecular" surface definition; no smoothing 290s Solvent probe radius: 1.400 A 290s Temperature: 298.150 K 290s Electrostatic energies will be calculated 290s Total electrostatic energy = 8.799304557596E+02 kJ/mol 290s Calculating forces... 290s [focusFillBound()]: WARNING: 290s Unusually large potential values 290s detected on the focusing boundary! 290s Convergence not guaranteed for NPBE/NRPBE calculations! 290s 290s ---------------------------------------- 290s CALCULATION #6 (reference): MULTIGRID 290s Setting up problem... 290s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 290s Debye length: 0 A 290s Current memory usage: 61.189 MB total, 122.067 MB high water 290s Using cubic spline charge discretization. 290s Partition overlap fraction = 0.1 290s Processor array = 2 x 2 x 1 290s Grid dimensions: 65 x 65 x 65 290s Grid spacings: 0.112 x 0.112 x 0.188 290s Grid lengths: 7.178 x 7.178 x 12.000 290s Grid center: (-2.411, 2.411, 0.000) 290s Multigrid levels: 5 290s Molecule ID: 1 290s Linearized traditional PBE 290s Boundary conditions from focusing 290s 0 ion species (0.000 M ionic strength): 290s Solute dielectric: 1.000 290s Solvent dielectric: 1.000 290s Using "molecular" surface definition; no smoothing 290s Solvent probe radius: 1.400 A 290s Temperature: 298.150 K 290s Electrostatic energies will be calculated 290s Total electrostatic energy = 1.542873949141E+03 kJ/mol 290s Calculating forces... 290s ---------------------------------------- 290s PRINT STATEMENTS 290s 290s print energy 1 (solvated) - 2 (reference) end 290s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 290s Global net ELEC energy = -5.761864257239E+01 kJ/mol 290s ---------------------------------------- 290s CLEANING UP AND SHUTTING DOWN... 290s Destroying force arrays. 290s No energy arrays to destroy. 290s Destroying multigrid structures. 290s Destroying finite element structures. 290s Destroying 1 molecules 290s Final memory usage: 0.001 MB total, 122.067 MB high water 290s 290s 290s Thanks for using APBS! 290s 290s Processor 2 results: 290s 2.401768459091e+02 290s 8.142935605696e+02 290s 1.485255306569e+03 290s 2.977178707146e+02 290s 8.799304557596e+02 290s 1.542873949141e+03 290s -5.761864257239e+01 290s 295s Processor 3 results: 295s 2.401768459091e+02 295s 8.142778325440e+02 295s 1.485246665692e+03 295s 2.977178707146e+02 295s 8.799304557596e+02 295s 1.542873949141e+03 295s -5.762728344954e+01 295s 295s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 295s *** PASSED *** 295s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 295s *** PASSED *** 295s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 295s *** PASSED *** 295s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 295s *** PASSED *** 295s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 295s *** PASSED *** 295s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 295s *** PASSED *** 295s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 295s *** PASSED *** 295s Elapsed time: 22.168531 seconds 295s -------------------------------------------------------------------------------- 295s -------------------------------------------------------------------------------- 295s Testing input file apbs-smol-parallel.in 295s 295s Splitting the input file into 4 separate files using the inputgen utility 295s 295s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 295s BINARY: /usr/bin/apbs 295s INPUT: apbs-mol-parallel-PE3.in 295s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 295s asc_getToken: Error occurred (bailing out). 295s Vio_scanf: Format problem with input. 295s 295s 295s ---------------------------------------------------------------------- 295s APBS -- Adaptive Poisson-Boltzmann Solver 295s Version APBS 3.4.1 295s 295s Nathan A. Baker (nathan.baker@pnnl.gov) 295s Pacific Northwest National Laboratory 295s 295s Additional contributing authors listed in the code documentation. 295s 295s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 295s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 295s Northwest Division for the U.S. Department of Energy. 295s 295s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 295s Portions Copyright (c) 2002-2020, Nathan A. Baker. 295s Portions Copyright (c) 1999-2002, The Regents of the University of California. 295s Portions Copyright (c) 1995, Michael Holst. 295s All rights reserved. 295s 295s Redistribution and use in source and binary forms, with or without 295s modification, are permitted provided that the following conditions are met: 295s 295s * Redistributions of source code must retain the above copyright notice, this 295s list of conditions and the following disclaimer. 295s 295s * Redistributions in binary form must reproduce the above copyright notice, 295s this list of conditions and the following disclaimer in the documentation 295s and/or other materials provided with the distribution. 295s 295s * Neither the name of the developer nor the names of its contributors may be 295s used to endorse or promote products derived from this software without 295s specific prior written permission. 295s 295s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 295s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 295s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 295s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 295s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 295s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 295s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 295s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 295s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 295s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 295s ---------------------------------------------------------------------- 295s APBS uses FETK (the Finite Element ToolKit) to solve the 295s Poisson-Boltzmann equation numerically. FETK is a portable collection 295s of finite element modeling class libraries developed by the Michael Holst 295s research group and written in an object-oriented form of C. FEtk is 295s designed to solve general coupled systems of nonlinear partial differential 295s equations using adaptive finite element methods, inexact Newton methods, 295s and algebraic multilevel methods. More information about FEtk may be found 295s at . 295s ---------------------------------------------------------------------- 295s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 295s Aqua is a modified form of the Holst group PMG library 295s which has been modified by Patrice Koehl 295s for improved efficiency and 295s memory usage when solving the Poisson-Boltzmann equation. 295s ---------------------------------------------------------------------- 295s Please cite your use of APBS as: 295s 295s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 295s nanosystems: application to microtubules and the ribosome. Proc. 295s Natl. Acad. Sci. USA 98, 10037-10041 2001. 295s 295s 295s This executable compiled on Jan 3 2025 at 11:01:42 295s 295s Parsing input file apbs-mol-parallel-PE3.in... 295s rank 0 size 1... 295s Parsed input file. 295s Got paths for 1 molecules 295s Reading PQR-format atom data from ion.pqr. 295s 1 atoms 295s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 295s Net charge 1.00e+00 e 295s Preparing to run 6 PBE calculations. 295s ---------------------------------------- 295s CALCULATION #1 (solvated): MULTIGRID 295s Setting up problem... 295s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 295s Debye length: 0 A 295s Current memory usage: 61.262 MB total, 61.262 MB high water 295s Using cubic spline charge discretization. 295s Partition overlap fraction = 0.1 295s Processor array = 2 x 2 x 1 295s Grid dimensions: 65 x 65 x 65 295s Grid spacings: 0.781 x 0.781 x 0.781 295s Grid lengths: 50.000 x 50.000 x 50.000 295s Grid center: (0.000, 0.000, 0.000) 295s Multigrid levels: 5 295s Molecule ID: 1 295s Linearized traditional PBE 295s Multiple Debye-Huckel sphere boundary conditions 295s 0 ion species (0.000 M ionic strength): 295s Solute dielectric: 1.000 295s Solvent dielectric: 78.540 295s Using "molecular" surface definition; no smoothing 295s Solvent probe radius: 1.400 A 295s Temperature: 298.150 K 295s Electrostatic energies will be calculated 295s Total electrostatic energy = 2.401768459091E+02 kJ/mol 295s Calculating forces... 295s ---------------------------------------- 295s CALCULATION #2 (solvated): MULTIGRID 295s Setting up problem... 295s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 295s Debye length: 0 A 295s Current memory usage: 61.262 MB total, 122.067 MB high water 295s Using cubic spline charge discretization. 295s Partition overlap fraction = 0.1 295s Processor array = 2 x 2 x 1 295s Grid dimensions: 65 x 65 x 65 295s Grid spacings: 0.296 x 0.296 x 0.383 295s Grid lengths: 18.944 x 18.944 x 24.495 295s Grid center: (2.411, 2.411, 0.000) 295s Multigrid levels: 5 295s Molecule ID: 1 295s Linearized traditional PBE 295s Boundary conditions from focusing 295s 0 ion species (0.000 M ionic strength): 295s Solute dielectric: 1.000 295s Solvent dielectric: 78.540 295s Using "molecular" surface definition; no smoothing 295s Solvent probe radius: 1.400 A 295s Temperature: 298.150 K 295s Electrostatic energies will be calculated 295s Total electrostatic energy = 8.142778325440E+02 kJ/mol 295s Calculating forces... 295s [focusFillBound()]: WARNING: 295s Unusually large potential values 295s detected on the focusing boundary! 295s Convergence not guaranteed for NPBE/NRPBE calculations! 295s 295s ---------------------------------------- 295s CALCULATION #3 (solvated): MULTIGRID 295s Setting up problem... 295s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 295s Debye length: 0 A 295s Current memory usage: 61.262 MB total, 122.067 MB high water 295s Using cubic spline charge discretization. 295s Partition overlap fraction = 0.1 295s Processor array = 2 x 2 x 1 295s Grid dimensions: 65 x 65 x 65 295s Grid spacings: 0.112 x 0.112 x 0.188 295s Grid lengths: 7.178 x 7.178 x 12.000 295s Grid center: (2.411, 2.411, 0.000) 295s Multigrid levels: 5 295s Molecule ID: 1 295s Linearized traditional PBE 295s Boundary conditions from focusing 295s 0 ion species (0.000 M ionic strength): 295s Solute dielectric: 1.000 295s Solvent dielectric: 78.540 295s Using "molecular" surface definition; no smoothing 295s Solvent probe radius: 1.400 A 295s Temperature: 298.150 K 295s Electrostatic energies will be calculated 295s Total electrostatic energy = 1.485246665692E+03 kJ/mol 295s Calculating forces... 295s ---------------------------------------- 295s CALCULATION #4 (reference): MULTIGRID 295s Setting up problem... 295s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 295s Debye length: 0 A 295s Current memory usage: 61.189 MB total, 122.067 MB high water 295s Using cubic spline charge discretization. 295s Partition overlap fraction = 0.1 295s Processor array = 2 x 2 x 1 295s Grid dimensions: 65 x 65 x 65 295s Grid spacings: 0.781 x 0.781 x 0.781 295s Grid lengths: 50.000 x 50.000 x 50.000 295s Grid center: (0.000, 0.000, 0.000) 295s Multigrid levels: 5 295s Molecule ID: 1 295s Linearized traditional PBE 295s Multiple Debye-Huckel sphere boundary conditions 295s 0 ion species (0.000 M ionic strength): 295s Solute dielectric: 1.000 295s Solvent dielectric: 1.000 295s Using "molecular" surface definition; no smoothing 295s Solvent probe radius: 1.400 A 295s Temperature: 298.150 K 295s Electrostatic energies will be calculated 295s Total electrostatic energy = 2.977178707146E+02 kJ/mol 295s Calculating forces... 295s ---------------------------------------- 295s CALCULATION #5 (reference): MULTIGRID 295s Setting up problem... 295s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 295s Debye length: 0 A 295s Current memory usage: 61.189 MB total, 122.067 MB high water 295s Using cubic spline charge discretization. 295s Partition overlap fraction = 0.1 295s Processor array = 2 x 2 x 1 295s Grid dimensions: 65 x 65 x 65 295s Grid spacings: 0.296 x 0.296 x 0.383 295s Grid lengths: 18.944 x 18.944 x 24.495 295s Grid center: (2.411, 2.411, 0.000) 295s Multigrid levels: 5 295s Molecule ID: 1 295s Linearized traditional PBE 295s Boundary conditions from focusing 295s 0 ion species (0.000 M ionic strength): 295s Solute dielectric: 1.000 295s Solvent dielectric: 1.000 295s Using "molecular" surface definition; no smoothing 295s Solvent probe radius: 1.400 A 295s Temperature: 298.150 K 295s Electrostatic energies will be calculated 295s Total electrostatic energy = 8.799304557596E+02 kJ/mol 295s Calculating forces... 295s [focusFillBound()]: WARNING: 295s Unusually large potential values 295s detected on the focusing boundary! 295s Convergence not guaranteed for NPBE/NRPBE calculations! 295s 295s ---------------------------------------- 295s CALCULATION #6 (reference): MULTIGRID 295s Setting up problem... 295s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 295s Debye length: 0 A 295s Current memory usage: 61.189 MB total, 122.067 MB high water 295s Using cubic spline charge discretization. 295s Partition overlap fraction = 0.1 295s Processor array = 2 x 2 x 1 295s Grid dimensions: 65 x 65 x 65 295s Grid spacings: 0.112 x 0.112 x 0.188 295s Grid lengths: 7.178 x 7.178 x 12.000 295s Grid center: (2.411, 2.411, 0.000) 295s Multigrid levels: 5 295s Molecule ID: 1 295s Linearized traditional PBE 295s Boundary conditions from focusing 295s 0 ion species (0.000 M ionic strength): 295s Solute dielectric: 1.000 295s Solvent dielectric: 1.000 295s Using "molecular" surface definition; no smoothing 295s Solvent probe radius: 1.400 A 295s Temperature: 298.150 K 295s Electrostatic energies will be calculated 295s Total electrostatic energy = 1.542873949141E+03 kJ/mol 295s Calculating forces... 295s ---------------------------------------- 295s PRINT STATEMENTS 295s 295s print energy 1 (solvated) - 2 (reference) end 295s Local net energy (PE 0) = -5.762728344954E+01 kJ/mol 295s Global net ELEC energy = -5.762728344954E+01 kJ/mol 295s ---------------------------------------- 295s CLEANING UP AND SHUTTING DOWN... 295s Destroying force arrays. 295s No energy arrays to destroy. 295s Destroying multigrid structures. 295s Destroying finite element structures. 295s Destroying 1 molecules 295s Final memory usage: 0.001 MB total, 122.067 MB high water 295s 295s 295s Thanks for using APBS! 295s 301s Processor 0 results: 301s 2.383232191816e+02 301s 8.145369591602e+02 301s 1.485524998001e+03 301s 2.977178707009e+02 301s 8.799304557588e+02 301s 1.542873949131e+03 301s -5.734895113069e+01 301s 301s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 301s EXPECTED COMPUTED: 7 301s EXPECTED EXPECTED: 7 301s COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] 301s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 301s COMPUTED RESULT 960.7073836226 301s COMPUTED RESULT 3257.1427835731997 301s COMPUTED RESULT 5941.0039478710005 301s COMPUTED RESULT 1190.8714828309999 301s COMPUTED RESULT 3519.7218230368003 301s COMPUTED RESULT 6171.495796544 301s COMPUTED RESULT -230.49184867463003 301s BINARY: /usr/bin/apbs 301s INPUT: apbs-smol-parallel-PE0.in 301s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.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-PE0.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 = 2.383232191816E+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 = 8.145369591602E+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 = 1.485524998001E+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 = 2.977178707009E+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 = 8.799304557588E+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 = 1.542873949131E+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) = -5.734895113069E+01 kJ/mol 301s Global net ELEC energy = -5.734895113069E+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 306s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 306s BINARY: /usr/bin/apbs 306s INPUT: apbs-smol-parallel-PE1.in 306s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 306s asc_getToken: Error occurred (bailing out). 306s Vio_scanf: Format problem with input. 306s 306s 306s ---------------------------------------------------------------------- 306s APBS -- Adaptive Poisson-Boltzmann Solver 306s Version APBS 3.4.1 306s 306s Nathan A. Baker (nathan.baker@pnnl.gov) 306s Pacific Northwest National Laboratory 306s 306s Additional contributing authors listed in the code documentation. 306s 306s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 306s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 306s Northwest Division for the U.S. Department of Energy. 306s 306s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 306s Portions Copyright (c) 2002-2020, Nathan A. Baker. 306s Portions Copyright (c) 1999-2002, The Regents of the University of California. 306s Portions Copyright (c) 1995, Michael Holst. 306s All rights reserved. 306s 306s Redistribution and use in source and binary forms, with or without 306s modification, are permitted provided that the following conditions are met: 306s 306s * Redistributions of source code must retain the above copyright notice, this 306s list of conditions and the following disclaimer. 306s 306s * Redistributions in binary form must reproduce the above copyright notice, 306s this list of conditions and the following disclaimer in the documentation 306s and/or other materials provided with the distribution. 306s 306s * Neither the name of the developer nor the names of its contributors may be 306s used to endorse or promote products derived from this software without 306s specific prior written permission. 306s 306s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 306s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 306s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 306s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 306s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 306s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 306s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 306s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 306s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 306s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 306s ---------------------------------------------------------------------- 306s APBS uses FETK (the Finite Element ToolKit) to solve the 306s Poisson-Boltzmann equation numerically. FETK is a portable collection 306s of finite element modeling class libraries developed by the Michael Holst 306s research group and written in an object-oriented form of C. FEtk is 306s designed to solve general coupled systems of nonlinear partial differential 306s equations using adaptive finite element methods, inexact Newton methods, 306s and algebraic multilevel methods. More information about FEtk may be found 306s at . 306s ---------------------------------------------------------------------- 306s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 306s Aqua is a modified form of the Holst group PMG library 306s which has been modified by Patrice Koehl 306s for improved efficiency and 306s memory usage when solving the Poisson-Boltzmann equation. 306s ---------------------------------------------------------------------- 306s Please cite your use of APBS as: 306s 306s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 306s nanosystems: application to microtubules and the ribosome. Proc. 306s Natl. Acad. Sci. USA 98, 10037-10041 2001. 306s 306s 306s This executable compiled on Jan 3 2025 at 11:01:42 306s 306s Parsing input file apbs-smol-parallel-PE1.in... 306s rank 0 sizeProcessor 1 results: 306s 2.383232191816e+02 306s 8.145419898332e+02 306s 1.485529328612e+03 306s 2.977178707009e+02 306s 8.799304557588e+02 306s 1.542873949131e+03 306s -5.734462051928e+01 306s 306s 1... 306s Parsed input file. 306s Got paths for 1 molecules 306s Reading PQR-format atom data from ion.pqr. 306s 1 atoms 306s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 306s Net charge 1.00e+00 e 306s Preparing to run 6 PBE calculations. 306s ---------------------------------------- 306s CALCULATION #1 (solvated): MULTIGRID 306s Setting up problem... 306s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 306s Debye length: 0 A 306s Current memory usage: 61.262 MB total, 61.262 MB high water 306s Using cubic spline charge discretization. 306s Partition overlap fraction = 0.1 306s Processor array = 2 x 2 x 1 306s Grid dimensions: 65 x 65 x 65 306s Grid spacings: 0.781 x 0.781 x 0.781 306s Grid lengths: 50.000 x 50.000 x 50.000 306s Grid center: (0.000, 0.000, 0.000) 306s Multigrid levels: 5 306s Molecule ID: 1 306s Linearized traditional PBE 306s Multiple Debye-Huckel sphere boundary conditions 306s 0 ion species (0.000 M ionic strength): 306s Solute dielectric: 1.000 306s Solvent dielectric: 78.540 306s Using "molecular" surface definition;harmonic average smoothing 306s Solvent probe radius: 1.400 A 306s Temperature: 298.150 K 306s Electrostatic energies will be calculated 306s Total electrostatic energy = 2.383232191816E+02 kJ/mol 306s Calculating forces... 306s ---------------------------------------- 306s CALCULATION #2 (solvated): MULTIGRID 306s Setting up problem... 306s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 306s Debye length: 0 A 306s Current memory usage: 61.262 MB total, 122.067 MB high water 306s Using cubic spline charge discretization. 306s Partition overlap fraction = 0.1 306s Processor array = 2 x 2 x 1 306s Grid dimensions: 65 x 65 x 65 306s Grid spacings: 0.296 x 0.296 x 0.383 306s Grid lengths: 18.944 x 18.944 x 24.495 306s Grid center: (2.411, -2.411, 0.000) 306s Multigrid levels: 5 306s Molecule ID: 1 306s Linearized traditional PBE 306s Boundary conditions from focusing 306s 0 ion species (0.000 M ionic strength): 306s Solute dielectric: 1.000 306s Solvent dielectric: 78.540 306s Using "molecular" surface definition;harmonic average smoothing 306s Solvent probe radius: 1.400 A 306s Temperature: 298.150 K 306s Electrostatic energies will be calculated 306s Total electrostatic energy = 8.145419898332E+02 kJ/mol 306s Calculating forces... 306s [focusFillBound()]: WARNING: 306s Unusually large potential values 306s detected on the focusing boundary! 306s Convergence not guaranteed for NPBE/NRPBE calculations! 306s 306s ---------------------------------------- 306s CALCULATION #3 (solvated): MULTIGRID 306s Setting up problem... 306s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 306s Debye length: 0 A 306s Current memory usage: 61.262 MB total, 122.067 MB high water 306s Using cubic spline charge discretization. 306s Partition overlap fraction = 0.1 306s Processor array = 2 x 2 x 1 306s Grid dimensions: 65 x 65 x 65 306s Grid spacings: 0.112 x 0.112 x 0.188 306s Grid lengths: 7.178 x 7.178 x 12.000 306s Grid center: (2.411, -2.411, 0.000) 306s Multigrid levels: 5 306s Molecule ID: 1 306s Linearized traditional PBE 306s Boundary conditions from focusing 306s 0 ion species (0.000 M ionic strength): 306s Solute dielectric: 1.000 306s Solvent dielectric: 78.540 306s Using "molecular" surface definition;harmonic average smoothing 306s Solvent probe radius: 1.400 A 306s Temperature: 298.150 K 306s Electrostatic energies will be calculated 306s Total electrostatic energy = 1.485529328612E+03 kJ/mol 306s Calculating forces... 306s ---------------------------------------- 306s CALCULATION #4 (reference): MULTIGRID 306s Setting up problem... 306s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 306s Debye length: 0 A 306s Current memory usage: 61.189 MB total, 122.067 MB high water 306s Using cubic spline charge discretization. 306s Partition overlap fraction = 0.1 306s Processor array = 2 x 2 x 1 306s Grid dimensions: 65 x 65 x 65 306s Grid spacings: 0.781 x 0.781 x 0.781 306s Grid lengths: 50.000 x 50.000 x 50.000 306s Grid center: (0.000, 0.000, 0.000) 306s Multigrid levels: 5 306s Molecule ID: 1 306s Linearized traditional PBE 306s Multiple Debye-Huckel sphere boundary conditions 306s 0 ion species (0.000 M ionic strength): 306s Solute dielectric: 1.000 306s Solvent dielectric: 1.000 306s Using "molecular" surface definition;harmonic average smoothing 306s Solvent probe radius: 1.400 A 306s Temperature: 298.150 K 306s Electrostatic energies will be calculated 306s Total electrostatic energy = 2.977178707009E+02 kJ/mol 306s Calculating forces... 306s ---------------------------------------- 306s CALCULATION #5 (reference): MULTIGRID 306s Setting up problem... 306s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 306s Debye length: 0 A 306s Current memory usage: 61.189 MB total, 122.067 MB high water 306s Using cubic spline charge discretization. 306s Partition overlap fraction = 0.1 306s Processor array = 2 x 2 x 1 306s Grid dimensions: 65 x 65 x 65 306s Grid spacings: 0.296 x 0.296 x 0.383 306s Grid lengths: 18.944 x 18.944 x 24.495 306s Grid center: (2.411, -2.411, 0.000) 306s Multigrid levels: 5 306s Molecule ID: 1 306s Linearized traditional PBE 306s Boundary conditions from focusing 306s 0 ion species (0.000 M ionic strength): 306s Solute dielectric: 1.000 306s Solvent dielectric: 1.000 306s Using "molecular" surface definition;harmonic average smoothing 306s Solvent probe radius: 1.400 A 306s Temperature: 298.150 K 306s Electrostatic energies will be calculated 306s Total electrostatic energy = 8.799304557588E+02 kJ/mol 306s Calculating forces... 306s [focusFillBound()]: WARNING: 306s Unusually large potential values 306s detected on the focusing boundary! 306s Convergence not guaranteed for NPBE/NRPBE calculations! 306s 306s ---------------------------------------- 306s CALCULATION #6 (reference): MULTIGRID 306s Setting up problem... 306s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 306s Debye length: 0 A 306s Current memory usage: 61.189 MB total, 122.067 MB high water 306s Using cubic spline charge discretization. 306s Partition overlap fraction = 0.1 306s Processor array = 2 x 2 x 1 306s Grid dimensions: 65 x 65 x 65 306s Grid spacings: 0.112 x 0.112 x 0.188 306s Grid lengths: 7.178 x 7.178 x 12.000 306s Grid center: (2.411, -2.411, 0.000) 306s Multigrid levels: 5 306s Molecule ID: 1 306s Linearized traditional PBE 306s Boundary conditions from focusing 306s 0 ion species (0.000 M ionic strength): 306s Solute dielectric: 1.000 306s Solvent dielectric: 1.000 306s Using "molecular" surface definition;harmonic average smoothing 306s Solvent probe radius: 1.400 A 306s Temperature: 298.150 K 306s Electrostatic energies will be calculated 306s Total electrostatic energy = 1.542873949131E+03 kJ/mol 306s Calculating forces... 306s ---------------------------------------- 306s PRINT STATEMENTS 306s 306s print energy 1 (solvated) - 2 (reference) end 306s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 306s Global net ELEC energy = -5.734462051928E+01 kJ/mol 306s ---------------------------------------- 306s CLEANING UP AND SHUTTING DOWN... 306s Destroying force arrays. 306s No energy arrays to destroy. 306s Destroying multigrid structures. 306s Destroying finite element structures. 306s Destroying 1 molecules 306s Final memory usage: 0.001 MB total, 122.067 MB high water 306s 306s 306s Thanks for using APBS! 306s 311s Processor 2 results: 311s 2.383232191909e+02 311s 8.145369593489e+02 311s 1.485524997676e+03 311s 2.977178707146e+02 311s 8.799304557596e+02 311s 1.542873949141e+03 311s -5.734895146550e+01 311s 311s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 311s BINARY: /usr/bin/apbs 311s INPUT: apbs-smol-parallel-PE2.in 311s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 311s asc_getToken: Error occurred (bailing out). 311s Vio_scanf: Format problem with input. 311s 311s 311s ---------------------------------------------------------------------- 311s APBS -- Adaptive Poisson-Boltzmann Solver 311s Version APBS 3.4.1 311s 311s Nathan A. Baker (nathan.baker@pnnl.gov) 311s Pacific Northwest National Laboratory 311s 311s Additional contributing authors listed in the code documentation. 311s 311s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 311s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 311s Northwest Division for the U.S. Department of Energy. 311s 311s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 311s Portions Copyright (c) 2002-2020, Nathan A. Baker. 311s Portions Copyright (c) 1999-2002, The Regents of the University of California. 311s Portions Copyright (c) 1995, Michael Holst. 311s All rights reserved. 311s 311s Redistribution and use in source and binary forms, with or without 311s modification, are permitted provided that the following conditions are met: 311s 311s * Redistributions of source code must retain the above copyright notice, this 311s list of conditions and the following disclaimer. 311s 311s * Redistributions in binary form must reproduce the above copyright notice, 311s this list of conditions and the following disclaimer in the documentation 311s and/or other materials provided with the distribution. 311s 311s * Neither the name of the developer nor the names of its contributors may be 311s used to endorse or promote products derived from this software without 311s specific prior written permission. 311s 311s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 311s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 311s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 311s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 311s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 311s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 311s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 311s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 311s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 311s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 311s ---------------------------------------------------------------------- 311s APBS uses FETK (the Finite Element ToolKit) to solve the 311s Poisson-Boltzmann equation numerically. FETK is a portable collection 311s of finite element modeling class libraries developed by the Michael Holst 311s research group and written in an object-oriented form of C. FEtk is 311s designed to solve general coupled systems of nonlinear partial differential 311s equations using adaptive finite element methods, inexact Newton methods, 311s and algebraic multilevel methods. More information about FEtk may be found 311s at . 311s ---------------------------------------------------------------------- 311s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 311s Aqua is a modified form of the Holst group PMG library 311s which has been modified by Patrice Koehl 311s for improved efficiency and 311s memory usage when solving the Poisson-Boltzmann equation. 311s ---------------------------------------------------------------------- 311s Please cite your use of APBS as: 311s 311s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 311s nanosystems: application to microtubules and the ribosome. Proc. 311s Natl. Acad. Sci. USA 98, 10037-10041 2001. 311s 311s 311s This executable compiled on Jan 3 2025 at 11:01:42 311s 311s Parsing input file apbs-smol-parallel-PE2.in... 311s rank 0 size 1... 311s Parsed input file. 311s Got paths for 1 molecules 311s Reading PQR-format atom data from ion.pqr. 311s 1 atoms 311s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 311s Net charge 1.00e+00 e 311s Preparing to run 6 PBE calculations. 311s ---------------------------------------- 311s CALCULATION #1 (solvated): MULTIGRID 311s Setting up problem... 311s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 311s Debye length: 0 A 311s Current memory usage: 61.262 MB total, 61.262 MB high water 311s Using cubic spline charge discretization. 311s Partition overlap fraction = 0.1 311s Processor array = 2 x 2 x 1 311s Grid dimensions: 65 x 65 x 65 311s Grid spacings: 0.781 x 0.781 x 0.781 311s Grid lengths: 50.000 x 50.000 x 50.000 311s Grid center: (0.000, 0.000, 0.000) 311s Multigrid levels: 5 311s Molecule ID: 1 311s Linearized traditional PBE 311s Multiple Debye-Huckel sphere boundary conditions 311s 0 ion species (0.000 M ionic strength): 311s Solute dielectric: 1.000 311s Solvent dielectric: 78.540 311s Using "molecular" surface definition;harmonic average smoothing 311s Solvent probe radius: 1.400 A 311s Temperature: 298.150 K 311s Electrostatic energies will be calculated 311s Total electrostatic energy = 2.383232191909E+02 kJ/mol 311s Calculating forces... 311s ---------------------------------------- 311s CALCULATION #2 (solvated): MULTIGRID 311s Setting up problem... 311s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 311s Debye length: 0 A 311s Current memory usage: 61.262 MB total, 122.067 MB high water 311s Using cubic spline charge discretization. 311s Partition overlap fraction = 0.1 311s Processor array = 2 x 2 x 1 311s Grid dimensions: 65 x 65 x 65 311s Grid spacings: 0.296 x 0.296 x 0.383 311s Grid lengths: 18.944 x 18.944 x 24.495 311s Grid center: (-2.411, 2.411, 0.000) 311s Multigrid levels: 5 311s Molecule ID: 1 311s Linearized traditional PBE 311s Boundary conditions from focusing 311s 0 ion species (0.000 M ionic strength): 311s Solute dielectric: 1.000 311s Solvent dielectric: 78.540 311s Using "molecular" surface definition;harmonic average smoothing 311s Solvent probe radius: 1.400 A 311s Temperature: 298.150 K 311s Electrostatic energies will be calculated 311s Total electrostatic energy = 8.145369593489E+02 kJ/mol 311s Calculating forces... 311s [focusFillBound()]: WARNING: 311s Unusually large potential values 311s detected on the focusing boundary! 311s Convergence not guaranteed for NPBE/NRPBE calculations! 311s 311s ---------------------------------------- 311s CALCULATION #3 (solvated): MULTIGRID 311s Setting up problem... 311s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 311s Debye length: 0 A 311s Current memory usage: 61.262 MB total, 122.067 MB high water 311s Using cubic spline charge discretization. 311s Partition overlap fraction = 0.1 311s Processor array = 2 x 2 x 1 311s Grid dimensions: 65 x 65 x 65 311s Grid spacings: 0.112 x 0.112 x 0.188 311s Grid lengths: 7.178 x 7.178 x 12.000 311s Grid center: (-2.411, 2.411, 0.000) 311s Multigrid levels: 5 311s Molecule ID: 1 311s Linearized traditional PBE 311s Boundary conditions from focusing 311s 0 ion species (0.000 M ionic strength): 311s Solute dielectric: 1.000 311s Solvent dielectric: 78.540 311s Using "molecular" surface definition;harmonic average smoothing 311s Solvent probe radius: 1.400 A 311s Temperature: 298.150 K 311s Electrostatic energies will be calculated 311s Total electrostatic energy = 1.485524997676E+03 kJ/mol 311s Calculating forces... 311s ---------------------------------------- 311s CALCULATION #4 (reference): MULTIGRID 311s Setting up problem... 311s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 311s Debye length: 0 A 311s Current memory usage: 61.189 MB total, 122.067 MB high water 311s Using cubic spline charge discretization. 311s Partition overlap fraction = 0.1 311s Processor array = 2 x 2 x 1 311s Grid dimensions: 65 x 65 x 65 311s Grid spacings: 0.781 x 0.781 x 0.781 311s Grid lengths: 50.000 x 50.000 x 50.000 311s Grid center: (0.000, 0.000, 0.000) 311s Multigrid levels: 5 311s Molecule ID: 1 311s Linearized traditional PBE 311s Multiple Debye-Huckel sphere boundary conditions 311s 0 ion species (0.000 M ionic strength): 311s Solute dielectric: 1.000 311s Solvent dielectric: 1.000 311s Using "molecular" surface definition;harmonic average smoothing 311s Solvent probe radius: 1.400 A 311s Temperature: 298.150 K 311s Electrostatic energies will be calculated 311s Total electrostatic energy = 2.977178707146E+02 kJ/mol 311s Calculating forces... 311s ---------------------------------------- 311s CALCULATION #5 (reference): MULTIGRID 311s Setting up problem... 311s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 311s Debye length: 0 A 311s Current memory usage: 61.189 MB total, 122.067 MB high water 311s Using cubic spline charge discretization. 311s Partition overlap fraction = 0.1 311s Processor array = 2 x 2 x 1 311s Grid dimensions: 65 x 65 x 65 311s Grid spacings: 0.296 x 0.296 x 0.383 311s Grid lengths: 18.944 x 18.944 x 24.495 311s Grid center: (-2.411, 2.411, 0.000) 311s Multigrid levels: 5 311s Molecule ID: 1 311s Linearized traditional PBE 311s Boundary conditions from focusing 311s 0 ion species (0.000 M ionic strength): 311s Solute dielectric: 1.000 311s Solvent dielectric: 1.000 311s Using "molecular" surface definition;harmonic average smoothing 311s Solvent probe radius: 1.400 A 311s Temperature: 298.150 K 311s Electrostatic energies will be calculated 311s Total electrostatic energy = 8.799304557596E+02 kJ/mol 311s Calculating forces... 311s [focusFillBound()]: WARNING: 311s Unusually large potential values 311s detected on the focusing boundary! 311s Convergence not guaranteed for NPBE/NRPBE calculations! 311s 311s ---------------------------------------- 311s CALCULATION #6 (reference): MULTIGRID 311s Setting up problem... 311s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 311s Debye length: 0 A 311s Current memory usage: 61.189 MB total, 122.067 MB high water 311s Using cubic spline charge discretization. 311s Partition overlap fraction = 0.1 311s Processor array = 2 x 2 x 1 311s Grid dimensions: 65 x 65 x 65 311s Grid spacings: 0.112 x 0.112 x 0.188 311s Grid lengths: 7.178 x 7.178 x 12.000 311s Grid center: (-2.411, 2.411, 0.000) 311s Multigrid levels: 5 311s Molecule ID: 1 311s Linearized traditional PBE 311s Boundary conditions from focusing 311s 0 ion species (0.000 M ionic strength): 311s Solute dielectric: 1.000 311s Solvent dielectric: 1.000 311s Using "molecular" surface definition;harmonic average smoothing 311s Solvent probe radius: 1.400 A 311s Temperature: 298.150 K 311s Electrostatic energies will be calculated 311s Total electrostatic energy = 1.542873949141E+03 kJ/mol 311s Calculating forces... 311s ---------------------------------------- 311s PRINT STATEMENTS 311s 311s print energy 1 (solvated) - 2 (reference) end 311s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 311s Global net ELEC energy = -5.734895146550E+01 kJ/mol 311s ---------------------------------------- 311s CLEANING UP AND SHUTTING DOWN... 311s Destroying force arrays. 311s No energy arrays to destroy. 311s Destroying multigrid structures. 311s Destroying finite element structures. 311s Destroying 1 molecules 311s Final memory usage: 0.001 MB total, 122.067 MB high water 311s 311s 311s Thanks for using APBS! 311s 316s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 316s BINARY: /usr/bin/apbs 316s INPUT: apbs-smol-parallel-PE3.in 316s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 316s Processor 3 results: 316s 2.383232191909e+02 316s 8.145419900310e+02 316s 1.485529328301e+03 316s 2.977178707146e+02 316s 8.799304557596e+02 316s 1.542873949141e+03 316s -5.734462084052e+01 316s 316s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 316s *** PASSED *** 316s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 316s *** PASSED *** 316s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 316s *** PASSED *** 316s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 316s *** PASSED *** 316s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 316s *** PASSED *** 316s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 316s *** PASSED *** 316s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 316s *** PASSED *** 316s Elapsed time: 21.206769 seconds 316s -------------------------------------------------------------------------------- 316s Total elapsed time: 53.544727 seconds 316s Test results have been logged 316s -------------------------------------------------------------------------------- 316s -------------------------------------------------------------------------------- 316s Testing input file apbs-mol-auto.in 316s 316s asc_getToken: Error occurred (bailing out). 316s Vio_scanf: Format problem with input. 316s 316s 316s ---------------------------------------------------------------------- 316s APBS -- Adaptive Poisson-Boltzmann Solver 316s Version APBS 3.4.1 316s 316s Nathan A. Baker (nathan.baker@pnnl.gov) 316s Pacific Northwest National Laboratory 316s 316s Additional contributing authors listed in the code documentation. 316s 316s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 316s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 316s Northwest Division for the U.S. Department of Energy. 316s 316s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 316s Portions Copyright (c) 2002-2020, Nathan A. Baker. 316s Portions Copyright (c) 1999-2002, The Regents of the University of California. 316s Portions Copyright (c) 1995, Michael Holst. 316s All rights reserved. 316s 316s Redistribution and use in source and binary forms, with or without 316s modification, are permitted provided that the following conditions are met: 316s 316s * Redistributions of source code must retain the above copyright notice, this 316s list of conditions and the following disclaimer. 316s 316s * Redistributions in binary form must reproduce the above copyright notice, 316s this list of conditions and the following disclaimer in the documentation 316s and/or other materials provided with the distribution. 316s 316s * Neither the name of the developer nor the names of its contributors may be 316s used to endorse or promote products derived from this software without 316s specific prior written permission. 316s 316s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 316s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 316s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 316s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 316s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 316s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 316s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 316s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 316s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 316s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 316s ---------------------------------------------------------------------- 316s APBS uses FETK (the Finite Element ToolKit) to solve the 316s Poisson-Boltzmann equation numerically. FETK is a portable collection 316s of finite element modeling class libraries developed by the Michael Holst 316s research group and written in an object-oriented form of C. FEtk is 316s designed to solve general coupled systems of nonlinear partial differential 316s equations using adaptive finite element methods, inexact Newton methods, 316s and algebraic multilevel methods. More information about FEtk may be found 316s at . 316s ---------------------------------------------------------------------- 316s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 316s Aqua is a modified form of the Holst group PMG library 316s which has been modified by Patrice Koehl 316s for improved efficiency and 316s memory usage when solving the Poisson-Boltzmann equation. 316s ---------------------------------------------------------------------- 316s Please cite your use of APBS as: 316s 316s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 316s nanosystems: application to microtubules and the ribosome. Proc. 316s Natl. Acad. Sci. USA 98, 10037-10041 2001. 316s 316s 316s This executable compiled on Jan 3 2025 at 11:01:42 316s 316s Parsing input file apbs-smol-parallel-PE3.in... 316s rank 0 size 1... 316s Parsed input file. 316s Got paths for 1 molecules 316s Reading PQR-format atom data from ion.pqr. 316s 1 atoms 316s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 316s Net charge 1.00e+00 e 316s Preparing to run 6 PBE calculations. 316s ---------------------------------------- 316s CALCULATION #1 (solvated): MULTIGRID 316s Setting up problem... 316s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 316s Debye length: 0 A 316s Current memory usage: 61.262 MB total, 61.262 MB high water 316s Using cubic spline charge discretization. 316s Partition overlap fraction = 0.1 316s Processor array = 2 x 2 x 1 316s Grid dimensions: 65 x 65 x 65 316s Grid spacings: 0.781 x 0.781 x 0.781 316s Grid lengths: 50.000 x 50.000 x 50.000 316s Grid center: (0.000, 0.000, 0.000) 316s Multigrid levels: 5 316s Molecule ID: 1 316s Linearized traditional PBE 316s Multiple Debye-Huckel sphere boundary conditions 316s 0 ion species (0.000 M ionic strength): 316s Solute dielectric: 1.000 316s Solvent dielectric: 78.540 316s Using "molecular" surface definition;harmonic average smoothing 316s Solvent probe radius: 1.400 A 316s Temperature: 298.150 K 316s Electrostatic energies will be calculated 316s Total electrostatic energy = 2.383232191909E+02 kJ/mol 316s Calculating forces... 316s ---------------------------------------- 316s CALCULATION #2 (solvated): MULTIGRID 316s Setting up problem... 316s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 316s Debye length: 0 A 316s Current memory usage: 61.262 MB total, 122.067 MB high water 316s Using cubic spline charge discretization. 316s Partition overlap fraction = 0.1 316s Processor array = 2 x 2 x 1 316s Grid dimensions: 65 x 65 x 65 316s Grid spacings: 0.296 x 0.296 x 0.383 316s Grid lengths: 18.944 x 18.944 x 24.495 316s Grid center: (2.411, 2.411, 0.000) 316s Multigrid levels: 5 316s Molecule ID: 1 316s Linearized traditional PBE 316s Boundary conditions from focusing 316s 0 ion species (0.000 M ionic strength): 316s Solute dielectric: 1.000 316s Solvent dielectric: 78.540 316s Using "molecular" surface definition;harmonic average smoothing 316s Solvent probe radius: 1.400 A 316s Temperature: 298.150 K 316s Electrostatic energies will be calculated 316s Total electrostatic energy = 8.145419900310E+02 kJ/mol 316s Calculating forces... 316s [focusFillBound()]: WARNING: 316s Unusually large potential values 316s detected on the focusing boundary! 316s Convergence not guaranteed for NPBE/NRPBE calculations! 316s 316s ---------------------------------------- 316s CALCULATION #3 (solvated): MULTIGRID 316s Setting up problem... 316s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 316s Debye length: 0 A 316s Current memory usage: 61.262 MB total, 122.067 MB high water 316s Using cubic spline charge discretization. 316s Partition overlap fraction = 0.1 316s Processor array = 2 x 2 x 1 316s Grid dimensions: 65 x 65 x 65 316s Grid spacings: 0.112 x 0.112 x 0.188 316s Grid lengths: 7.178 x 7.178 x 12.000 316s Grid center: (2.411, 2.411, 0.000) 316s Multigrid levels: 5 316s Molecule ID: 1 316s Linearized traditional PBE 316s Boundary conditions from focusing 316s 0 ion species (0.000 M ionic strength): 316s Solute dielectric: 1.000 316s Solvent dielectric: 78.540 316s Using "molecular" surface definition;harmonic average smoothing 316s Solvent probe radius: 1.400 A 316s Temperature: 298.150 K 316s Electrostatic energies will be calculated 316s Total electrostatic energy = 1.485529328301E+03 kJ/mol 316s Calculating forces... 316s ---------------------------------------- 316s CALCULATION #4 (reference): MULTIGRID 316s Setting up problem... 316s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 316s Debye length: 0 A 316s Current memory usage: 61.189 MB total, 122.067 MB high water 316s Using cubic spline charge discretization. 316s Partition overlap fraction = 0.1 316s Processor array = 2 x 2 x 1 316s Grid dimensions: 65 x 65 x 65 316s Grid spacings: 0.781 x 0.781 x 0.781 316s Grid lengths: 50.000 x 50.000 x 50.000 316s Grid center: (0.000, 0.000, 0.000) 316s Multigrid levels: 5 316s Molecule ID: 1 316s Linearized traditional PBE 316s Multiple Debye-Huckel sphere boundary conditions 316s 0 ion species (0.000 M ionic strength): 316s Solute dielectric: 1.000 316s Solvent dielectric: 1.000 316s Using "molecular" surface definition;harmonic average smoothing 316s Solvent probe radius: 1.400 A 316s Temperature: 298.150 K 316s Electrostatic energies will be calculated 316s Total electrostatic energy = 2.977178707146E+02 kJ/mol 316s Calculating forces... 316s ---------------------------------------- 316s CALCULATION #5 (reference): MULTIGRID 316s Setting up problem... 316s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 316s Debye length: 0 A 316s Current memory usage: 61.189 MB total, 122.067 MB high water 316s Using cubic spline charge discretization. 316s Partition overlap fraction = 0.1 316s Processor array = 2 x 2 x 1 316s Grid dimensions: 65 x 65 x 65 316s Grid spacings: 0.296 x 0.296 x 0.383 316s Grid lengths: 18.944 x 18.944 x 24.495 316s Grid center: (2.411, 2.411, 0.000) 316s Multigrid levels: 5 316s Molecule ID: 1 316s Linearized traditional PBE 316s Boundary conditions from focusing 316s 0 ion species (0.000 M ionic strength): 316s Solute dielectric: 1.000 316s Solvent dielectric: 1.000 316s Using "molecular" surface definition;harmonic average smoothing 316s Solvent probe radius: 1.400 A 316s Temperature: 298.150 K 316s Electrostatic energies will be calculated 316s Total electrostatic energy = 8.799304557596E+02 kJ/mol 316s Calculating forces... 316s [focusFillBound()]: WARNING: 316s Unusually large potential values 316s detected on the focusing boundary! 316s Convergence not guaranteed for NPBE/NRPBE calculations! 316s 316s ---------------------------------------- 316s CALCULATION #6 (reference): MULTIGRID 316s Setting up problem... 316s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 316s Debye length: 0 A 316s Current memory usage: 61.189 MB total, 122.067 MB high water 316s Using cubic spline charge discretization. 316s Partition overlap fraction = 0.1 316s Processor array = 2 x 2 x 1 316s Grid dimensions: 65 x 65 x 65 316s Grid spacings: 0.112 x 0.112 x 0.188 316s Grid lengths: 7.178 x 7.178 x 12.000 316s Grid center: (2.411, 2.411, 0.000) 316s Multigrid levels: 5 316s Molecule ID: 1 316s Linearized traditional PBE 316s Boundary conditions from focusing 316s 0 ion species (0.000 M ionic strength): 316s Solute dielectric: 1.000 316s Solvent dielectric: 1.000 316s Using "molecular" surface definition;harmonic average smoothing 316s Solvent probe radius: 1.400 A 316s Temperature: 298.150 K 316s Electrostatic energies will be calculated 316s Total electrostatic energy = 1.542873949141E+03 kJ/mol 316s Calculating forces... 316s ---------------------------------------- 316s PRINT STATEMENTS 316s 316s print energy 1 (solvated) - 2 (reference) end 316s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 316s Global net ELEC energy = -5.734462084052E+01 kJ/mol 316s ---------------------------------------- 316s CLEANING UP AND SHUTTING DOWN... 316s Destroying force arrays. 316s No energy arrays to destroy. 316s Destroying multigrid structures. 316s Destroying finite element structures. 316s Destroying 1 molecules 316s Final memory usage: 0.001 MB total, 122.067 MB high water 316s 316s 316s Thanks for using APBS! 316s 494s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 494s EXPECTED COMPUTED: 7 494s EXPECTED EXPECTED: 7 494s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 494s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 494s COMPUTED RESULT 953.292876745 494s COMPUTED RESULT 3258.1578983732998 494s COMPUTED RESULT 5942.108652589999 494s COMPUTED RESULT 1190.8714828309999 494s COMPUTED RESULT 3519.7218230368003 494s COMPUTED RESULT 6171.495796544 494s COMPUTED RESULT -229.38714395599 494s Running tests for actin-dimer-auto section 494s BINARY: /usr/bin/apbs 494s INPUT: apbs-mol-auto.in 494s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 494s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 494s *** PASSED *** 494s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 494s *** PASSED *** 494s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 494s *** PASSED *** 494s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 494s *** PASSED *** 494s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 494s *** PASSED *** 494s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 494s *** PASSED *** 494s Testing computed result against expected result (1.048683058628e+02, 1.048683060915e+02) 494s *** PASSED *** 494s Elapsed time: 177.833713 seconds 494s -------------------------------------------------------------------------------- 494s -------------------------------------------------------------------------------- 494s Testing input file apbs-smol-auto.in 494s 494s asc_getToken: Error occurred (bailing out). 494s Vio_scanf: Format problem with input. 494s 494s 494s ---------------------------------------------------------------------- 494s APBS -- Adaptive Poisson-Boltzmann Solver 494s Version APBS 3.4.1 494s 494s Nathan A. Baker (nathan.baker@pnnl.gov) 494s Pacific Northwest National Laboratory 494s 494s Additional contributing authors listed in the code documentation. 494s 494s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 494s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 494s Northwest Division for the U.S. Department of Energy. 494s 494s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 494s Portions Copyright (c) 2002-2020, Nathan A. Baker. 494s Portions Copyright (c) 1999-2002, The Regents of the University of California. 494s Portions Copyright (c) 1995, Michael Holst. 494s All rights reserved. 494s 494s Redistribution and use in source and binary forms, with or without 494s modification, are permitted provided that the following conditions are met: 494s 494s * Redistributions of source code must retain the above copyright notice, this 494s list of conditions and the following disclaimer. 494s 494s * Redistributions in binary form must reproduce the above copyright notice, 494s this list of conditions and the following disclaimer in the documentation 494s and/or other materials provided with the distribution. 494s 494s * Neither the name of the developer nor the names of its contributors may be 494s used to endorse or promote products derived from this software without 494s specific prior written permission. 494s 494s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 494s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 494s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 494s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 494s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 494s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 494s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 494s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 494s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 494s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 494s ---------------------------------------------------------------------- 494s APBS uses FETK (the Finite Element ToolKit) to solve the 494s Poisson-Boltzmann equation numerically. FETK is a portable collection 494s of finite element modeling class libraries developed by the Michael Holst 494s research group and written in an object-oriented form of C. FEtk is 494s designed to solve general coupled systems of nonlinear partial differential 494s equations using adaptive finite element methods, inexact Newton methods, 494s and algebraic multilevel methods. More information about FEtk may be found 494s at . 494s ---------------------------------------------------------------------- 494s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 494s Aqua is a modified form of the Holst group PMG library 494s which has been modified by Patrice Koehl 494s for improved efficiency and 494s memory usage when solving the Poisson-Boltzmann equation. 494s ---------------------------------------------------------------------- 494s Please cite your use of APBS as: 494s 494s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 494s nanosystems: application to microtubules and the ribosome. Proc. 494s Natl. Acad. Sci. USA 98, 10037-10041 2001. 494s 494s 494s This executable compiled on Jan 3 2025 at 11:01:42 494s 494s Parsing input file apbs-mol-auto.in... 494s rank 0 size 1... 494s Parsed input file. 494s Got paths for 3 molecules 494s Reading PQR-format atom data from mol1.pqr. 494s asc_getToken: Error occurred (bailing out). 494s Vio_scanf: Format problem with input. 494s 5877 atoms 494s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 494s Net charge -1.20e+01 e 494s Reading PQR-format atom data from mol2.pqr. 494s asc_getToken: Error occurred (bailing out). 494s Vio_scanf: Format problem with input. 494s 5877 atoms 494s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 494s Net charge -1.20e+01 e 494s Reading PQR-format atom data from complex.pqr. 494s 11754 atoms 494s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 494s Net charge -2.40e+01 e 494s Preparing to run 6 PBE calculations. 494s ---------------------------------------- 494s CALCULATION #1 (mol1): MULTIGRID 494s Setting up problem... 494s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 494s Debye length: 13.5959 A 494s Current memory usage: 1004.896 MB total, 1004.896 MB high water 494s Using linear spline charge discretization. 494s Grid dimensions: 161 x 161 x 161 494s Grid spacings: 0.975 x 0.756 x 1.012 494s Grid lengths: 156.000 x 121.000 x 162.000 494s Grid center: (2.518, -2.465, 16.742) 494s Multigrid levels: 4 494s Molecule ID: 1 494s Nonlinear traditional PBE 494s Single Debye-Huckel sphere boundary conditions 494s 2 ion species (0.050 M ionic strength): 494s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 494s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 494s Solute dielectric: 2.000 494s Solvent dielectric: 78.400 494s Using "molecular" surface definition; no smoothing 494s Solvent probe radius: 1.400 A 494s Temperature: 298.150 K 494s Electrostatic energies will be calculated 494s Total electrostatic energy = 1.527617850342E+05 kJ/mol 494s Calculating forces... 494s ---------------------------------------- 494s CALCULATION #2 (mol1): MULTIGRID 494s Setting up problem... 494s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 494s Debye length: 13.5959 A 494s Current memory usage: 1004.896 MB total, 1995.284 MB high water 494s Using linear spline charge discretization. 494s Grid dimensions: 161 x 161 x 161 494s Grid spacings: 0.700 x 0.569 x 0.725 494s Grid lengths: 112.000 x 91.000 x 116.000 494s Grid center: (2.518, -2.465, 16.742) 494s Multigrid levels: 4 494s Molecule ID: 1 494s Nonlinear traditional PBE 494s Boundary conditions from focusing 494s 2 ion species (0.050 M ionic strength): 494s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 494s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 494s Solute dielectric: 2.000 494s Solvent dielectric: 78.400 494s Using "molecular" surface definition; no smoothing 494s Solvent probe radius: 1.400 A 494s Temperature: 298.150 K 494s Electrostatic energies will be calculated 494s Total electrostatic energy = 2.919510754196E+05 kJ/mol 494s Calculating forces... 494s ---------------------------------------- 494s CALCULATION #3 (mol2): MULTIGRID 494s Setting up problem... 494s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 494s Debye length: 13.5959 A 494s Current memory usage: 1005.881 MB total, 1995.284 MB high water 494s Using linear spline charge discretization. 494s Grid dimensions: 161 x 161 x 161 494s Grid spacings: 0.975 x 0.756 x 1.012 494s Grid lengths: 156.000 x 121.000 x 162.000 494s Grid center: (2.518, -2.465, 16.742) 494s Multigrid levels: 4 494s Molecule ID: 2 494s Nonlinear traditional PBE 494s Single Debye-Huckel sphere boundary conditions 494s 2 ion species (0.050 M ionic strength): 494s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 494s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 494s Solute dielectric: 2.000 494s Solvent dielectric: 78.400 494s Using "molecular" surface definition; no smoothing 494s Solvent probe radius: 1.400 A 494s Temperature: 298.150 K 494s Electrostatic energies will be calculated 494s Total electrostatic energy = 1.527671844880E+05 kJ/mol 494s Calculating forces... 494s ---------------------------------------- 494s CALCULATION #4 (mol2): MULTIGRID 494s Setting up problem... 494s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 494s Debye length: 13.5959 A 494s Current memory usage: 1005.881 MB total, 1997.252 MB high water 494s Using linear spline charge discretization. 494s Grid dimensions: 161 x 161 x 161 494s Grid spacings: 0.700 x 0.569 x 0.725 494s Grid lengths: 112.000 x 91.000 x 116.000 494s Grid center: (2.518, -2.465, 16.742) 494s Multigrid levels: 4 494s Molecule ID: 2 494s Nonlinear traditional PBE 494s Boundary conditions from focusing 494s 2 ion species (0.050 M ionic strength): 494s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 494s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 494s Solute dielectric: 2.000 494s Solvent dielectric: 78.400 494s Using "molecular" surface definition; no smoothing 494s Solvent probe radius: 1.400 A 494s Temperature: 298.150 K 494s Electrostatic energies will be calculated 494s Total electrostatic energy = 2.915468859278E+05 kJ/mol 494s Calculating forces... 494s ---------------------------------------- 494s CALCULATION #5 (complex): MULTIGRID 494s Setting up problem... 494s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 494s Debye length: 13.5959 A 494s Current memory usage: 1018.381 MB total, 1997.252 MB high water 494s Using linear spline charge discretization. 494s Grid dimensions: 161 x 161 x 161 494s Grid spacings: 0.975 x 0.756 x 1.012 494s Grid lengths: 156.000 x 121.000 x 162.000 494s Grid center: (2.518, -2.465, 16.742) 494s Multigrid levels: 4 494s Molecule ID: 3 494s Nonlinear traditional PBE 494s Single Debye-Huckel sphere boundary conditions 494s 2 ion species (0.050 M ionic strength): 494s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 494s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 494s Solute dielectric: 2.000 494s Solvent dielectric: 78.400 494s Using "molecular" surface definition; no smoothing 494s Solvent probe radius: 1.400 A 494s Temperature: 298.150 K 494s Electrostatic energies will be calculated 494s Total electrostatic energy = 3.056317807611E+05 kJ/mol 494s Calculating forces... 494s ---------------------------------------- 494s CALCULATION #6 (complex): MULTIGRID 494s Setting up problem... 494s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 494s Debye length: 13.5959 A 494s Current memory usage: 1018.381 MB total, 2013.407 MB high water 494s Using linear spline charge discretization. 494s Grid dimensions: 161 x 161 x 161 494s Grid spacings: 0.700 x 0.569 x 0.725 494s Grid lengths: 112.000 x 91.000 x 116.000 494s Grid center: (2.518, -2.465, 16.742) 494s Multigrid levels: 4 494s Molecule ID: 3 494s Nonlinear traditional PBE 494s Boundary conditions from focusing 494s 2 ion species (0.050 M ionic strength): 494s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 494s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 494s Solute dielectric: 2.000 494s Solvent dielectric: 78.400 494s Using "molecular" surface definition; no smoothing 494s Solvent probe radius: 1.400 A 494s Temperature: 298.150 K 494s Electrostatic energies will be calculated 494s Total electrostatic energy = 5.836028296532E+05 kJ/mol 494s Calculating forces... 494s ---------------------------------------- 494s PRINT STATEMENTS 494s 494s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 494s Local net energy (PE 0) = 1.048683058628E+02 kJ/mol 494s Global net ELEC energy = 1.048683058628E+02 kJ/mol 494s ---------------------------------------- 494s CLEANING UP AND SHUTTING DOWN... 494s Destroying force arrays. 494s No energy arrays to destroy. 494s Destroying multigrid structures. 494s Destroying finite element structures. 494s Destroying 3 molecules 494s Final memory usage: 0.001 MB total, 2013.407 MB high water 494s 494s 494s Thanks for using APBS! 494s 630s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 630s *** PASSED *** 630s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 630s *** PASSED *** 630s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 630s *** PASSED *** 630s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 630s *** PASSED *** 630s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 630s *** PASSED *** 630s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 630s *** PASSED *** 630s Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) 630s *** PASSED *** 630s Elapsed time: 135.51499 seconds 630s -------------------------------------------------------------------------------- 630s Total elapsed time: 313.348703 seconds 630s Test results have been logged 630s -------------------------------------------------------------------------------- 630s -------------------------------------------------------------------------------- 630s Testing input file alkanes.in 630s 630s Checking for intermediate energies in input file apbs-mol-auto.out 630s EXPECTED COMPUTED: 7 630s EXPECTED EXPECTED: 7 630s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058628] 630s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 630s COMPUTED RESULT 152761.7850342 630s COMPUTED RESULT 291951.0754196 630s COMPUTED RESULT 152767.184488 630s COMPUTED RESULT 291546.8859278 630s COMPUTED RESULT 305631.7807611 630s COMPUTED RESULT 583602.8296532 630s COMPUTED RESULT 104.8683058628 630s BINARY: /usr/bin/apbs 630s INPUT: apbs-smol-auto.in 630s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 630s asc_getToken: Error occurred (bailing out). 630s Vio_scanf: Format problem with input. 630s 630s 630s ---------------------------------------------------------------------- 630s APBS -- Adaptive Poisson-Boltzmann Solver 630s Version APBS 3.4.1 630s 630s Nathan A. Baker (nathan.baker@pnnl.gov) 630s Pacific Northwest National Laboratory 630s 630s Additional contributing authors listed in the code documentation. 630s 630s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 630s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 630s Northwest Division for the U.S. Department of Energy. 630s 630s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 630s Portions Copyright (c) 2002-2020, Nathan A. Baker. 630s Portions Copyright (c) 1999-2002, The Regents of the University of California. 630s Portions Copyright (c) 1995, Michael Holst. 630s All rights reserved. 630s 630s Redistribution and use in source and binary forms, with or without 630s modification, are permitted provided that the following conditions are met: 630s 630s * Redistributions of source code must retain the above copyright notice, this 630s list of conditions and the following disclaimer. 630s 630s * Redistributions in binary form must reproduce the above copyright notice, 630s this list of conditions and the following disclaimer in the documentation 630s and/or other materials provided with the distribution. 630s 630s * Neither the name of the developer nor the names of its contributors may be 630s used to endorse or promote products derived from this software without 630s specific prior written permission. 630s 630s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 630s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 630s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 630s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 630s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 630s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 630s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 630s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 630s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 630s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 630s ---------------------------------------------------------------------- 630s APBS uses FETK (the Finite Element ToolKit) to solve the 630s Poisson-Boltzmann equation numerically. FETK is a portable collection 630s of finite element modeling class libraries developed by the Michael Holst 630s research group and written in an object-oriented form of C. FEtk is 630s designed to solve general coupled systems of nonlinear partial differential 630s equations using adaptive finite element methods, inexact Newton methods, 630s and algebraic multilevel methods. More information about FEtk may be found 630s at . 630s ---------------------------------------------------------------------- 630s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 630s Aqua is a modified form of the Holst group PMG library 630s which has been modified by Patrice Koehl 630s for improved efficiency and 630s memory usage when solving the Poisson-Boltzmann equation. 630s ---------------------------------------------------------------------- 630s Please cite your use of APBS as: 630s 630s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 630s nanosystems: application to microtubules and the ribosome. Proc. 630s Natl. Acad. Sci. USA 98, 10037-10041 2001. 630s 630s 630s This executable compiled on Jan 3 2025 at 11:01:42 630s 630s Parsing input file apbs-smol-auto.in... 630s rank 0 size 1... 630s Parsed input file. 630s Got paths for 3 molecules 630s Reading PQR-format atom data from mol1.pqr. 630s asc_getToken: Error occurred (bailing out). 630s Vio_scanf: Format problem with input. 630s 5877 atoms 630s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 630s Net charge -1.20e+01 e 630s Reading PQR-format atom data from mol2.pqr. 630s asc_getToken: Error occurred (bailing out). 630s Vio_scanf: Format problem with input. 630s 5877 atoms 630s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 630s Net charge -1.20e+01 e 630s Reading PQR-format atom data from complex.pqr. 630s 11754 atoms 630s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 630s Net charge -2.40e+01 e 630s Preparing to run 6 PBE calculations. 630s ---------------------------------------- 630s CALCULATION #1 (mol1): MULTIGRID 630s Setting up problem... 630s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 630s Debye length: 13.5959 A 630s Current memory usage: 1004.896 MB total, 1004.896 MB high water 630s Using linear spline charge discretization. 630s Grid dimensions: 161 x 161 x 161 630s Grid spacings: 0.975 x 0.756 x 1.012 630s Grid lengths: 156.000 x 121.000 x 162.000 630s Grid center: (2.518, -2.465, 16.742) 630s Multigrid levels: 4 630s Molecule ID: 1 630s Nonlinear traditional PBE 630s Single Debye-Huckel sphere boundary conditions 630s 2 ion species (0.050 M ionic strength): 630s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 630s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 630s Solute dielectric: 2.000 630s Solvent dielectric: 78.400 630s Using "molecular" surface definition;harmonic average smoothing 630s Solvent probe radius: 1.400 A 630s Temperature: 298.150 K 630s Electrostatic energies will be calculated 630s Total electrostatic energy = 1.528632421825E+05 kJ/mol 630s Calculating forces... 630s ---------------------------------------- 630s CALCULATION #2 (mol1): MULTIGRID 630s Setting up problem... 630s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 630s Debye length: 13.5959 A 630s Current memory usage: 1004.896 MB total, 1995.284 MB high water 630s Using linear spline charge discretization. 630s Grid dimensions: 161 x 161 x 161 630s Grid spacings: 0.700 x 0.569 x 0.725 630s Grid lengths: 112.000 x 91.000 x 116.000 630s Grid center: (2.518, -2.465, 16.742) 630s Multigrid levels: 4 630s Molecule ID: 1 630s Nonlinear traditional PBE 630s Boundary conditions from focusing 630s 2 ion species (0.050 M ionic strength): 630s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 630s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 630s Solute dielectric: 2.000 630s Solvent dielectric: 78.400 630s Using "molecular" surface definition;harmonic average smoothing 630s Solvent probe radius: 1.400 A 630s Temperature: 298.150 K 630s Electrostatic energies will be calculated 630s Total electrostatic energy = 2.920618662320E+05 kJ/mol 630s Calculating forces... 630s ---------------------------------------- 630s CALCULATION #3 (mol2): MULTIGRID 630s Setting up problem... 630s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 630s Debye length: 13.5959 A 630s Current memory usage: 1005.881 MB total, 1995.284 MB high water 630s Using linear spline charge discretization. 630s Grid dimensions: 161 x 161 x 161 630s Grid spacings: 0.975 x 0.756 x 1.012 630s Grid lengths: 156.000 x 121.000 x 162.000 630s Grid center: (2.518, -2.465, 16.742) 630s Multigrid levels: 4 630s Molecule ID: 2 630s Nonlinear traditional PBE 630s Single Debye-Huckel sphere boundary conditions 630s 2 ion species (0.050 M ionic strength): 630s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 630s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 630s Solute dielectric: 2.000 630s Solvent dielectric: 78.400 630s Using "molecular" surface definition;harmonic average smoothing 630s Solvent probe radius: 1.400 A 630s Temperature: 298.150 K 630s Electrostatic energies will be calculated 630s Total electrostatic energy = 1.529297900572E+05 kJ/mol 630s Calculating forces... 630s ---------------------------------------- 630s CALCULATION #4 (mol2): MULTIGRID 630s Setting up problem... 630s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 630s Debye length: 13.5959 A 630s Current memory usage: 1005.881 MB total, 1997.252 MB high water 630s Using linear spline charge discretization. 630s Grid dimensions: 161 x 161 x 161 630s Grid spacings: 0.700 x 0.569 x 0.725 630s Grid lengths: 112.000 x 91.000 x 116.000 630s Grid center: (2.518, -2.465, 16.742) 630s Multigrid levels: 4 630s Molecule ID: 2 630s Nonlinear traditional PBE 630s Boundary conditions from focusing 630s 2 ion species (0.050 M ionic strength): 630s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 630s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 630s Solute dielectric: 2.000 630s Solvent dielectric: 78.400 630s Using "molecular" surface definition;harmonic average smoothing 630s Solvent probe radius: 1.400 A 630s Temperature: 298.150 K 630s Electrostatic energies will be calculated 630s Total electrostatic energy = 2.916592202835E+05 kJ/mol 630s Calculating forces... 630s ---------------------------------------- 630s CALCULATION #5 (complex): MULTIGRID 630s Setting up problem... 630s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 630s Debye length: 13.5959 A 630s Current memory usage: 1018.381 MB total, 1997.252 MB high water 630s Using linear spline charge discretization. 630s Grid dimensions: 161 x 161 x 161 630s Grid spacings: 0.975 x 0.756 x 1.012 630s Grid lengths: 156.000 x 121.000 x 162.000 630s Grid center: (2.518, -2.465, 16.742) 630s Multigrid levels: 4 630s Molecule ID: 3 630s Nonlinear traditional PBE 630s Single Debye-Huckel sphere boundary conditions 630s 2 ion species (0.050 M ionic strength): 630s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 630s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 630s Solute dielectric: 2.000 630s Solvent dielectric: 78.400 630s Using "molecular" surface definition;harmonic average smoothing 630s Solvent probe radius: 1.400 A 630s Temperature: 298.150 K 630s Electrostatic energies will be calculated 630s Total electrostatic energy = 3.059244262535E+05 kJ/mol 630s Calculating forces... 630s ---------------------------------------- 630s CALCULATION #6 (complex): MULTIGRID 630s Setting up problem... 630s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 630s Debye length: 13.5959 A 630s Current memory usage: 1018.381 MB total, 2013.407 MB high water 630s Using linear spline charge discretization. 630s Grid dimensions: 161 x 161 x 161 630s Grid spacings: 0.700 x 0.569 x 0.725 630s Grid lengths: 112.000 x 91.000 x 116.000 630s Grid center: (2.518, -2.465, 16.742) 630s Multigrid levels: 4 630s Molecule ID: 3 630s Nonlinear traditional PBE 630s Boundary conditions from focusing 630s 2 ion species (0.050 M ionic strength): 630s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 630s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 630s Solute dielectric: 2.000 630s Solvent dielectric: 78.400 630s Using "molecular" surface definition;harmonic average smoothing 630s Solvent probe radius: 1.400 A 630s Temperature: 298.150 K 630s Electrostatic energies will be calculated 630s Total electrostatic energy = 5.838306706232E+05 kJ/mol 630s Calculating forces... 630s ---------------------------------------- 630s PRINT STATEMENTS 630s 630s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 630s Local net energy (PE 0) = 1.095841077691E+02 kJ/mol 630s Global net ELEC energy = 1.095841077691E+02 kJ/mol 630s ---------------------------------------- 630s CLEANING UP AND SHUTTING DOWN... 630s Destroying force arrays. 630s No energy arrays to destroy. 630s Destroying multigrid structures. 630s Destroying finite element structures. 630s Destroying 3 molecules 630s Final memory usage: 0.001 MB total, 2013.407 MB high water 630s 630s 630s Thanks for using APBS! 630s 642s Checking for intermediate energies in input file apbs-smol-auto.out 642s EXPECTED COMPUTED: 7 642s EXPECTED EXPECTED: 7 642s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] 642s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 642s COMPUTED RESULT 152863.2421825 642s COMPUTED RESULT 292061.866232 642s COMPUTED RESULT 152929.7900572 642s COMPUTED RESULT 291659.2202835 642s COMPUTED RESULT 305924.4262535 642s COMPUTED RESULT 583830.6706232 642s COMPUTED RESULT 109.5841077691 642s Running tests for alkanes section 642s BINARY: /usr/bin/apbs 642s INPUT: alkanes.in 642s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 642s 642s ---------------------------------------------------------------------- 642s APBS -- Adaptive Poisson-Boltzmann Solver 642s Version APBS 3.4.1 642s 642s Nathan A. Baker (nathan.baker@pnnl.gov) 642s Pacific Northwest National Laboratory 642s 642s Additional contributing authors listed in the code documentation. 642s 642s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 642s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 642s Northwest Division for the U.S. Department of Energy. 642s 642s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 642s Portions Copyright (c) 2002-2020, Nathan A. Baker. 642s Portions Copyright (c) 1999-2002, The Regents of the University of California. 642s Portions Copyright (c) 1995, Michael Holst. 642s All rights reserved. 642s 642s Redistribution and use in source and binary forms, with or without 642s modification, are permitted provided that the following conditions are met: 642s 642s * Redistributions of source code must retain the above copyright notice, this 642s list of conditions and the following disclaimer. 642s 642s * Redistributions in binary form must reproduce the above copyright notice, 642s this list of conditions and the following disclaimer in the documentation 642s and/or other materials provided with the distribution. 642s 642s * Neither the name of the developer nor the names of its contributors may be 642s used to endorse or promote products derived from this software without 642s specific prior written permission. 642s 642s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 642s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 642s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 642s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 642s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 642s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 642s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 642s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 642s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 642s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 642s ---------------------------------------------------------------------- 642s APBS uses FETK (the Finite Element ToolKit) to solve the 642s Poisson-Boltzmann equation numerically. FETK is a portable collection 642s of finite element modeling class libraries developed by the Michael Holst 642s research group and written in an object-oriented form of C. FEtk is 642s designed to solve general coupled systems of nonlinear partial differential 642s equations using adaptive finite element methods, inexact Newton methods, 642s and algebraic multilevel methods. More information about FEtk may be found 642s at . 642s ---------------------------------------------------------------------- 642s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 642s Aqua is a modified form of the Holst group Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 642s *** PASSED *** 642s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 642s *** PASSED *** 642s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 642s *** PASSED *** 642s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 642s *** PASSED *** 642s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 642s *** PASSED *** 642s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 642s *** PASSED *** 642s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 642s *** PASSED *** 642s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 642s *** PASSED *** 642s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 642s *** PASSED *** 642s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 642s *** PASSED *** 642s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 642s *** PASSED *** 642s Elapsed time: 12.632613 seconds 642s -------------------------------------------------------------------------------- 642s Total elapsed time: 12.632613 seconds 642s Test results have been logged 642s -------------------------------------------------------------------------------- 642s -------------------------------------------------------------------------------- 642s Testing input file 1d7h-dmso-mol.in 642s 642s PMG library 642s which has been modified by Patrice Koehl 642s for improved efficiency and 642s memory usage when solving the Poisson-Boltzmann equation. 642s ---------------------------------------------------------------------- 642s Please cite your use of APBS as: 642s 642s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 642s nanosystems: application to microtubules and the ribosome. Proc. 642s Natl. Acad. Sci. USA 98, 10037-10041 2001. 642s 642s 642s This executable compiled on Jan 3 2025 at 11:01:42 642s 642s Parsing input file alkanes.in... 642s rank 0 size 1... 642s Parsed input file. 642s Reading parameter data from parm.dat. 642s Got paths for 11 molecules 642s Reading PDB-format atom data from 2-methylbutane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 17 atoms 642s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 642s Net charge 4.33e+00 e 642s Reading PDB-format atom data from butane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 14 atoms 642s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 642s Net charge 3.51e+00 e 642s Reading PDB-format atom data from cyclohexane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 18 atoms 642s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 642s Net charge 4.93e+00 e 642s Reading PDB-format atom data from cyclopentane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 13 atoms 642s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 642s Net charge 3.88e+00 e 642s Reading PDB-format atom data from ethane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 8 atoms 642s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 642s Net charge 1.87e+00 e 642s Reading PDB-format atom data from hexane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 20 atoms 642s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 642s Net charge 5.16e+00 e 642s Reading PDB-format atom data from isobutane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 14 atoms 642s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 642s Net charge 3.51e+00 e 642s Reading PDB-format atom data from methane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 5 atoms 642s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 642s Net charge 1.05e+00 e 642s Reading PDB-format atom data from neopentane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 17 atoms 642s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 642s Net charge 4.33e+00 e 642s Reading PDB-format atom data from pentane.pdb. 642s asc_getToken: Error occurred (bailing out). 642s Vio_scanf: Format problem with input. 642s 17 atoms 642s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 642s Net charge 4.33e+00 e 642s Reading PDB-format atom data from propane.pdb. 642s 11 atoms 642s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 642s Net charge 2.69e+00 e 642s Preparing to run 11 PBE calculations. 642s ---------------------------------------- 642s CALCULATION #1 (solvated-2-methylbutane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 3.815624614267E+00 642s SASA for atom 1: 0.000000000000E+00 642s SASA for atom 2: 6.122920124655E-01 642s SASA for atom 3: 3.957497153740E+00 642s SASA for atom 4: 4.308445014544E+00 642s SASA for atom 5: 1.843264951960E+01 642s SASA for atom 6: 1.837011296483E+01 642s SASA for atom 7: 1.666599184724E+01 642s SASA for atom 8: 1.480031796315E+01 642s SASA for atom 9: 1.603020354037E+01 642s SASA for atom 10: 1.473778140838E+01 642s SASA for atom 11: 1.611879699297E+01 642s SASA for atom 12: 1.810954398660E+01 642s SASA for atom 13: 1.420100931324E+01 642s SASA for atom 14: 1.437298483886E+01 642s SASA for atom 15: 1.814081226399E+01 642s SASA for atom 16: 2.152820898091E+01 642s 642s Total solvent accessible surface area: 214.202 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 3.243280922127E-02 642s Surface tension*area energy for atom 1: 0.000000000000E+00 642s Surface tension*area energy for atom 2: 5.204482105957E-03 642s Surface tension*area energy for atom 3: 3.363872580679E-02 642s Surface tension*area energy for atom 4: 3.662178262362E-02 642s Surface tension*area energy for atom 5: 1.566775209166E-01 642s Surface tension*area energy for atom 6: 1.561459602010E-01 642s Surface tension*area energy for atom 7: 1.416609307015E-01 642s Surface tension*area energy for atom 8: 1.258027026868E-01 642s Surface tension*area energy for atom 9: 1.362567300932E-01 642s Surface tension*area energy for atom 10: 1.252711419712E-01 642s Surface tension*area energy for atom 11: 1.370097744402E-01 642s Surface tension*area energy for atom 12: 1.539311238861E-01 642s Surface tension*area energy for atom 13: 1.207085791625E-01 642s Surface tension*area energy for atom 14: 1.221703711303E-01 642s Surface tension*area energy for atom 15: 1.541969042439E-01 642s Surface tension*area energy for atom 16: 1.829897763377E-01 642s 642s Total surface tension energy: 1.82072 kJ/mol 642s 642s Total solvent accessible volume: 253.665 A^3 642s 642s Total pressure*volume energy: 60.7274 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.271287875274E+00 642s WCA energy for atom 1: -5.600872869478E+00 642s WCA energy for atom 2: -5.773775123943E+00 642s WCA energy for atom 3: -6.072801488986E+00 642s WCA energy for atom 4: -6.378470721845E+00 642s WCA energy for atom 5: -1.573474558351E+00 642s WCA energy for atom 6: -1.582338715648E+00 642s WCA energy for atom 7: -1.504044838266E+00 642s WCA energy for atom 8: -1.351002262819E+00 642s WCA energy for atom 9: -1.437367175239E+00 642s WCA energy for atom 10: -1.384626257493E+00 642s WCA energy for atom 11: -1.468867560891E+00 642s WCA energy for atom 12: -1.557005662832E+00 642s WCA energy for atom 13: -1.473759654043E+00 642s WCA energy for atom 14: -1.502261431335E+00 642s WCA energy for atom 15: -1.550940901474E+00 642s WCA energy for atom 16: -1.667828659696E+00 642s 642s Total WCA energy: -48.1507 kJ/mol 642s 642s Total non-polar energy = 1.439739455792E+01 kJ/mol 642s ---------------------------------------- 642s CALCULATION #2 (solvated-butane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 4.405515699447E+00 642s SASA for atom 1: 8.213673337951E-01 642s SASA for atom 2: 8.064333822716E-01 642s SASA for atom 3: 4.375647796400E+00 642s SASA for atom 4: 1.855251124959E+01 642s SASA for atom 5: 2.147609518526E+01 642s SASA for atom 6: 1.852645435176E+01 642s SASA for atom 7: 1.660345529247E+01 642s SASA for atom 8: 1.658782115377E+01 642s SASA for atom 9: 1.658260977421E+01 642s SASA for atom 10: 1.658260977421E+01 642s SASA for atom 11: 2.145003828744E+01 642s SASA for atom 12: 1.852124297220E+01 642s SASA for atom 13: 1.856293400871E+01 642s 642s Total solvent accessible surface area: 193.855 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 3.744688344530E-02 642s Surface tension*area energy for atom 1: 6.981622337259E-03 642s Surface tension*area energy for atom 2: 6.854683749309E-03 642s Surface tension*area energy for atom 3: 3.719300626940E-02 642s Surface tension*area energy for atom 4: 1.576963456215E-01 642s Surface tension*area energy for atom 5: 1.825468090747E-01 642s Surface tension*area energy for atom 6: 1.574748619900E-01 642s Surface tension*area energy for atom 7: 1.411293699860E-01 642s Surface tension*area energy for atom 8: 1.409964798071E-01 642s Surface tension*area energy for atom 9: 1.409521830808E-01 642s Surface tension*area energy for atom 10: 1.409521830808E-01 642s Surface tension*area energy for atom 11: 1.823253254433E-01 642s Surface tension*area energy for atom 12: 1.574305652637E-01 642s Surface tension*area energy for atom 13: 1.577849390741E-01 642s 642s Total surface tension energy: 1.64777 kJ/mol 642s 642s Total solvent accessible volume: 217.863 A^3 642s 642s Total pressure*volume energy: 52.1564 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.728858147814E+00 642s WCA energy for atom 1: -6.204037472587E+00 642s WCA energy for atom 2: -6.202937735018E+00 642s WCA energy for atom 3: -6.728762249931E+00 642s WCA energy for atom 4: -1.623549989062E+00 642s WCA energy for atom 5: -1.709092300778E+00 642s WCA energy for atom 6: -1.625196457114E+00 642s WCA energy for atom 7: -1.484289341167E+00 642s WCA energy for atom 8: -1.485410538626E+00 642s WCA energy for atom 9: -1.485593139015E+00 642s WCA energy for atom 10: -1.484878734279E+00 642s WCA energy for atom 11: -1.708585062695E+00 642s WCA energy for atom 12: -1.625094916482E+00 642s WCA energy for atom 13: -1.624416805392E+00 642s 642s Total WCA energy: -41.7207 kJ/mol 642s 642s Total non-polar energy = 1.208346456826E+01 kJ/mol 642s ---------------------------------------- 642s CALCULATION #3 (solvated-cyclohexane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 7.840324549863E-01 642s SASA for atom 1: 8.064333822716E-01 642s SASA for atom 2: 8.288343095569E-01 642s SASA for atom 3: 7.840324549863E-01 642s SASA for atom 4: 7.989664065098E-01 642s SASA for atom 5: 8.363012853187E-01 642s SASA for atom 6: 2.001169752764E+01 642s SASA for atom 7: 1.616048802948E+01 642s SASA for atom 8: 2.001169752764E+01 642s SASA for atom 9: 1.619175630687E+01 642s SASA for atom 10: 1.616048802948E+01 642s SASA for atom 11: 1.993352683418E+01 642s SASA for atom 12: 2.001169752764E+01 642s SASA for atom 13: 1.618133354774E+01 642s SASA for atom 14: 1.617091078861E+01 642s SASA for atom 15: 2.001690890721E+01 642s SASA for atom 16: 1.993873821374E+01 642s SASA for atom 17: 1.617091078861E+01 642s 642s Total solvent accessible surface area: 221.799 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 6.664275867383E-03 642s Surface tension*area energy for atom 1: 6.854683749309E-03 642s Surface tension*area energy for atom 2: 7.045091631234E-03 642s Surface tension*area energy for atom 3: 6.664275867383E-03 642s Surface tension*area energy for atom 4: 6.791214455333E-03 642s Surface tension*area energy for atom 5: 7.108560925209E-03 642s Surface tension*area energy for atom 6: 1.700994289850E-01 642s Surface tension*area energy for atom 7: 1.373641482506E-01 642s Surface tension*area energy for atom 8: 1.700994289850E-01 642s Surface tension*area energy for atom 9: 1.376299286084E-01 642s Surface tension*area energy for atom 10: 1.373641482506E-01 642s Surface tension*area energy for atom 11: 1.694349780905E-01 642s Surface tension*area energy for atom 12: 1.700994289850E-01 642s Surface tension*area energy for atom 13: 1.375413351558E-01 642s Surface tension*area energy for atom 14: 1.374527417032E-01 642s Surface tension*area energy for atom 15: 1.701437257113E-01 642s Surface tension*area energy for atom 16: 1.694792748168E-01 642s Surface tension*area energy for atom 17: 1.374527417032E-01 642s 642s Total surface tension energy: 1.88529 kJ/mol 642s 642s Total solvent accessible volume: 267.435 A^3 642s 642s Total pressure*volume energy: 64.0239 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -5.793234697241E+00 642s WCA energy for atom 1: -5.784370526583E+00 642s WCA energy for atom 2: -5.791799130412E+00 642s WCA energy for atom 3: -5.788504399087E+00 642s WCA energy for atom 4: -5.797319672490E+00 642s WCA energy for atom 5: -5.787358035342E+00 642s WCA energy for atom 6: -1.523887929614E+00 642s WCA energy for atom 7: -1.413678912317E+00 642s WCA energy for atom 8: -1.521751604392E+00 642s WCA energy for atom 9: -1.414741802525E+00 642s WCA energy for atom 10: -1.413367854344E+00 642s WCA energy for atom 11: -1.523407238081E+00 642s WCA energy for atom 12: -1.523000623583E+00 642s WCA energy for atom 13: -1.413922068538E+00 642s WCA energy for atom 14: -1.416316744211E+00 642s WCA energy for atom 15: -1.524577474659E+00 642s WCA energy for atom 16: -1.523300410052E+00 642s WCA energy for atom 17: -1.414522566061E+00 642s 642s Total WCA energy: -52.3691 kJ/mol 642s 642s Total non-polar energy = 1.354016672221E+01 kJ/mol 642s ---------------------------------------- 642s CALCULATION #4 (solvated-cyclopentane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 9.490526193215E+00 642s SASA for atom 1: 9.512927120500E+00 642s SASA for atom 2: 2.299828534626E+00 642s SASA for atom 3: 1.919012770776E+00 642s SASA for atom 4: 2.307295510388E+00 642s SASA for atom 5: 2.325838699632E+01 642s SASA for atom 6: 2.325838699632E+01 642s SASA for atom 7: 2.045987617019E+01 642s SASA for atom 8: 2.067875411190E+01 642s SASA for atom 9: 2.028790064456E+01 642s SASA for atom 10: 1.897463299431E+01 642s SASA for atom 11: 2.048593306801E+01 642s SASA for atom 12: 2.070481100972E+01 642s 642s Total solvent accessible surface area: 193.638 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 8.066947264233E-02 642s Surface tension*area energy for atom 1: 8.085988052425E-02 642s Surface tension*area energy for atom 2: 1.954854254432E-02 642s Surface tension*area energy for atom 3: 1.631160855160E-02 642s Surface tension*area energy for atom 4: 1.961201183830E-02 642s Surface tension*area energy for atom 5: 1.976962894687E-01 642s Surface tension*area energy for atom 6: 1.976962894687E-01 642s Surface tension*area energy for atom 7: 1.739089474466E-01 642s Surface tension*area energy for atom 8: 1.757694099511E-01 642s Surface tension*area energy for atom 9: 1.724471554788E-01 642s Surface tension*area energy for atom 10: 1.612843804516E-01 642s Surface tension*area energy for atom 11: 1.741304310781E-01 642s Surface tension*area energy for atom 12: 1.759908935826E-01 642s 642s Total surface tension energy: 1.64593 kJ/mol 642s 642s Total solvent accessible volume: 217.998 A^3 642s 642s Total pressure*volume energy: 52.1887 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.343496616804E+00 642s WCA energy for atom 1: -6.327869601807E+00 642s WCA energy for atom 2: -6.334858040579E+00 642s WCA energy for atom 3: -6.296075406417E+00 642s WCA energy for atom 4: -6.345600816761E+00 642s WCA energy for atom 5: -1.663697465126E+00 642s WCA energy for atom 6: -1.662444032853E+00 642s WCA energy for atom 7: -1.572325104493E+00 642s WCA energy for atom 8: -1.604626551065E+00 642s WCA energy for atom 9: -1.586431484963E+00 642s WCA energy for atom 10: -1.554291291374E+00 642s WCA energy for atom 11: -1.574315220751E+00 642s WCA energy for atom 12: -1.604941679892E+00 642s 642s Total WCA energy: -44.471 kJ/mol 642s 642s Total non-polar energy = 9.363673200142E+00 kJ/mol 642s ---------------------------------------- 642s CALCULATION #5 (solvated-ethane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 5.995981536705E+00 642s SASA for atom 1: 5.966113633657E+00 642s SASA for atom 2: 2.121552620704E+01 642s SASA for atom 3: 2.124158310486E+01 642s SASA for atom 4: 2.125200586399E+01 642s SASA for atom 5: 2.123116034573E+01 642s SASA for atom 6: 2.125200586399E+01 642s SASA for atom 7: 2.127285138225E+01 642s 642s Total solvent accessible surface area: 139.427 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 5.096584306199E-02 642s Surface tension*area energy for atom 1: 5.071196588609E-02 642s Surface tension*area energy for atom 2: 1.803319727598E-01 642s Surface tension*area energy for atom 3: 1.805534563913E-01 642s Surface tension*area energy for atom 4: 1.806420498439E-01 642s Surface tension*area energy for atom 5: 1.804648629387E-01 642s Surface tension*area energy for atom 6: 1.806420498439E-01 642s Surface tension*area energy for atom 7: 1.808192367491E-01 642s 642s Total surface tension energy: 1.18513 kJ/mol 642s 642s Total solvent accessible volume: 140.346 A^3 642s 642s Total pressure*volume energy: 33.5988 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -7.360066353115E+00 642s WCA energy for atom 1: -7.355483516201E+00 642s WCA energy for atom 2: -1.776106201066E+00 642s WCA energy for atom 3: -1.773973940651E+00 642s WCA energy for atom 4: -1.775401936843E+00 642s WCA energy for atom 5: -1.773464835521E+00 642s WCA energy for atom 6: -1.774382856097E+00 642s WCA energy for atom 7: -1.772366599434E+00 642s 642s Total WCA energy: -25.3612 kJ/mol 642s 642s Total non-polar energy = 9.422717598546E+00 kJ/mol 642s ---------------------------------------- 642s CALCULATION #6 (solvated-hexane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 4.405515699447E+00 642s SASA for atom 1: 8.213673337951E-01 642s SASA for atom 2: 3.285469335181E-01 642s SASA for atom 3: 2.986790304710E-01 642s SASA for atom 4: 1.855251124959E+01 642s SASA for atom 5: 2.147609518526E+01 642s SASA for atom 6: 1.852645435176E+01 642s SASA for atom 7: 1.655655287639E+01 642s SASA for atom 8: 1.655134149682E+01 642s SASA for atom 9: 1.360170066332E+01 642s SASA for atom 10: 1.357043238593E+01 642s SASA for atom 11: 1.381536722546E+01 642s SASA for atom 12: 1.384142412329E+01 642s SASA for atom 13: 7.765654792245E-01 642s SASA for atom 14: 1.684839013200E+01 642s SASA for atom 15: 1.682233323417E+01 642s SASA for atom 16: 4.166572475070E+00 642s SASA for atom 17: 2.179398933870E+01 642s SASA for atom 18: 1.877660057086E+01 642s SASA for atom 19: 1.876096643216E+01 642s 642s Total solvent accessible surface area: 250.291 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 3.744688344530E-02 642s Surface tension*area energy for atom 1: 6.981622337259E-03 642s Surface tension*area energy for atom 2: 2.792648934903E-03 642s Surface tension*area energy for atom 3: 2.538771759003E-03 642s Surface tension*area energy for atom 4: 1.576963456215E-01 642s Surface tension*area energy for atom 5: 1.825468090747E-01 642s Surface tension*area energy for atom 6: 1.574748619900E-01 642s Surface tension*area energy for atom 7: 1.407306994493E-01 642s Surface tension*area energy for atom 8: 1.406864027230E-01 642s Surface tension*area energy for atom 9: 1.156144556382E-01 642s Surface tension*area energy for atom 10: 1.153486752804E-01 642s Surface tension*area energy for atom 11: 1.174306214164E-01 642s Surface tension*area energy for atom 12: 1.176521050479E-01 642s Surface tension*area energy for atom 13: 6.600806573408E-03 642s Surface tension*area energy for atom 14: 1.432113161220E-01 642s Surface tension*area energy for atom 15: 1.429898324905E-01 642s Surface tension*area energy for atom 16: 3.541586603809E-02 642s Surface tension*area energy for atom 17: 1.852489093789E-01 642s Surface tension*area energy for atom 18: 1.596011048523E-01 642s Surface tension*area energy for atom 19: 1.594682146734E-01 642s 642s Total surface tension energy: 2.12748 kJ/mol 642s 642s Total solvent accessible volume: 298.053 A^3 642s 642s Total pressure*volume energy: 71.3539 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.635406071935E+00 642s WCA energy for atom 1: -5.957247427848E+00 642s WCA energy for atom 2: -5.524801144538E+00 642s WCA energy for atom 3: -5.522294168859E+00 642s WCA energy for atom 4: -1.605314409440E+00 642s WCA energy for atom 5: -1.701051761776E+00 642s WCA energy for atom 6: -1.606669162773E+00 642s WCA energy for atom 7: -1.442505934938E+00 642s WCA energy for atom 8: -1.443059002759E+00 642s WCA energy for atom 9: -1.328947132810E+00 642s WCA energy for atom 10: -1.328906972440E+00 642s WCA energy for atom 11: -1.331566344214E+00 642s WCA energy for atom 12: -1.328041776815E+00 642s WCA energy for atom 13: -5.937562025661E+00 642s WCA energy for atom 14: -1.442277774427E+00 642s WCA energy for atom 15: -1.442777091510E+00 642s WCA energy for atom 16: -6.602262542378E+00 642s WCA energy for atom 17: -1.698172146664E+00 642s WCA energy for atom 18: -1.600970858835E+00 642s WCA energy for atom 19: -1.600841970217E+00 642s 642s Total WCA energy: -57.0807 kJ/mol 642s 642s Total non-polar energy = 1.640068943201E+01 kJ/mol 642s ---------------------------------------- 642s CALCULATION #7 (solvated-isobutane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 3.464676753463E+00 642s SASA for atom 1: 1.984493338158E+01 642s SASA for atom 2: 1.778643845361E+01 642s SASA for atom 3: 1.671289426332E+01 642s SASA for atom 4: 0.000000000000E+00 642s SASA for atom 5: 3.531879535319E+00 642s SASA for atom 6: 1.673895116114E+01 642s SASA for atom 7: 1.793756846098E+01 642s SASA for atom 8: 1.973549441072E+01 642s SASA for atom 9: 1.710895911022E+01 642s SASA for atom 10: 4.599657069253E+00 642s SASA for atom 11: 1.937069784121E+01 642s SASA for atom 12: 1.654613011726E+01 642s SASA for atom 13: 1.936548646165E+01 642s 642s Total solvent accessible surface area: 192.744 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 2.944975240444E-02 642s Surface tension*area energy for atom 1: 1.686819337434E-01 642s Surface tension*area energy for atom 2: 1.511847268556E-01 642s Surface tension*area energy for atom 3: 1.420596012382E-01 642s Surface tension*area energy for atom 4: 0.000000000000E+00 642s Surface tension*area energy for atom 5: 3.002097605021E-02 642s Surface tension*area energy for atom 6: 1.422810848697E-01 642s Surface tension*area energy for atom 7: 1.524693319183E-01 642s Surface tension*area energy for atom 8: 1.677517024912E-01 642s Surface tension*area energy for atom 9: 1.454261524369E-01 642s Surface tension*area energy for atom 10: 3.909708508865E-02 642s Surface tension*area energy for atom 11: 1.646509316503E-01 642s Surface tension*area energy for atom 12: 1.406421059967E-01 642s Surface tension*area energy for atom 13: 1.646066349240E-01 642s 642s Total surface tension energy: 1.63832 kJ/mol 642s 642s Total solvent accessible volume: 218.943 A^3 642s 642s Total pressure*volume energy: 52.415 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.381016335247E+00 642s WCA energy for atom 1: -1.612317964554E+00 642s WCA energy for atom 2: -1.588013719598E+00 642s WCA energy for atom 3: -1.532162371190E+00 642s WCA energy for atom 4: -5.987950445279E+00 642s WCA energy for atom 5: -6.393089030861E+00 642s WCA energy for atom 6: -1.533454887042E+00 642s WCA energy for atom 7: -1.587650918485E+00 642s WCA energy for atom 8: -1.614083521570E+00 642s WCA energy for atom 9: -1.442402031577E+00 642s WCA energy for atom 10: -6.408813541353E+00 642s WCA energy for atom 11: -1.605830214390E+00 642s WCA energy for atom 12: -1.529385873788E+00 642s WCA energy for atom 13: -1.605662490385E+00 642s 642s Total WCA energy: -40.8218 kJ/mol 642s 642s Total non-polar energy = 1.323144287435E+01 kJ/mol 642s ---------------------------------------- 642s CALCULATION #8 (solvated-methane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 1.231304303117E+01 642s SASA for atom 1: 2.323233009850E+01 642s SASA for atom 2: 2.345641941977E+01 642s SASA for atom 3: 2.377431357320E+01 642s SASA for atom 4: 2.264344420771E+01 642s 642s Total solvent accessible surface area: 105.42 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 1.046608657649E-01 642s Surface tension*area energy for atom 1: 1.974748058372E-01 642s Surface tension*area energy for atom 2: 1.993795650680E-01 642s Surface tension*area energy for atom 3: 2.020816653722E-01 642s Surface tension*area energy for atom 4: 1.924692757655E-01 642s 642s Total surface tension energy: 0.896066 kJ/mol 642s 642s Total solvent accessible volume: 95.985 A^3 642s 642s Total pressure*volume energy: 22.9788 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -8.133807570805E+00 642s WCA energy for atom 1: -1.962181541765E+00 642s WCA energy for atom 2: -1.964078319162E+00 642s WCA energy for atom 3: -1.963015006647E+00 642s WCA energy for atom 4: -1.957425549100E+00 642s 642s Total WCA energy: -15.9805 kJ/mol 642s 642s Total non-polar energy = 7.894367190329E+00 kJ/mol 642s ---------------------------------------- 642s CALCULATION #9 (solvated-neopentane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 2.441701074100E+00 642s SASA for atom 1: 1.663993494942E+01 642s SASA for atom 2: 1.715586152630E+01 642s SASA for atom 3: 1.645753666466E+01 642s SASA for atom 4: 0.000000000000E+00 642s SASA for atom 5: 2.389432243768E+00 642s SASA for atom 6: 1.638457735076E+01 642s SASA for atom 7: 1.667641460637E+01 642s SASA for atom 8: 1.721839808108E+01 642s SASA for atom 9: 2.419300146815E+00 642s SASA for atom 10: 1.640021148945E+01 642s SASA for atom 11: 1.666599184724E+01 642s SASA for atom 12: 1.719234118325E+01 642s SASA for atom 13: 2.449168049862E+00 642s SASA for atom 14: 1.723403221977E+01 642s SASA for atom 15: 1.639500010989E+01 642s SASA for atom 16: 1.663472356985E+01 642s 642s Total solvent accessible surface area: 210.755 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 2.075445912985E-02 642s Surface tension*area energy for atom 1: 1.414394470700E-01 642s Surface tension*area energy for atom 2: 1.458248229736E-01 642s Surface tension*area energy for atom 3: 1.398890616496E-01 642s Surface tension*area energy for atom 4: 0.000000000000E+00 642s Surface tension*area energy for atom 5: 2.031017407203E-02 642s Surface tension*area energy for atom 6: 1.392689074814E-01 642s Surface tension*area energy for atom 7: 1.417495241541E-01 642s Surface tension*area energy for atom 8: 1.463563836891E-01 642s Surface tension*area energy for atom 9: 2.056405124793E-02 642s Surface tension*area energy for atom 10: 1.394017976603E-01 642s Surface tension*area energy for atom 11: 1.416609307015E-01 642s Surface tension*area energy for atom 12: 1.461349000577E-01 642s Surface tension*area energy for atom 13: 2.081792842383E-02 642s Surface tension*area energy for atom 14: 1.464892738680E-01 642s Surface tension*area energy for atom 15: 1.393575009340E-01 642s Surface tension*area energy for atom 16: 1.413951503437E-01 642s 642s Total surface tension energy: 1.79141 kJ/mol 642s 642s Total solvent accessible volume: 251.127 A^3 642s 642s Total pressure*volume energy: 60.1198 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.011082520236E+00 642s WCA energy for atom 1: -1.497367782613E+00 642s WCA energy for atom 2: -1.498546483218E+00 642s WCA energy for atom 3: -1.492562171495E+00 642s WCA energy for atom 4: -5.447325863939E+00 642s WCA energy for atom 5: -6.004516149175E+00 642s WCA energy for atom 6: -1.492776531092E+00 642s WCA energy for atom 7: -1.496078170066E+00 642s WCA energy for atom 8: -1.501529655270E+00 642s WCA energy for atom 9: -5.996267554365E+00 642s WCA energy for atom 10: -1.492194267752E+00 642s WCA energy for atom 11: -1.496027211216E+00 642s WCA energy for atom 12: -1.500561393960E+00 642s WCA energy for atom 13: -6.000218612907E+00 642s WCA energy for atom 14: -1.500859921426E+00 642s WCA energy for atom 15: -1.492908499790E+00 642s WCA energy for atom 16: -1.494057174414E+00 642s 642s Total WCA energy: -47.4149 kJ/mol 642s 642s Total non-polar energy = 1.449633815052E+01 kJ/mol 642s ---------------------------------------- 642s CALCULATION #10 (solvated-pentane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 4.405515699447E+00 642s SASA for atom 1: 8.213673337951E-01 642s SASA for atom 2: 3.285469335181E-01 642s SASA for atom 3: 7.466975761774E-01 642s SASA for atom 4: 1.855251124959E+01 642s SASA for atom 5: 2.147609518526E+01 642s SASA for atom 6: 1.852645435176E+01 642s SASA for atom 7: 1.655655287639E+01 642s SASA for atom 8: 1.655134149682E+01 642s SASA for atom 9: 1.360170066332E+01 642s SASA for atom 10: 1.357043238593E+01 642s SASA for atom 11: 1.685881289113E+01 642s SASA for atom 12: 1.687444702982E+01 642s SASA for atom 13: 4.196440378117E+00 642s SASA for atom 14: 1.881308022781E+01 642s SASA for atom 15: 1.882350298694E+01 642s SASA for atom 16: 2.182004623652E+01 642s 642s Total solvent accessible surface area: 222.524 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 3.744688344530E-02 642s Surface tension*area energy for atom 1: 6.981622337259E-03 642s Surface tension*area energy for atom 2: 2.792648934903E-03 642s Surface tension*area energy for atom 3: 6.346929397508E-03 642s Surface tension*area energy for atom 4: 1.576963456215E-01 642s Surface tension*area energy for atom 5: 1.825468090747E-01 642s Surface tension*area energy for atom 6: 1.574748619900E-01 642s Surface tension*area energy for atom 7: 1.407306994493E-01 642s Surface tension*area energy for atom 8: 1.406864027230E-01 642s Surface tension*area energy for atom 9: 1.156144556382E-01 642s Surface tension*area energy for atom 10: 1.153486752804E-01 642s Surface tension*area energy for atom 11: 1.432999095746E-01 642s Surface tension*area energy for atom 12: 1.434327997535E-01 642s Surface tension*area energy for atom 13: 3.566974321399E-02 642s Surface tension*area energy for atom 14: 1.599111819364E-01 642s Surface tension*area energy for atom 15: 1.599997753890E-01 642s Surface tension*area energy for atom 16: 1.854703930104E-01 642s 642s Total surface tension energy: 1.89145 kJ/mol 642s 642s Total solvent accessible volume: 258.93 A^3 642s 642s Total pressure*volume energy: 61.9878 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.655804319869E+00 642s WCA energy for atom 1: -6.027315962813E+00 642s WCA energy for atom 2: -5.696430965386E+00 642s WCA energy for atom 3: -6.016749084714E+00 642s WCA energy for atom 4: -1.608595384643E+00 642s WCA energy for atom 5: -1.703300955380E+00 642s WCA energy for atom 6: -1.609931495887E+00 642s WCA energy for atom 7: -1.457107525189E+00 642s WCA energy for atom 8: -1.457741620594E+00 642s WCA energy for atom 9: -1.354235498709E+00 642s WCA energy for atom 10: -1.354106470090E+00 642s WCA energy for atom 11: -1.456736412636E+00 642s WCA energy for atom 12: -1.455995435596E+00 642s WCA energy for atom 13: -6.633650611186E+00 642s WCA energy for atom 14: -1.605996088477E+00 642s WCA energy for atom 15: -1.606549890103E+00 642s WCA energy for atom 16: -1.700042300035E+00 642s 642s Total WCA energy: -49.4003 kJ/mol 642s 642s Total non-polar energy = 1.447900211546E+01 kJ/mol 642s ---------------------------------------- 642s CALCULATION #11 (solvated-propane): APOLAR 642s 642s Solvent Accessible Surface Area (SASA) for each atom: 642s SASA for atom 0: 3.173464698754E+00 642s SASA for atom 1: 1.931858404557E+01 642s SASA for atom 2: 2.014198201675E+01 642s SASA for atom 3: 2.149694070352E+01 642s SASA for atom 4: 1.904078819252E+00 642s SASA for atom 5: 2.067354273233E+01 642s SASA for atom 6: 1.937590922077E+01 642s SASA for atom 7: 3.098794941136E+00 642s SASA for atom 8: 1.942802301642E+01 642s SASA for atom 9: 1.973028303116E+01 642s SASA for atom 10: 2.204934693736E+01 642s 642s Total solvent accessible surface area: 170.391 A^2 642s 642s Surface tension*area energies (gamma * SASA) for each atom: 642s Surface tension*area energy for atom 0: 2.697444993941E-02 642s Surface tension*area energy for atom 1: 1.642079643873E-01 642s Surface tension*area energy for atom 2: 1.712068471424E-01 642s Surface tension*area energy for atom 3: 1.827239959799E-01 642s Surface tension*area energy for atom 4: 1.618466996365E-02 642s Surface tension*area energy for atom 5: 1.757251132248E-01 642s Surface tension*area energy for atom 6: 1.646952283766E-01 642s Surface tension*area energy for atom 7: 2.633975699966E-02 642s Surface tension*area energy for atom 8: 1.651381956396E-01 642s Surface tension*area energy for atom 9: 1.677074057649E-01 642s Surface tension*area energy for atom 10: 1.874194489675E-01 642s 642s Total surface tension energy: 1.44832 kJ/mol 642s 642s Total solvent accessible volume: 183.573 A^3 642s 642s Total pressure*volume energy: 43.9474 kJ/mol 642s 642s WCA dispersion Energies for each atom: 642s WCA energy for atom 0: -6.818670105515E+00 642s WCA energy for atom 1: -1.641297645338E+00 642s WCA energy for atom 2: -1.649584120441E+00 642s WCA energy for atom 3: -1.711408141255E+00 642s WCA energy for atom 4: -6.624720142882E+00 642s WCA energy for atom 5: -1.610117050515E+00 642s WCA energy for atom 6: -1.596858009746E+00 642s WCA energy for atom 7: -6.816460624835E+00 642s WCA energy for atom 8: -1.642782751806E+00 642s WCA energy for atom 9: -1.645779566650E+00 642s WCA energy for atom 10: -1.714436154542E+00 642s 642s Total WCA energy: -33.4721 kJ/mol 642s 642s Total non-polar energy = 1.192358496286E+01 kJ/mol 642s ---------------------------------------- 642s PRINT STATEMENTS 642s 642s print APOL energy 1 (solvated-2-methylbutane) end 642s Global net APOL energy = 1.439739455792E+01 kJ/mol 642s 642s print APOL energy 2 (solvated-butane) end 642s Global net APOL energy = 1.208346456826E+01 kJ/mol 642s 642s print APOL energy 3 (solvated-cyclohexane) end 642s Global net APOL energy = 1.354016672221E+01 kJ/mol 642s 642s print APOL energy 4 (solvated-cyclopentane) end 642s Global net APOL energy = 9.363673200142E+00 kJ/mol 642s 642s print APOL energy 5 (solvated-ethane) end 642s Global net APOL energy = 9.422717598546E+00 kJ/mol 642s 642s print APOL energy 6 (solvated-hexane) end 642s Global net APOL energy = 1.640068943201E+01 kJ/mol 642s 642s print APOL energy 7 (solvated-isobutane) end 642s Global net APOL energy = 1.323144287435E+01 kJ/mol 642s 642s print APOL energy 8 (solvated-methane) end 642s Global net APOL energy = 7.894367190329E+00 kJ/mol 642s 642s print APOL energy 9 (solvated-neopentane) end 642s Global net APOL energy = 1.449633815052E+01 kJ/mol 642s 642s print APOL energy 10 (solvated-pentane) end 642s Global net APOL energy = 1.447900211546E+01 kJ/mol 642s 642s print APOL energy 11 (solvated-propane) end 642s Global net APOL energy = 1.192358496286E+01 kJ/mol 642s ---------------------------------------- 642s CLEANING UP AND SHUTTING DOWN... 642s Destroying force arrays. 642s No energy arrays to destroy. 642s Destroying multigrid structures. 642s Destroying finite element structures. 642s Destroying 11 molecules 642s Final memory usage: 0.001 MB total, 2.204 MB high water 642s 642s 642s Thanks for using APBS! 642s 660s Checking for intermediate energies in input file alkanes.out 660s EXPECTED COMPUTED: 11 660s EXPECTED EXPECTED: 11 660s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 660s 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'] 660s COMPUTED RESULT 14.39739455792 660s COMPUTED RESULT 12.08346456826 660s COMPUTED RESULT 13.54016672221 660s COMPUTED RESULT 9.363673200142 660s COMPUTED RESULT 9.422717598546 660s COMPUTED RESULT 16.40068943201 660s COMPUTED RESULT 13.23144287435 660s COMPUTED RESULT 7.894367190329 660s COMPUTED RESULT 14.49633815052 660s COMPUTED RESULT 14.47900211546 660s COMPUTED RESULT 11.92358496286 660s Running tests for FKBP section 660s BINARY: /usr/bin/apbs 660s INPUT: 1d7h-dmso-mol.in 660s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 660s asc_getToken: Error occurred (bailing out). 660s Vio_scanf: Format problem with input. 660s 660s 660s ---------------------------------------------------------------------- 660s APBS -- Adaptive Poisson-Boltzmann Solver 660s Version APBS 3.4.1 660s 660s Nathan A. Baker (nathan.baker@pnnl.gov) 660s Pacific Northwest National Laboratory 660s 660s Additional contributing authors listed in the code documentation. 660s 660s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 660s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 660s Northwest Division for the U.S. Department of Energy. 660s 660s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 660s Portions Copyright (c) 2002-2020, Nathan A. Baker. 660s Portions Copyright (c) 1999-2002, The Regents of the University of California. 660s Portions Copyright (c) 1995, Michael Holst. 660s All rights reserved. 660s 660s Redistribution and use in source and binary forms, with or without 660s modification, are permitted provided that the following conditions are met: 660s 660s * Redistributions of source code must retain the above copyright notice, this 660s list of conditions and the following disclaimer. 660s 660s * Redistributions in binary form must reproduce the above copyright notice, 660s this list of conditions and the following disclaimer in the documentation 660s and/or other materials provided with the distribution. 660s 660s * Neither the name of the developer nor the names of its contributors may be 660s used to endorse or promote products derived from this software without 660s specific prior written permission. 660s 660s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 660s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 660s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 660s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 660s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 660s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 660s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 660s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 660s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 660s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 660s ---------------------------------------------------------------------- 660s APBS uses FETK (the Finite Element ToolKit) to solve the 660s Poisson-Boltzmann equation numerically. FETK is a portable collection 660s of finite element modeling class libraries developed by the Michael Holst 660s research group and written in an object-oriented form of C. FEtk is 660s designed to solve general coupled systems of nonlinear partial differential 660s equations using adaptive finite element methods, inexact Newton methods, 660s and algebraic multilevel methods. More information about FEtk may be found 660s at . 660s ---------------------------------------------------------------------- 660s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 660s Aqua is a modified form of the Holst group PMG library 660s which has been modified by Patrice Koehl 660s for improved efficiency and 660s memory usage when solving the Poisson-Boltzmann equation. 660s ---------------------------------------------------------------------- 660s Please cite your use of APBS as: 660s 660s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 660s nanosystems: application to microtubules and the ribosome. Proc. 660s Natl. Acad. Sci. USA 98, 10037-10041 2001. 660s 660s 660s This executable compiled on Jan 3 2025 at 11:01:42 660s 660s Parsing input file 1d7h-dmso-mol.in... 660s rank 0 size 1... 660s Parsed input file. 660s Got paths for 3 molecules 660s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 660s asc_getToken: Error occurred (bailing out). 660s Vio_scanf: Format problem with input. 660s 1673 atoms 660s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 660s Net charge 9.91e-01 e 660s Reading PQR-format atom data from dmso-min.pqr. 660s asc_getToken: Error occurred (bailing out). 660s Vio_scanf: Format problem with input. 660s 10 atoms 660s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 660s Net charge 2.78e-17 e 660s Reading PQR-format atom data from 1d7h-min.pqr. 660s 1663 atoms 660s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 660s Net charge 9.91e-01 e 660s Preparing to run 12 PBE calculations. 660s ---------------------------------------- 660s CALCULATION #1 (complex-solv-coarse): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 30.4176 A 660s Current memory usage: 102.625 MB total, 102.625 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 1.500 x 1.500 x 1.500 660s Grid lengths: 96.000 x 96.000 x 96.000 660s Grid center: (25.875, 18.349, 19.112) 660s Multigrid levels: 5 660s Molecule ID: 1 660s Linearized traditional PBE 660s Multiple Debye-Huckel sphere boundary conditions 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 78.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 1.060899690259E+04 kJ/mol 660s Calculating forces... 660s [focusFillBound()]: WARNING: 660s Unusually large potential values 660s detected on the focusing boundary! 660s Convergence not guaranteed for NPBE/NRPBE calculations! 660s 660s ---------------------------------------- 660s CALCULATION #2 (complex-solv-fine): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 30.4176 A 660s Current memory usage: 102.625 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 0.225 x 0.225 x 0.225 660s Grid lengths: 14.400 x 14.400 x 14.400 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 1 660s Linearized traditional PBE 660s Boundary conditions from focusing 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 78.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 4.276523673491E+04 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s CALCULATION #3 (complex-ref-coarse): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 4.87072 A 660s Current memory usage: 102.625 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 1.500 x 1.500 x 1.500 660s Grid lengths: 96.000 x 96.000 x 96.000 660s Grid center: (25.875, 18.349, 19.112) 660s Multigrid levels: 5 660s Molecule ID: 1 660s Linearized traditional PBE 660s Multiple Debye-Huckel sphere boundary conditions 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 2.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 1.399234956777E+04 kJ/mol 660s Calculating forces... 660s [focusFillBound()]: WARNING: 660s Unusually large potential values 660s detected on the focusing boundary! 660s Convergence not guaranteed for NPBE/NRPBE calculations! 660s 660s ---------------------------------------- 660s CALCULATION #4 (complex-ref-fine): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 4.87072 A 660s Current memory usage: 102.625 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 0.225 x 0.225 x 0.225 660s Grid lengths: 14.400 x 14.400 x 14.400 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 1 660s Linearized traditional PBE 660s Boundary conditions from focusing 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 2.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 4.610066575192E+04 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 30.4176 A 660s Current memory usage: 62.396 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 1.500 x 1.500 x 1.500 660s Grid lengths: 96.000 x 96.000 x 96.000 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 2 660s Linearized traditional PBE 660s Multiple Debye-Huckel sphere boundary conditions 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 78.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 3.961107503213E+01 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s CALCULATION #6 (dmso-solv-fine): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 30.4176 A 660s Current memory usage: 62.396 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 0.225 x 0.225 x 0.225 660s Grid lengths: 14.400 x 14.400 x 14.400 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 2 660s Linearized traditional PBE 660s Boundary conditions from focusing 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 78.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 7.121048606059E+02 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 4.87072 A 660s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 660s *** PASSED *** 660s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 660s *** PASSED *** 660s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 660s *** PASSED *** 660s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 660s *** PASSED *** 660s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 660s *** PASSED *** 660s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 660s *** PASSED *** 660s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 660s *** PASSED *** 660s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 660s *** PASSED *** 660s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 660s *** PASSED *** 660s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 660s *** PASSED *** 660s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 660s *** PASSED *** 660s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 660s *** PASSED *** 660s Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) 660s *** PASSED *** 660s Elapsed time: 17.442175 seconds 660s -------------------------------------------------------------------------------- 660s -------------------------------------------------------------------------------- 660s Testing input file 1d7h-dmso-smol.in 660s 660s Current memory usage: 62.396 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 1.500 x 1.500 x 1.500 660s Grid lengths: 96.000 x 96.000 x 96.000 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 2 660s Linearized traditional PBE 660s Multiple Debye-Huckel sphere boundary conditions 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 2.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 6.751571424823E+01 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s CALCULATION #8 (dmso-ref-fine): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 4.87072 A 660s Current memory usage: 62.396 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 0.225 x 0.225 x 0.225 660s Grid lengths: 14.400 x 14.400 x 14.400 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 2 660s Linearized traditional PBE 660s Boundary conditions from focusing 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 2.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 7.339101343121E+02 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 30.4176 A 660s Current memory usage: 102.404 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 1.500 x 1.500 x 1.500 660s Grid lengths: 96.000 x 96.000 x 96.000 660s Grid center: (25.875, 18.349, 19.112) 660s Multigrid levels: 5 660s Molecule ID: 3 660s Linearized traditional PBE 660s Multiple Debye-Huckel sphere boundary conditions 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 78.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 1.058410584089E+04 kJ/mol 660s Calculating forces... 660s [focusFillBound()]: WARNING: 660s Unusually large potential values 660s detected on the focusing boundary! 660s Convergence not guaranteed for NPBE/NRPBE calculations! 660s 660s ---------------------------------------- 660s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 30.4176 A 660s Current memory usage: 102.404 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 0.225 x 0.225 x 0.225 660s Grid lengths: 14.400 x 14.400 x 14.400 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 3 660s Linearized traditional PBE 660s Boundary conditions from focusing 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 78.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 4.205385249581E+04 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 4.87072 A 660s Current memory usage: 102.404 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 1.500 x 1.500 x 1.500 660s Grid lengths: 96.000 x 96.000 x 96.000 660s Grid center: (25.875, 18.349, 19.112) 660s Multigrid levels: 5 660s Molecule ID: 3 660s Linearized traditional PBE 660s Multiple Debye-Huckel sphere boundary conditions 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 2.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 1.395961902233E+04 kJ/mol 660s Calculating forces... 660s [focusFillBound()]: WARNING: 660s Unusually large potential values 660s detected on the focusing boundary! 660s Convergence not guaranteed for NPBE/NRPBE calculations! 660s 660s ---------------------------------------- 660s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 660s Setting up problem... 660s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 660s Debye length: 4.87072 A 660s Current memory usage: 102.404 MB total, 182.834 MB high water 660s Using linear spline charge discretization. 660s Grid dimensions: 65 x 65 x 65 660s Grid spacings: 0.225 x 0.225 x 0.225 660s Grid lengths: 14.400 x 14.400 x 14.400 660s Grid center: (17.751, 17.770, 20.492) 660s Multigrid levels: 5 660s Molecule ID: 3 660s Linearized traditional PBE 660s Boundary conditions from focusing 660s 2 ion species (0.010 M ionic strength): 660s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 660s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 660s Solute dielectric: 2.000 660s Solvent dielectric: 2.000 660s Using "molecular" surface definition; no smoothing 660s Solvent probe radius: 0.000 A 660s Temperature: 300.000 K 660s Electrostatic energies will be calculated 660s Total electrostatic energy = 4.538248433997E+04 kJ/mol 660s Calculating forces... 660s ---------------------------------------- 660s PRINT STATEMENTS 660s 660s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 660s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 660s Global net ELEC energy = -3.335429017008E+03 kJ/mol 660s 660s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 660s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 660s Global net ELEC energy = -2.180527370616E+01 kJ/mol 660s 660s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 660s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 660s Global net ELEC energy = -3.328631844166E+03 kJ/mol 660s 660s 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 660s Local net energy (PE 0) = 1.500810086371E+01 kJ/mol 660s Global net ELEC energy = 1.500810086371E+01 kJ/mol 660s ---------------------------------------- 660s CLEANING UP AND SHUTTING DOWN... 660s Destroying force arrays. 660s No energy arrays to destroy. 660s Destroying multigrid structures. 660s Destroying finite element structures. 660s Destroying 3 molecules 660s Final memory usage: 0.001 MB total, 182.834 MB high water 660s 660s 660s Thanks for using APBS! 660s 676s Checking for intermediate energies in input file 1d7h-dmso-mol.out 676s EXPECTED COMPUTED: 16 676s EXPECTED EXPECTED: 16 676s 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] 676s 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'] 676s COMPUTED RESULT 10608.99690259 676s COMPUTED RESULT 42765.23673491 676s COMPUTED RESULT 13992.34956777 676s COMPUTED RESULT 46100.66575192 676s COMPUTED RESULT 39.61107503213 676s COMPUTED RESULT 712.1048606059 676s COMPUTED RESULT 67.51571424823 676s COMPUTED RESULT 733.9101343121 676s COMPUTED RESULT 10584.10584089 676s COMPUTED RESULT 42053.85249581 676s COMPUTED RESULT 13959.61902233 676s COMPUTED RESULT 45382.48433997 676s COMPUTED RESULT -3335.429017008 676s COMPUTED RESULT -21.80527370616 676s COMPUTED RESULT -3328.631844166 676s COMPUTED RESULT 15.00810086371 676s BINARY: /usr/bin/apbs 676s INPUT: 1d7h-dmso-smol.in 676s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.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 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 1d7h-dmso-smol.in... 676s rank 0 size 1... 676s Parsed input file. 676s Got paths for 3 molecules 676s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 676s asc_getToken: Error occurred (bailing out). 676s Vio_scanf: Format problem with input. 676s 1673 atoms 676s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 676s Net charge 9.91e-01 e 676s Reading PQR-format atom data from dmso-min.pqr. 676s asc_getToken: Error occurred (bailing out). 676s Vio_scanf: Format problem with input. 676s 10 atoms 676s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 676s Net charge 2.78e-17 e 676s Reading PQR-format atom data from 1d7h-min.pqr. 676s 1663 atoms 676s Centered at (2.587e+01, 1.835e+01, 1.911e+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: 102.625 MB total, 102.625 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: (25.875, 18.349, 19.112) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.074948704824E+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 #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: 102.625 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 4.289487256481E+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: 102.625 MB total, 182.834 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: (25.875, 18.349, 19.112) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.399234956777E+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:Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 676s *** PASSED *** 676s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 676s *** PASSED *** 676s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 676s *** PASSED *** 676s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 676s *** PASSED *** 676s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 676s *** PASSED *** 676s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 676s *** PASSED *** 676s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 676s *** PASSED *** 676s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 676s *** PASSED *** 676s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 676s *** PASSED *** 676s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 676s *** PASSED *** 676s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 676s *** PASSED *** 676s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 676s *** PASSED *** 676s Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) 676s *** PASSED *** 676s Elapsed time: 16.199526 seconds 676s -------------------------------------------------------------------------------- 676s -------------------------------------------------------------------------------- 676s Testing input file 1d7i-dss-mol.in 676s 676s 4.87072 A 676s Current memory usage: 102.625 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 4.610066575192E+04 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #5 (dmso-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: 62.396 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 3.719709905887E+01 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #6 (dmso-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: 62.396 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 7.125747080979E+02 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #7 (dmso-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: 62.396 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 6.751571424823E+01 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #8 (dmso-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: 62.396 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 7.339101343121E+02 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #9 (1d7h-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: 102.404 MB total, 182.834 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: (25.875, 18.349, 19.112) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.071654753674E+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 #10 (1d7h-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: 102.404 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 4.218178203716E+04 kJ/mol 676s Calculating forces... 676s ---------------------------------------- 676s CALCULATION #11 (1d7h-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: 102.404 MB total, 182.834 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: (25.875, 18.349, 19.112) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 1.395961902233E+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 (1d7h-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: 102.404 MB total, 182.834 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: (17.751, 17.770, 20.492) 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;harmonic average smoothing 676s Solvent probe radius: 0.000 A 676s Temperature: 300.000 K 676s Electrostatic energies will be calculated 676s Total electrostatic energy = 4.538248433997E+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) = -3.205793187109E+03 kJ/mol 676s Global net ELEC energy = -3.205793187109E+03 kJ/mol 676s 676s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 676s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 676s Global net ELEC energy = -2.133542621421E+01 kJ/mol 676s 676s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 676s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 676s Global net ELEC energy = -3.200702302816E+03 kJ/mol 676s 676s 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 676s Local net energy (PE 0) = 1.624454192073E+01 kJ/mol 676s Global net ELEC energy = 1.624454192073E+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, 182.834 MB high water 676s 676s 676s Thanks for using APBS! 676s 695s Checking for intermediate energies in input file 1d7h-dmso-smol.out 695s EXPECTED COMPUTED: 16 695s EXPECTED EXPECTED: 16 695s 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] 695s 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'] 695s COMPUTED RESULT 10749.48704824 695s COMPUTED RESULT 42894.87256481 695s COMPUTED RESULT 13992.34956777 695s COMPUTED RESULT 46100.66575192 695s COMPUTED RESULT 37.19709905887 695s COMPUTED RESULT 712.5747080979 695s COMPUTED RESULT 67.51571424823 695s COMPUTED RESULT 733.9101343121 695s COMPUTED RESULT 10716.54753674 695s COMPUTED RESULT 42181.78203716 695s COMPUTED RESULT 13959.61902233 695s COMPUTED RESULT 45382.48433997 695s COMPUTED RESULT -3205.793187109 695s COMPUTED RESULT -21.33542621421 695s COMPUTED RESULT -3200.702302816 695s COMPUTED RESULT 16.24454192073 695s BINARY: /usr/bin/apbs 695s INPUT: 1d7i-dss-mol.in 695s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 695s asc_getToken: Error occurred (bailing out). 695s Vio_scanf: Format problem with input. 695s 695s 695s ---------------------------------------------------------------------- 695s APBS -- Adaptive Poisson-Boltzmann Solver 695s Version APBS 3.4.1 695s 695s Nathan A. Baker (nathan.baker@pnnl.gov) 695s Pacific Northwest National Laboratory 695s 695s Additional contributing authors listed in the code documentation. 695s 695s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 695s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 695s Northwest Division for the U.S. Department of Energy. 695s 695s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 695s Portions Copyright (c) 2002-2020, Nathan A. Baker. 695s Portions Copyright (c) 1999-2002, The Regents of the University of California. 695s Portions Copyright (c) 1995, Michael Holst. 695s All rights reserved. 695s 695s Redistribution and use in source and binary forms, with or without 695s modification, are permitted provided that the following conditions are met: 695s 695s * Redistributions of source code must retain the above copyright notice, this 695s list of conditions and the following disclaimer. 695s 695s * Redistributions in binary form must reproduce the above copyright notice, 695s this list of conditions and the following disclaimer in the documentation 695s and/or other materials provided with the distribution. 695s 695s * Neither the name of the developer nor the names of its contributors may be 695s used to endorse or promote products derived from this software without 695s specific prior written permission. 695s 695s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 695s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 695s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 695s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 695s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 695s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 695s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 695s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 695s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 695s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 695s ---------------------------------------------------------------------- 695s APBS uses FETK (the Finite Element ToolKit) to solve the 695s Poisson-Boltzmann equation numerically. FETK is a portable collection 695s of finite element modeling class libraries developed by the Michael Holst 695s research group and written in an object-oriented form of C. FEtk is 695s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 695s *** PASSED *** 695s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 695s *** PASSED *** 695s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 695s *** PASSED *** 695s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 695s *** PASSED *** 695s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 695s *** PASSED *** 695s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 695s *** PASSED *** 695s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 695s *** PASSED *** 695s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 695s *** PASSED *** 695s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 695s *** PASSED *** 695s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 695s *** PASSED *** 695s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 695s *** PASSED *** 695s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 695s *** PASSED *** 695s Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) 695s *** PASSED *** 695s Elapsed time: 18.9437 seconds 695s -------------------------------------------------------------------------------- 695s -------------------------------------------------------------------------------- 695s Testing input file 1d7i-dss-smol.in 695s 695s designed to solve general coupled systems of nonlinear partial differential 695s equations using adaptive finite element methods, inexact Newton methods, 695s and algebraic multilevel methods. More information about FEtk may be found 695s at . 695s ---------------------------------------------------------------------- 695s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 695s Aqua is a modified form of the Holst group PMG library 695s which has been modified by Patrice Koehl 695s for improved efficiency and 695s memory usage when solving the Poisson-Boltzmann equation. 695s ---------------------------------------------------------------------- 695s Please cite your use of APBS as: 695s 695s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 695s nanosystems: application to microtubules and the ribosome. Proc. 695s Natl. Acad. Sci. USA 98, 10037-10041 2001. 695s 695s 695s This executable compiled on Jan 3 2025 at 11:01:42 695s 695s Parsing input file 1d7i-dss-mol.in... 695s rank 0 size 1... 695s Parsed input file. 695s Got paths for 3 molecules 695s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 695s asc_getToken: Error occurred (bailing out). 695s Vio_scanf: Format problem with input. 695s 1677 atoms 695s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 695s Net charge 9.91e-01 e 695s Reading PQR-format atom data from dss-min.pqr. 695s asc_getToken: Error occurred (bailing out). 695s Vio_scanf: Format problem with input. 695s 14 atoms 695s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 695s Net charge -8.33e-17 e 695s Reading PQR-format atom data from 1d7i-min.pqr. 695s 1663 atoms 695s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 695s Net charge 9.91e-01 e 695s Preparing to run 12 PBE calculations. 695s ---------------------------------------- 695s CALCULATION #1 (complex-solv-coarse): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 30.4176 A 695s Current memory usage: 102.869 MB total, 102.869 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 1.500 x 1.500 x 1.500 695s Grid lengths: 96.000 x 96.000 x 96.000 695s Grid center: (25.264, 18.988, 19.122) 695s Multigrid levels: 5 695s Molecule ID: 1 695s Linearized traditional PBE 695s Multiple Debye-Huckel sphere boundary conditions 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 78.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 9.160578033846E+03 kJ/mol 695s Calculating forces... 695s [focusFillBound()]: WARNING: 695s Unusually large potential values 695s detected on the focusing boundary! 695s Convergence not guaranteed for NPBE/NRPBE calculations! 695s 695s ---------------------------------------- 695s CALCULATION #2 (complex-solv-fine): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 30.4176 A 695s Current memory usage: 102.869 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 0.225 x 0.225 x 0.225 695s Grid lengths: 14.400 x 14.400 x 14.400 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 1 695s Linearized traditional PBE 695s Boundary conditions from focusing 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 78.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 3.955701871716E+04 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s CALCULATION #3 (complex-ref-coarse): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 4.87072 A 695s Current memory usage: 102.869 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 1.500 x 1.500 x 1.500 695s Grid lengths: 96.000 x 96.000 x 96.000 695s Grid center: (25.264, 18.988, 19.122) 695s Multigrid levels: 5 695s Molecule ID: 1 695s Linearized traditional PBE 695s Multiple Debye-Huckel sphere boundary conditions 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 2.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 1.264965939588E+04 kJ/mol 695s Calculating forces... 695s [focusFillBound()]: WARNING: 695s Unusually large potential values 695s detected on the focusing boundary! 695s Convergence not guaranteed for NPBE/NRPBE calculations! 695s 695s ---------------------------------------- 695s CALCULATION #4 (complex-ref-fine): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 4.87072 A 695s Current memory usage: 102.869 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 0.225 x 0.225 x 0.225 695s Grid lengths: 14.400 x 14.400 x 14.400 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 1 695s Linearized traditional PBE 695s Boundary conditions from focusing 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 2.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 4.301801664829E+04 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s CALCULATION #5 (dss-solv-coarse): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 30.4176 A 695s Current memory usage: 62.482 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 1.500 x 1.500 x 1.500 695s Grid lengths: 96.000 x 96.000 x 96.000 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 2 695s Linearized traditional PBE 695s Multiple Debye-Huckel sphere boundary conditions 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 78.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 9.431133325426E+01 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s CALCULATION #6 (dss-solv-fine): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 30.4176 A 695s Current memory usage: 62.482 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 0.225 x 0.225 x 0.225 695s Grid lengths: 14.400 x 14.400 x 14.400 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 2 695s Linearized traditional PBE 695s Boundary conditions from focusing 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 78.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 1.677348113184E+03 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s CALCULATION #7 (dss-ref-coarse): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 4.87072 A 695s Current memory usage: 62.482 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 1.500 x 1.500 x 1.500 695s Grid lengths: 96.000 x 96.000 x 96.000 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 2 695s Linearized traditional PBE 695s Multiple Debye-Huckel sphere boundary conditions 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 2.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 1.171079106781E+02 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s CALCULATION #8 (dss-ref-fine): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 4.87072 A 695s Current memory usage: 62.482 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 0.225 x 0.225 x 0.225 695s Grid lengths: 14.400 x 14.400 x 14.400 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 2 695s Linearized traditional PBE 695s Boundary conditions from focusing 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 2.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 1.697869784185E+03 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 30.4176 A 695s Current memory usage: 102.566 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 1.500 x 1.500 x 1.500 695s Grid lengths: 96.000 x 96.000 x 96.000 695s Grid center: (25.264, 18.988, 19.122) 695s Multigrid levels: 5 695s Molecule ID: 3 695s Linearized traditional PBE 695s Multiple Debye-Huckel sphere boundary conditions 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 78.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 9.040108332204E+03 kJ/mol 695s Calculating forces... 695s [focusFillBound()]: WARNING: 695s Unusually large potential values 695s detected on the focusing boundary! 695s Convergence not guaranteed for NPBE/NRPBE calculations! 695s 695s ---------------------------------------- 695s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 30.4176 A 695s Current memory usage: 102.566 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 0.225 x 0.225 x 0.225 695s Grid lengths: 14.400 x 14.400 x 14.400 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 3 695s Linearized traditional PBE 695s Boundary conditions from focusing 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 78.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 3.787747796627E+04 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 4.87072 A 695s Current memory usage: 102.566 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 1.500 x 1.500 x 1.500 695s Grid lengths: 96.000 x 96.000 x 96.000 695s Grid center: (25.264, 18.988, 19.122) 695s Multigrid levels: 5 695s Molecule ID: 3 695s Linearized traditional PBE 695s Multiple Debye-Huckel sphere boundary conditions 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 2.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 1.252495566243E+04 kJ/mol 695s Calculating forces... 695s [focusFillBound()]: WARNING: 695s Unusually large potential values 695s detected on the focusing boundary! 695s Convergence not guaranteed for NPBE/NRPBE calculations! 695s 695s ---------------------------------------- 695s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 695s Setting up problem... 695s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 695s Debye length: 4.87072 A 695s Current memory usage: 102.566 MB total, 183.200 MB high water 695s Using linear spline charge discretization. 695s Grid dimensions: 65 x 65 x 65 695s Grid spacings: 0.225 x 0.225 x 0.225 695s Grid lengths: 14.400 x 14.400 x 14.400 695s Grid center: (17.340, 19.211, 20.503) 695s Multigrid levels: 5 695s Molecule ID: 3 695s Linearized traditional PBE 695s Boundary conditions from focusing 695s 2 ion species (0.010 M ionic strength): 695s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 695s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 695s Solute dielectric: 2.000 695s Solvent dielectric: 2.000 695s Using "molecular" surface definition; no smoothing 695s Solvent probe radius: 0.000 A 695s Temperature: 300.000 K 695s Electrostatic energies will be calculated 695s Total electrostatic energy = 4.133237922574E+04 kJ/mol 695s Calculating forces... 695s ---------------------------------------- 695s PRINT STATEMENTS 695s 695s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 695s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 695s Global net ELEC energy = -3.460997931137E+03 kJ/mol 695s 695s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 695s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 695s Global net ELEC energy = -2.052167100108E+01 kJ/mol 695s 695s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 695s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 695s Global net ELEC energy = -3.454901259473E+03 kJ/mol 695s 695s 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 695s Local net energy (PE 0) = 1.442499933668E+01 kJ/mol 695s Global net ELEC energy = 1.442499933668E+01 kJ/mol 695s ---------------------------------------- 695s CLEANING UP AND SHUTTING DOWN... 695s Destroying force arrays. 695s No energy arrays to destroy. 695s Destroying multigrid structures. 695s Destroying finite element structures. 695s Destroying 3 molecules 695s Final memory usage: 0.001 MB total, 183.200 MB high water 695s 695s 695s Thanks for using APBS! 695s 710s Checking for intermediate energies in input file 1d7i-dss-mol.out 710s EXPECTED COMPUTED: 16 710s EXPECTED EXPECTED: 16 710s 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] 710s 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'] 710s COMPUTED RESULT 9160.578033846 710s COMPUTED RESULT 39557.01871716 710s COMPUTED RESULT 12649.65939588 710s COMPUTED RESULT 43018.01664829 710s COMPUTED RESULT 94.31133325426 710s COMPUTED RESULT 1677.348113184 710s COMPUTED RESULT 117.1079106781 710s COMPUTED RESULT 1697.869784185 710s COMPUTED RESULT 9040.108332204 710s COMPUTED RESULT 37877.47796627 710s COMPUTED RESULT 12524.95566243 710s COMPUTED RESULT 41332.37922574 710s COMPUTED RESULT -3460.997931137 710s COMPUTED RESULT -20.52167100108 710s COMPUTED RESULT -3454.901259473 710s COMPUTED RESULT 14.42499933668 710s BINARY: /usr/bin/apbs 710s INPUT: 1d7i-dss-smol.in 710s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 710s asc_getToken: Error occurred (bailing out). 710s Vio_scanf: Format problem with input. 710s 710s 710s ---------------------------------------------------------------------- 710s APBS -- Adaptive Poisson-Boltzmann Solver 710s Version APBS 3.4.1 710s 710s Nathan A. Baker (nathan.baker@pnnl.gov) 710s Pacific Northwest National Laboratory 710s 710s Additional contributing authors listed in the code documentation. 710s 710s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 710s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 710s Northwest Division for the U.S. Department of Energy. 710s 710s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 710s Portions Copyright (c) 2002-2020, Nathan A. Baker. 710s Portions Copyright (c) 1999-2002, The Regents of the University of California. 710s Portions Copyright (c) 1995, Michael Holst. 710s All rights reserved. 710s 710s Redistribution and use in source and binary forms, with or without 710s modification, are permitted provided that the following conditions are met: 710s 710s * Redistributions of source code must retain the above copyright notice, this 710s list of conditions and the following disclaimer. 710s 710s * Redistributions in binary form must reproduce the above copyright notice, 710s this list of conditions and the following disclaimer in the documentation 710s and/or other materials provided with the distribution. 710s 710s * Neither the name of the developer nor the names of its contributors may be 710s used to endorse or promote products derived from this software without 710s specific prior written permission. 710s 710s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 710s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 710s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 710s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 710s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 710s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 710s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 710s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 710s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 710s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 710s ---------------------------------------------------------------------- 710s APBS uses FETK (the Finite Element ToolKit) to solve the 710s Poisson-Boltzmann equation numerically. FETK is a portable collection 710s of finite element modeling class libraries developed by the Michael Holst 710s research group and written in an object-oriented form of C. FEtk is 710s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 710s *** PASSED *** 710s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 710s *** PASSED *** 710s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 710s *** PASSED *** 710s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 710s *** PASSED *** 710s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 710s *** PASSED *** 710s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 710s *** PASSED *** 710s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 710s *** PASSED *** 710s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 710s *** PASSED *** 710s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 710s *** PASSED *** 710s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 710s *** PASSED *** 710s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 710s *** PASSED *** 710s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 710s *** PASSED *** 710s Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) 710s *** PASSED *** 710s Elapsed time: 14.809215 seconds 710s -------------------------------------------------------------------------------- 710s Total elapsed time: 67.394616 seconds 710s Test results have been logged 710s -------------------------------------------------------------------------------- 710s -------------------------------------------------------------------------------- 710s Testing input file apbs-mol.in 710s 710s designed to solve general coupled systems of nonlinear partial differential 710s equations using adaptive finite element methods, inexact Newton methods, 710s and algebraic multilevel methods. More information about FEtk may be found 710s at . 710s ---------------------------------------------------------------------- 710s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 710s Aqua is a modified form of the Holst group PMG library 710s which has been modified by Patrice Koehl 710s for improved efficiency and 710s memory usage when solving the Poisson-Boltzmann equation. 710s ---------------------------------------------------------------------- 710s Please cite your use of APBS as: 710s 710s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 710s nanosystems: application to microtubules and the ribosome. Proc. 710s Natl. Acad. Sci. USA 98, 10037-10041 2001. 710s 710s 710s This executable compiled on Jan 3 2025 at 11:01:42 710s 710s Parsing input file 1d7i-dss-smol.in... 710s rank 0 size 1... 710s Parsed input file. 710s Got paths for 3 molecules 710s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 710s asc_getToken: Error occurred (bailing out). 710s Vio_scanf: Format problem with input. 710s 1677 atoms 710s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 710s Net charge 9.91e-01 e 710s Reading PQR-format atom data from dss-min.pqr. 710s asc_getToken: Error occurred (bailing out). 710s Vio_scanf: Format problem with input. 710s 14 atoms 710s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 710s Net charge -8.33e-17 e 710s Reading PQR-format atom data from 1d7i-min.pqr. 710s 1663 atoms 710s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 710s Net charge 9.91e-01 e 710s Preparing to run 12 PBE calculations. 710s ---------------------------------------- 710s CALCULATION #1 (complex-solv-coarse): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 30.4176 A 710s Current memory usage: 102.869 MB total, 102.869 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 1.500 x 1.500 x 1.500 710s Grid lengths: 96.000 x 96.000 x 96.000 710s Grid center: (25.264, 18.988, 19.122) 710s Multigrid levels: 5 710s Molecule ID: 1 710s Linearized traditional PBE 710s Multiple Debye-Huckel sphere boundary conditions 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 78.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 9.634884642408E+03 kJ/mol 710s Calculating forces... 710s [focusFillBound()]: WARNING: 710s Unusually large potential values 710s detected on the focusing boundary! 710s Convergence not guaranteed for NPBE/NRPBE calculations! 710s 710s ---------------------------------------- 710s CALCULATION #2 (complex-solv-fine): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 30.4176 A 710s Current memory usage: 102.869 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 0.225 x 0.225 x 0.225 710s Grid lengths: 14.400 x 14.400 x 14.400 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 1 710s Linearized traditional PBE 710s Boundary conditions from focusing 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 78.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 4.003177540425E+04 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s CALCULATION #3 (complex-ref-coarse): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 4.87072 A 710s Current memory usage: 102.869 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 1.500 x 1.500 x 1.500 710s Grid lengths: 96.000 x 96.000 x 96.000 710s Grid center: (25.264, 18.988, 19.122) 710s Multigrid levels: 5 710s Molecule ID: 1 710s Linearized traditional PBE 710s Multiple Debye-Huckel sphere boundary conditions 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 2.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 1.264965939588E+04 kJ/mol 710s Calculating forces... 710s [focusFillBound()]: WARNING: 710s Unusually large potential values 710s detected on the focusing boundary! 710s Convergence not guaranteed for NPBE/NRPBE calculations! 710s 710s ---------------------------------------- 710s CALCULATION #4 (complex-ref-fine): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 4.87072 A 710s Current memory usage: 102.869 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 0.225 x 0.225 x 0.225 710s Grid lengths: 14.400 x 14.400 x 14.400 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 1 710s Linearized traditional PBE 710s Boundary conditions from focusing 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 2.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 4.301801664829E+04 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s CALCULATION #5 (dss-solv-coarse): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 30.4176 A 710s Current memory usage: 62.482 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 1.500 x 1.500 x 1.500 710s Grid lengths: 96.000 x 96.000 x 96.000 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 2 710s Linearized traditional PBE 710s Multiple Debye-Huckel sphere boundary conditions 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 78.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 7.942232645345E+01 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s CALCULATION #6 (dss-solv-fine): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 30.4176 A 710s Current memory usage: 62.482 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 0.225 x 0.225 x 0.225 710s Grid lengths: 14.400 x 14.400 x 14.400 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 2 710s Linearized traditional PBE 710s Boundary conditions from focusing 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 78.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 1.677798535473E+03 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s CALCULATION #7 (dss-ref-coarse): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 4.87072 A 710s Current memory usage: 62.482 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 1.500 x 1.500 x 1.500 710s Grid lengths: 96.000 x 96.000 x 96.000 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 2 710s Linearized traditional PBE 710s Multiple Debye-Huckel sphere boundary conditions 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 2.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 1.171079106781E+02 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s CALCULATION #8 (dss-ref-fine): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 4.87072 A 710s Current memory usage: 62.482 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 0.225 x 0.225 x 0.225 710s Grid lengths: 14.400 x 14.400 x 14.400 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 2 710s Linearized traditional PBE 710s Boundary conditions from focusing 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 2.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 1.697869784185E+03 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 30.4176 A 710s Current memory usage: 102.566 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 1.500 x 1.500 x 1.500 710s Grid lengths: 96.000 x 96.000 x 96.000 710s Grid center: (25.264, 18.988, 19.122) 710s Multigrid levels: 5 710s Molecule ID: 3 710s Linearized traditional PBE 710s Multiple Debye-Huckel sphere boundary conditions 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 78.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 9.507068451372E+03 kJ/mol 710s Calculating forces... 710s [focusFillBound()]: WARNING: 710s Unusually large potential values 710s detected on the focusing boundary! 710s Convergence not guaranteed for NPBE/NRPBE calculations! 710s 710s ---------------------------------------- 710s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 30.4176 A 710s Current memory usage: 102.566 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 0.225 x 0.225 x 0.225 710s Grid lengths: 14.400 x 14.400 x 14.400 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 3 710s Linearized traditional PBE 710s Boundary conditions from focusing 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 78.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 3.835075772299E+04 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 4.87072 A 710s Current memory usage: 102.566 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 1.500 x 1.500 x 1.500 710s Grid lengths: 96.000 x 96.000 x 96.000 710s Grid center: (25.264, 18.988, 19.122) 710s Multigrid levels: 5 710s Molecule ID: 3 710s Linearized traditional PBE 710s Multiple Debye-Huckel sphere boundary conditions 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 2.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 1.252495566243E+04 kJ/mol 710s Calculating forces... 710s [focusFillBound()]: WARNING: 710s Unusually large potential values 710s detected on the focusing boundary! 710s Convergence not guaranteed for NPBE/NRPBE calculations! 710s 710s ---------------------------------------- 710s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 710s Setting up problem... 710s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 710s Debye length: 4.87072 A 710s Current memory usage: 102.566 MB total, 183.200 MB high water 710s Using linear spline charge discretization. 710s Grid dimensions: 65 x 65 x 65 710s Grid spacings: 0.225 x 0.225 x 0.225 710s Grid lengths: 14.400 x 14.400 x 14.400 710s Grid center: (17.340, 19.211, 20.503) 710s Multigrid levels: 5 710s Molecule ID: 3 710s Linearized traditional PBE 710s Boundary conditions from focusing 710s 2 ion species (0.010 M ionic strength): 710s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 710s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 710s Solute dielectric: 2.000 710s Solvent dielectric: 2.000 710s Using "molecular" surface definition;harmonic average smoothing 710s Solvent probe radius: 0.000 A 710s Temperature: 300.000 K 710s Electrostatic energies will be calculated 710s Total electrostatic energy = 4.133237922574E+04 kJ/mol 710s Calculating forces... 710s ---------------------------------------- 710s PRINT STATEMENTS 710s 710s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 710s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 710s Global net ELEC energy = -2.986241244040E+03 kJ/mol 710s 710s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 710s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 710s Global net ELEC energy = -2.007124871262E+01 kJ/mol 710s 710s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 710s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 710s Global net ELEC energy = -2.981621502756E+03 kJ/mol 710s 710s 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 710s Local net energy (PE 0) = 1.545150742844E+01 kJ/mol 710s Global net ELEC energy = 1.545150742844E+01 kJ/mol 710s ---------------------------------------- 710s CLEANING UP AND SHUTTING DOWN... 710s Destroying force arrays. 710s No energy arrays to destroy. 710s Destroying multigrid structures. 710s Destroying finite element structures. 710s Destroying 3 molecules 710s Final memory usage: 0.001 MB total, 183.200 MB high water 710s 710s 710s Thanks for using APBS! 710s 728s Checking for intermediate energies in input file 1d7i-dss-smol.out 728s EXPECTED COMPUTED: 16 728s EXPECTED EXPECTED: 16 728s 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] 728s 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'] 728s COMPUTED RESULT 9634.884642408 728s COMPUTED RESULT 40031.77540425 728s COMPUTED RESULT 12649.65939588 728s COMPUTED RESULT 43018.01664829 728s COMPUTED RESULT 79.42232645345 728s COMPUTED RESULT 1677.798535473 728s COMPUTED RESULT 117.1079106781 728s COMPUTED RESULT 1697.869784185 728s COMPUTED RESULT 9507.068451372 728s COMPUTED RESULT 38350.75772299 728s COMPUTED RESULT 12524.95566243 728s COMPUTED RESULT 41332.37922574 728s COMPUTED RESULT -2986.24124404 728s COMPUTED RESULT -20.07124871262 728s COMPUTED RESULT -2981.621502756 728s COMPUTED RESULT 15.45150742844 728s Running tests for hca-bind section 728s BINARY: /usr/bin/apbs 728s INPUT: apbs-mol.in 728s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 728s asc_getToken: Error occurred (bailing out). 728s Vio_scanf: Format problem with input. 728s 728s 728s ---------------------------------------------------------------------- 728s APBS -- Adaptive Poisson-Boltzmann Solver 728s Version APBS 3.4.1 728s 728s Nathan A. Baker (nathan.baker@pnnl.gov) 728s Pacific Northwest National Laboratory 728s 728s Additional contributing authors listed in the code documentation. 728s 728s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 728s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 728s Northwest Division for the U.S. Department of Energy. 728s 728s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 728s Portions Copyright (c) 2002-2020, Nathan A. Baker. 728s Portions Copyright (c) 1999-2002, The Regents of the University of California. 728s Portions Copyright (c) 1995, Michael Holst. 728s All rights reserved. 728s 728s Redistribution and use in source and binary forms, with or without 728s modification, are permitted provided that the following conditions are met: 728s 728s * Redistributions of source code must retain the above copyright notice, this 728s list of conditions and the following disclaimer. 728s 728s * Redistributions in binary form must reproduce the above copyright notice, 728s this list of conditions and the following disclaimer in the documentation 728s and/or other materials provided with the distribution. 728s 728s * Neither the name of the developer nor the names of its contributors may be 728s used to endorse or promote products derived from this software without 728s specific prior written permission. 728s 728s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 728s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 728s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 728s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 728s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 728s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 728s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 728s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 728s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 728s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 728s ---------------------------------------------------------------------- 728s APBS uses FETK (the Finite Element ToolKit) to solve the 728s Poisson-Boltzmann equation numerically. FETK is a portable collection 728s of finite element modeling class libraries developed by the Michael Holst 728s research group and written in an object-oriented form of C. FEtk is 728s designed to solve general coupled systems of nonlinear partial differential 728s equations using adaptive finite element methods, inexact Newton methods, 728s and algebraic multilevel methods. More information about FEtk may be found 728s at . 728s ---------------------------------------------------------------------- 728s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 728s Aqua is a modified form of the Holst group PMG library 728s which has been modified by Patrice Koehl 728s for improved efficiency and 728s memory usage when solving the Poisson-Boltzmann equation. 728s ---------------------------------------------------------------------- 728s Please cite your use of APBS as: 728s 728s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 728s nanosystems: application to microtubules and the ribosome. Proc. 728s Natl. Acad. Sci. USA 98, 10037-10041 2001. 728s 728s 728s This executable compiled on Jan 3 2025 at 11:01:42 728s 728s Parsing input file apbs-mol.in... 728s rank 0 size 1... 728s Parsed input file. 728s Got paths for 3 molecules 728s Reading PQR-format atom data from acet.pqr. 728s asc_getToken: Error occurred (bailing out). 728s Vio_scanf: Format problem with input. 728s 18 atoms 728s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 728s Net charge -1.00e+00 e 728s Reading PQR-format atom data from hca.pqr. 728s asc_getToken: Error occurred (bailing out). 728s Vio_scanf: Format problem with input. 728s 2482 atoms 728s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 728s Net charge 1.00e+00 e 728s Reading PQR-format atom data from complex.pqr. 728s 2500 atoms 728s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 728s Net charge -1.02e-14 e 728s Preparing to run 9 PBE calculations. 728s ---------------------------------------- 728s CALCULATION #1 (acet): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 62.632 MB total, 62.632 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 1.500 x 1.500 x 1.500 728s Grid lengths: 96.000 x 96.000 x 96.000 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 1 728s Linearized traditional PBE 728s Single Debye-Huckel sphere boundary conditions 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 2.213600726771E+02 kJ/mol 728s Calculating forces... 728s ---------------------------------------- 728s CALCULATION #2 (acet): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 62.632 MB total, 123.513 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 0.581 x 0.581 x 0.581 728s Grid lengths: 37.181 x 37.181 x 37.181 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 1 728s Linearized traditional PBE 728s Boundary conditions from focusing 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 1.825764811255E+03 kJ/mol 728s Calculating forces... 728s ---------------------------------------- 728s CALCULATION #3 (acet): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 62.632 MB total, 123.513 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 0.225 x 0.225 x 0.225 728s Grid lengths: 14.400 x 14.400 x 14.400 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 1 728s Linearized traditional PBE 728s Boundary conditions from focusing 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 6.458471211905E+03 kJ/mol 728s Calculating forces... 728s ---------------------------------------- 728s CALCULATION #4 (hca): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 127.616 MB total, 127.616 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 1.500 x 1.500 x 1.500 728s Grid lengths: 96.000 x 96.000 x 96.000 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 2 728s Linearized traditional PBE 728s Single Debye-Huckel sphere boundary conditions 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 2.093606095527E+04 kJ/mol 728s Calculating forces... 728s [focusFillBound()]: WARNING: 728s Unusually large potential values 728s detected on the focusing boundary! 728s Convergence not guaranteed for NPBE/NRPBE calculations! 728s 728s ---------------------------------------- 728s CALCULATION #5 (hca): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 127.616 MB total, 207.303 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 0.581 x 0.581 x 0.581 728s Grid lengths: 37.181 x 37.181 x 37.181 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 2 728s Linearized traditional PBE 728s Boundary conditions from focusing 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 1.515433544464E+05 kJ/mol 728s Calculating forces... 728s [focusFillBound()]: WARNING: 728s Unusually large potential values 728s detected on the focusing boundary! 728s Convergence not guaranteed for NPBE/NRPBE calculations! 728s 728s ---------------------------------------- 728s CALCULATION #6 (hca): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 127.616 MB total, 207.303 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 0.225 x 0.225 x 0.225 728s Grid lengths: 14.400 x 14.400 x 14.400 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 2 728s Linearized traditional PBE 728s Boundary conditions from focusing 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 1.786369323561E+05 kJ/mol 728s Calculating forces... 728s ---------------------------------------- 728s CALCULATION #7 (complex): MULTIGRID 728s Setting up probleTesting computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 728s *** PASSED *** 728s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 728s *** PASSED *** 728s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 728s *** PASSED *** 728s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 728s *** PASSED *** 728s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 728s *** PASSED *** 728s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 728s *** PASSED *** 728s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 728s *** PASSED *** 728s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 728s *** PASSED *** 728s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 728s *** PASSED *** 728s Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) 728s *** PASSED *** 728s Elapsed time: 18.357177 seconds 728s -------------------------------------------------------------------------------- 728s -------------------------------------------------------------------------------- 728s Testing input file apbs-smol.in 728s 728s m... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 127.915 MB total, 207.303 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 1.500 x 1.500 x 1.500 728s Grid lengths: 96.000 x 96.000 x 96.000 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 3 728s Linearized traditional PBE 728s Single Debye-Huckel sphere boundary conditions 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 2.105322784838E+04 kJ/mol 728s Calculating forces... 728s [focusFillBound()]: WARNING: 728s Unusually large potential values 728s detected on the focusing boundary! 728s Convergence not guaranteed for NPBE/NRPBE calculations! 728s 728s ---------------------------------------- 728s CALCULATION #8 (complex): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 127.915 MB total, 207.713 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 0.581 x 0.581 x 0.581 728s Grid lengths: 37.181 x 37.181 x 37.181 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 3 728s Linearized traditional PBE 728s Boundary conditions from focusing 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 1.533304996252E+05 kJ/mol 728s Calculating forces... 728s [focusFillBound()]: WARNING: 728s Unusually large potential values 728s detected on the focusing boundary! 728s Convergence not guaranteed for NPBE/NRPBE calculations! 728s 728s ---------------------------------------- 728s CALCULATION #9 (complex): MULTIGRID 728s Setting up problem... 728s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 728s Debye length: 0 A 728s Current memory usage: 127.915 MB total, 207.713 MB high water 728s Using linear spline charge discretization. 728s Grid dimensions: 65 x 65 x 65 728s Grid spacings: 0.225 x 0.225 x 0.225 728s Grid lengths: 14.400 x 14.400 x 14.400 728s Grid center: (-6.028, 3.898, 15.179) 728s Multigrid levels: 5 728s Molecule ID: 3 728s Linearized traditional PBE 728s Boundary conditions from focusing 728s 2 ion species (0.000 M ionic strength): 728s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 728s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 728s Solute dielectric: 2.000 728s Solvent dielectric: 78.540 728s Using "molecular" surface definition; no smoothing 728s Solvent probe radius: 0.000 A 728s Temperature: 298.150 K 728s Electrostatic energies will be calculated 728s Total electrostatic energy = 1.850429388099E+05 kJ/mol 728s Calculating forces... 728s ---------------------------------------- 728s PRINT STATEMENTS 728s 728s print energy 3 (complex) - 1 (acet) - 2 (hca) end 728s Local net energy (PE 0) = -5.246475812665E+01 kJ/mol 728s Global net ELEC energy = -5.246475812665E+01 kJ/mol 728s ---------------------------------------- 728s CLEANING UP AND SHUTTING DOWN... 728s Destroying force arrays. 728s No energy arrays to destroy. 728s Destroying multigrid structures. 728s Destroying finite element structures. 728s Destroying 3 molecules 728s Final memory usage: 0.001 MB total, 207.713 MB high water 728s 728s 728s Thanks for using APBS! 728s 742s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 742s *** PASSED *** 742s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 742s *** PASSED *** 742s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 742s *** PASSED *** 742s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 742s *** PASSED *** 742s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 742s *** PASSED *** 742s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 742s *** PASSED *** 742s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 742s *** PASSED *** 742s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 742s *** PASSED *** 742s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 742s *** PASSED *** 742s Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) 742s *** PASSED *** 742s Elapsed time: 13.491095 seconds 742s -------------------------------------------------------------------------------- 742s Total elapsed time: 31.848272 seconds 742s Test results have been logged 742s -------------------------------------------------------------------------------- 742s -------------------------------------------------------------------------------- 742s Testing input file apbs-mol.in 742s 742s Checking for intermediate energies in input file apbs-mol.out 742s EXPECTED COMPUTED: 10 742s EXPECTED EXPECTED: 10 742s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] 742s 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'] 742s COMPUTED RESULT 221.3600726771 742s COMPUTED RESULT 1825.764811255 742s COMPUTED RESULT 6458.471211905 742s COMPUTED RESULT 20936.06095527 742s COMPUTED RESULT 151543.3544464 742s COMPUTED RESULT 178636.9323561 742s COMPUTED RESULT 21053.22784838 742s COMPUTED RESULT 153330.4996252 742s COMPUTED RESULT 185042.9388099 742s COMPUTED RESULT -52.46475812665 742s BINARY: /usr/bin/apbs 742s INPUT: apbs-smol.in 742s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 742s asc_getToken: Error occurred (bailing out). 742s Vio_scanf: Format problem with input. 742s 742s 742s ---------------------------------------------------------------------- 742s APBS -- Adaptive Poisson-Boltzmann Solver 742s Version APBS 3.4.1 742s 742s Nathan A. Baker (nathan.baker@pnnl.gov) 742s Pacific Northwest National Laboratory 742s 742s Additional contributing authors listed in the code documentation. 742s 742s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 742s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 742s Northwest Division for the U.S. Department of Energy. 742s 742s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 742s Portions Copyright (c) 2002-2020, Nathan A. Baker. 742s Portions Copyright (c) 1999-2002, The Regents of the University of California. 742s Portions Copyright (c) 1995, Michael Holst. 742s All rights reserved. 742s 742s Redistribution and use in source and binary forms, with or without 742s modification, are permitted provided that the following conditions are met: 742s 742s * Redistributions of source code must retain the above copyright notice, this 742s list of conditions and the following disclaimer. 742s 742s * Redistributions in binary form must reproduce the above copyright notice, 742s this list of conditions and the following disclaimer in the documentation 742s and/or other materials provided with the distribution. 742s 742s * Neither the name of the developer nor the names of its contributors may be 742s used to endorse or promote products derived from this software without 742s specific prior written permission. 742s 742s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 742s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 742s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 742s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 742s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 742s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 742s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 742s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 742s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 742s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 742s ---------------------------------------------------------------------- 742s APBS uses FETK (the Finite Element ToolKit) to solve the 742s Poisson-Boltzmann equation numerically. FETK is a portable collection 742s of finite element modeling class libraries developed by the Michael Holst 742s research group and written in an object-oriented form of C. FEtk is 742s designed to solve general coupled systems of nonlinear partial differential 742s equations using adaptive finite element methods, inexact Newton methods, 742s and algebraic multilevel methods. More information about FEtk may be found 742s at . 742s ---------------------------------------------------------------------- 742s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 742s Aqua is a modified form of the Holst group PMG library 742s which has been modified by Patrice Koehl 742s for improved efficiency and 742s memory usage when solving the Poisson-Boltzmann equation. 742s ---------------------------------------------------------------------- 742s Please cite your use of APBS as: 742s 742s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 742s nanosystems: application to microtubules and the ribosome. Proc. 742s Natl. Acad. Sci. USA 98, 10037-10041 2001. 742s 742s 742s This executable compiled on Jan 3 2025 at 11:01:42 742s 742s Parsing input file apbs-smol.in... 742s rank 0 size 1... 742s Parsed input file. 742s Got paths for 3 molecules 742s Reading PQR-format atom data from acet.pqr. 742s asc_getToken: Error occurred (bailing out). 742s Vio_scanf: Format problem with input. 742s 18 atoms 742s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 742s Net charge -1.00e+00 e 742s Reading PQR-format atom data from hca.pqr. 742s asc_getToken: Error occurred (bailing out). 742s Vio_scanf: Format problem with input. 742s 2482 atoms 742s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 742s Net charge 1.00e+00 e 742s Reading PQR-format atom data from complex.pqr. 742s 2500 atoms 742s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 742s Net charge -1.02e-14 e 742s Preparing to run 9 PBE calculations. 742s ---------------------------------------- 742s CALCULATION #1 (acet): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 62.632 MB total, 62.632 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 1.500 x 1.500 x 1.500 742s Grid lengths: 96.000 x 96.000 x 96.000 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 1 742s Linearized traditional PBE 742s Single Debye-Huckel sphere boundary conditions 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 1.884888131017E+02 kJ/mol 742s Calculating forces... 742s ---------------------------------------- 742s CALCULATION #2 (acet): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 62.632 MB total, 123.513 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 0.581 x 0.581 x 0.581 742s Grid lengths: 37.181 x 37.181 x 37.181 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 1 742s Linearized traditional PBE 742s Boundary conditions from focusing 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 1.820045922544E+03 kJ/mol 742s Calculating forces... 742s ---------------------------------------- 742s CALCULATION #3 (acet): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 62.632 MB total, 123.513 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 0.225 x 0.225 x 0.225 742s Grid lengths: 14.400 x 14.400 x 14.400 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 1 742s Linearized traditional PBE 742s Boundary conditions from focusing 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 6.460002606908E+03 kJ/mol 742s Calculating forces... 742s ---------------------------------------- 742s CALCULATION #4 (hca): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 127.616 MB total, 127.616 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 1.500 x 1.500 x 1.500 742s Grid lengths: 96.000 x 96.000 x 96.000 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 2 742s Linearized traditional PBE 742s Single Debye-Huckel sphere boundary conditions 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 2.189161497021E+04 kJ/mol 742s Calculating forces... 742s [focusFillBound()]: WARNING: 742s Unusually large potential values 742s detected on the focusing boundary! 742s Convergence not guaranteed for NPBE/NRPBE calculations! 742s 742s ---------------------------------------- 742s CALCULATION #5 (hca): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 127.616 MB total, 207.303 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 0.581 x 0.581 x 0.581 742s Grid lengths: 37.181 x 37.181 x 37.181 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 2 742s Linearized traditional PBE 742s Boundary conditions from focusing 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 1.520000494925E+05 kJ/mol 742s Calculating forces... 742s [focusFillBound()]: WARNING: 742s Unusually large potential values 742s detected on the focusing boundary! 742s Convergence not guaranteed for NPBE/NRPBE calculations! 742s 742s ---------------------------------------- 742s CALCULATION #6 (hca): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 127.616 MB total, 207.303 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 0.225 x 0.225 x 0.225 742s Grid lengths: 14.400 x 14.400 x 14.400 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 2 742s Linearized traditional PBE 742s Boundary conditions from focusing 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 1.790436191580E+05 kJ/mol 742s Calculating forces... 742s ---------------------------------------- 742s CALCULATION #7 (complex): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 127.915 MB total, 207.303 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 1.500 x 1.500 x 1.500 742s Grid lengths: 96.000 x 96.000 x 96.000 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 3 742s Linearized traditional PBE 742s Single Debye-Huckel sphere boundary conditions 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 2.195842512312E+04 kJ/mol 742s Calculating forces... 742s [focusFillBound()]: WARNING: 742s Unusually large potential values 742s detected on the focusing boundary! 742s Convergence not guaranteed for NPBE/NRPBE calculations! 742s 742s ---------------------------------------- 742s CALCULATION #8 (complex): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 127.915 MB total, 207.713 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 0.581 x 0.581 x 0.581 742s Grid lengths: 37.181 x 37.181 x 37.181 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 3 742s Linearized traditional PBE 742s Boundary conditions from focusing 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 1.537771604355E+05 kJ/mol 742s Calculating forces... 742s [focusFillBound()]: WARNING: 742s Unusually large potential values 742s detected on the focusing boundary! 742s Convergence not guaranteed for NPBE/NRPBE calculations! 742s 742s ---------------------------------------- 742s CALCULATION #9 (complex): MULTIGRID 742s Setting up problem... 742s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 742s Debye length: 0 A 742s Current memory usage: 127.915 MB total, 207.713 MB high water 742s Using linear spline charge discretization. 742s Grid dimensions: 65 x 65 x 65 742s Grid spacings: 0.225 x 0.225 x 0.225 742s Grid lengths: 14.400 x 14.400 x 14.400 742s Grid center: (-6.028, 3.898, 15.179) 742s Multigrid levels: 5 742s Molecule ID: 3 742s Linearized traditional PBE 742s Boundary conditions from focusing 742s 2 ion species (0.000 M ionic strength): 742s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 742s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 742s Solute dielectric: 2.000 742s Solvent dielectric: 78.540 742s Using "molecular" surface definition;harmonic average smoothing 742s Solvent probe radius: 0.000 A 742s Temperature: 298.150 K 742s Electrostatic energies will be calculated 742s Total electrostatic energy = 1.854495619747E+05 kJ/mol 742s Calculating forces... 742s ---------------------------------------- 742s PRINT STATEMENTS 742s 742s print energy 3 (complex) - 1 (acet) - 2 (hca) end 742s Local net energy (PE 0) = -5.405979017066E+01 kJ/mol 742s Global net ELEC energy = -5.405979017066E+01 kJ/mol 742s ---------------------------------------- 742s CLEANING UP AND SHUTTING DOWN... 742s Destroying force arrays. 742s No energy arrays to destroy. 742s Destroying multigrid structures. 742s Destroying finite element structures. 742s Destroying 3 molecules 742s Final memory usage: 0.001 MB total, 207.713 MB high water 742s 742s 742s Thanks for using APBS! 742s 751s Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 751s *** PASSED *** 751s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 751s *** PASSED *** 751s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 751s *** PASSED *** 751s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 751s *** PASSED *** 751s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 751s *** PASSED *** 751s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 751s *** PASSED *** 751s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 751s *** PASSED *** 751s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 751s *** PASSED *** 751s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 751s *** PASSED *** 751s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 751s *** PASSED *** 751s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 751s *** PASSED *** 751s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 751s *** PASSED *** 751s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 751s *** PASSED *** 751s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 751s *** PASSED *** 751s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 751s *** PASSED *** 751s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 751s *** PASSED *** 751s Elapsed time: 9.089702 seconds 751s -------------------------------------------------------------------------------- 751s -------------------------------------------------------------------------------- 751s Testing input file apbs-smol.in 751s 751s Checking for intermediate energies in input file apbs-smol.out 751s EXPECTED COMPUTED: 10 751s EXPECTED EXPECTED: 10 751s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] 751s 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'] 751s COMPUTED RESULT 188.4888131017 751s COMPUTED RESULT 1820.045922544 751s COMPUTED RESULT 6460.002606908 751s COMPUTED RESULT 21891.61497021 751s COMPUTED RESULT 152000.0494925 751s COMPUTED RESULT 179043.619158 751s COMPUTED RESULT 21958.42512312 751s COMPUTED RESULT 153777.1604355 751s COMPUTED RESULT 185449.5619747 751s COMPUTED RESULT -54.05979017066 751s Running tests for ionize section 751s BINARY: /usr/bin/apbs 751s INPUT: apbs-mol.in 751s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 751s asc_getToken: Error occurred (bailing out). 751s Vio_scanf: Format problem with input. 751s 751s 751s ---------------------------------------------------------------------- 751s APBS -- Adaptive Poisson-Boltzmann Solver 751s Version APBS 3.4.1 751s 751s Nathan A. Baker (nathan.baker@pnnl.gov) 751s Pacific Northwest National Laboratory 751s 751s Additional contributing authors listed in the code documentation. 751s 751s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 751s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 751s Northwest Division for the U.S. Department of Energy. 751s 751s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 751s Portions Copyright (c) 2002-2020, Nathan A. Baker. 751s Portions Copyright (c) 1999-2002, The Regents of the University of California. 751s Portions Copyright (c) 1995, Michael Holst. 751s All rights reserved. 751s 751s Redistribution and use in source and binary forms, with or without 751s modification, are permitted provided that the following conditions are met: 751s 751s * Redistributions of source code must retain the above copyright notice, this 751s list of conditions and the following disclaimer. 751s 751s * Redistributions in binary form must reproduce the above copyright notice, 751s this list of conditions and the following disclaimer in the documentation 751s and/or other materials provided with the distribution. 751s 751s * Neither the name of the developer nor the names of its contributors may be 751s used to endorse or promote products derived from this software without 751s specific prior written permission. 751s 751s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 751s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 751s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 751s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 751s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 751s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 751s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 751s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 751s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 751s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 751s ---------------------------------------------------------------------- 751s APBS uses FETK (the Finite Element ToolKit) to solve the 751s Poisson-Boltzmann equation numerically. FETK is a portable collection 751s of finite element modeling class libraries developed by the Michael Holst 751s research group and written in an object-oriented form of C. FEtk is 751s designed to solve general coupled systems of nonlinear partial differential 751s equations using adaptive finite element methods, inexact Newton methods, 751s and algebraic multilevel methods. More information about FEtk may be found 751s at . 751s ---------------------------------------------------------------------- 751s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 751s Aqua is a modified form of the Holst group PMG library 751s which has been modified by Patrice Koehl 751s for improved efficiency and 751s memory usage when solving the Poisson-Boltzmann equation. 751s ---------------------------------------------------------------------- 751s Please cite your use of APBS as: 751s 751s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 751s nanosystems: application to microtubules and the ribosome. Proc. 751s Natl. Acad. Sci. USA 98, 10037-10041 2001. 751s 751s 751s This executable compiled on Jan 3 2025 at 11:01:42 751s 751s Parsing input file apbs-mol.in... 751s rank 0 size 1... 751s Parsed input file. 751s Got paths for 3 molecules 751s Reading PQR-format atom data from acetic-acid.pqr. 751s asc_getToken: Error occurred (bailing out). 751s Vio_scanf: Format problem with input. 751s 8 atoms 751s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 751s Net charge -1.67e-16 e 751s Reading PQR-format atom data from acetate.pqr. 751s asc_getToken: Error occurred (bailing out). 751s Vio_scanf: Format problem with input. 751s 8 atoms 751s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 751s Net charge -1.00e+00 e 751s Reading PQR-format atom data from proton.pqr. 751s 1 atoms 751s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 751s Net charge 1.00e+00 e 751s Preparing to run 12 PBE calculations. 751s ---------------------------------------- 751s CALCULATION #1 (acetic-solv): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 7.76163 A 751s Current memory usage: 61.581 MB total, 61.581 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.188 x 0.188 x 0.188 751s Grid lengths: 12.000 x 12.000 x 12.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 1 751s Linearized traditional PBE 751s Multiple Debye-Huckel sphere boundary conditions 751s 2 ion species (0.150 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 78.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 5.823898055191E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #2 (acetic-solv): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 7.76163 A 751s Current memory usage: 61.581 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.094 x 0.094 x 0.094 751s Grid lengths: 6.000 x 6.000 x 6.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 1 751s Linearized traditional PBE 751s Boundary conditions from focusing 751s 2 ion species (0.150 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 78.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 9.793274462353E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #3 (acetic-ref): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 0 A 751s Current memory usage: 61.405 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.188 x 0.188 x 0.188 751s Grid lengths: 12.000 x 12.000 x 12.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 1 751s Linearized traditional PBE 751s Multiple Debye-Huckel sphere boundary conditions 751s 2 ion species (0.000 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 2.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 5.846917564309E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #4 (acetic-ref): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 0 A 751s Current memory usage: 61.405 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.094 x 0.094 x 0.094 751s Grid lengths: 6.000 x 6.000 x 6.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 1 751s Linearized traditional PBE 751s Boundary conditions from focusing 751s 2 ion species (0.000 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 2.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 9.815953282539E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #5 (acetate-solv): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 7.76163 A 751s Current memory usage: 61.581 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.188 x 0.188 x 0.188 751s Grid lengths: 12.000 x 12.000 x 12.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 2 751s Linearized traditional PBE 751s Multiple Debye-Huckel sphere boundary conditions 751s 2 ion species (0.150 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 78.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 8.219846763777E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #6 (acetate-solv): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 7.76163 A 751s Current memory usage: 61.581 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.094 x 0.094 x 0.094 751s Grid lengths: 6.000 x 6.000 x 6.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 2 751s Linearized traditional PBE 751s Boundary conditions from focusing 751s 2 ion species (0.150 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 78.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 1.392741988698E+04 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #7 (acetate-ref): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 0 A 751s Current memory usage: 61.405 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.188 x 0.188 x 0.188 751s Grid lengths: 12.000 x 12.000 x 12.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 2 751s Linearized traditional PBE 751s Multiple Debye-Huckel sphere boundary conditions 751s 2 ion species (0.000 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 2.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 8.420373979905E+03 kJ/mol 751s Calculating forces... 751s [focusFillBound()]: WARNING: 751s Unusually large potential values 751s detected on the focusing boundary! 751s Convergence not guaranteed for NPBE/NRPBE calculations! 751s 751s ---------------------------------------- 751s CALCULATION #8 (acetate-ref): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 0 A 751s Current memory usage: 61.405 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.094 x 0.094 x 0.094 751s Grid lengths: 6.000 x 6.000 x 6.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 2 751s Linearized traditional PBE 751s Boundary conditions from focusing 751s 2 ion species (0.000 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 2.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 1.412716615065E+04 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #9 (proton-solv): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 7.76163 A 751s Current memory usage: 61.410 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.188 x 0.188 x 0.188 751s Grid lengths: 12.000 x 12.000 x 12.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 3 751s Linearized traditional PBE 751s Multiple Debye-Huckel sphere boundary conditions 751s 2 ion species (0.150 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 78.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 3.862359524598E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #10 (proton-solv): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 7.76163 A 751s Current memory usage: 61.410 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.094 x 0.094 x 0.094 751s Grid lengths: 6.000 x 6.000 x 6.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 3 751s Linearized traditional PBE 751s Boundary conditions from focusing 751s 2 ion species (0.150 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 78.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 6.288156251610E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s CALCULATION #11 (proton-ref): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 0 A 751s Current memory usage: 61.371 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.188 x 0.188 x 0.188 751s Grid lengths: 12.000 x 12.000 x 12.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 3 751s Linearized traditional PBE 751s Multiple Debye-Huckel sphere boundary conditions 751s 2 ion species (0.000 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 2.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 4.162533113906E+03 kJ/mol 751s Calculating forces... 751s [focusFillBound()]: WARNING: 751s Unusually large potential values 751s detected on the focusing boundary! 751s Convergence not guaranteed for NPBE/NRPBE calculations! 751s 751s ---------------------------------------- 751s CALCULATION #12 (proton-ref): MULTIGRID 751s Setting up problem... 751s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 751s Debye length: 0 A 751s Current memory usage: 61.371 MB total, 122.371 MB high water 751s Using linear spline charge discretization. 751s Grid dimensions: 65 x 65 x 65 751s Grid spacings: 0.094 x 0.094 x 0.094 751s Grid lengths: 6.000 x 6.000 x 6.000 751s Grid center: (0.000, -0.154, 1.287) 751s Multigrid levels: 5 751s Molecule ID: 3 751s Linearized traditional PBE 751s Boundary conditions from focusing 751s 2 ion species (0.000 M ionic strength): 751s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 751s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 751s Solute dielectric: 2.000 751s Solvent dielectric: 2.000 751s Using "molecular" surface definition; no smoothing 751s Solvent probe radius: 0.000 A 751s Temperature: 293.000 K 751s Electrostatic energies will be calculated 751s Total electrostatic energy = 6.585616091973E+03 kJ/mol 751s Calculating forces... 751s ---------------------------------------- 751s PRINT STATEMENTS 751s 751s print energy 1 (acetic-solv) - 2 (acetic-ref) end 751s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 751s Global net ELEC energy = -2.267882018629E+01 kJ/mol 751s 751s print energy 3 (acetate-solv) - 4 (acetate-ref) end 751s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 751s Global net ELEC energy = -1.997462636633E+02 kJ/mol 751s 751s print energy 5 (proton-solv) - 6 (proton-ref) end 751s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 751s Global net ELEC energy = -2.974598403628E+02 kJ/mol 751s 751s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 751s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 751s Global net ELEC energy = -4.745272838398E+02 kJ/mol 751s ---------------------------------------- 751s CLEANING UP AND SHUTTING DOWN... 751s Destroying force arrays. 751s No energy arrays to destroy. 751s Destroying multigrid structures. 751s Destroying finite element structures. 751s Destroying 3 molecules 751s Final memory usage: 0.001 MB total, 122.371 MB high water 751s 751s 751s Thanks for using APBS! 751s 759s Checking for intermediate energies in input file apbs-mol.out 759s EXPECTED COMPUTED: 16 759s EXPECTED EXPECTED: 16 759s 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] 759s 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'] 759s COMPUTED RESULT 5823.898055191 759s COMPUTED RESULT 9793.274462353 759s COMPUTED RESULT 5846.917564309 759s COMPUTED RESULT 9815.953282539 759s COMPUTED RESULT 8219.846763777 759s COMPUTED RESULT 13927.41988698 759s COMPUTED RESULT 8420.373979905 759s COMPUTED RESULT 14127.16615065 759s COMPUTED RESULT 3862.359524598 759s COMPUTED RESULT 6288.15625161 759s COMPUTED RESULT 4162.533113906 759s COMPUTED RESULT 6585.616091973 759s COMPUTED RESULT -22.67882018629 759s COMPUTED RESULT -199.7462636633 759s COMPUTED RESULT -297.4598403628 759s COMPUTED RESULT -474.5272838398 759s BINARY: /usr/bin/apbs 759s INPUT: apbs-smol.in 759s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 759s asc_getToken: Error occurred (bailing out). 759s Vio_scanf: Format problem with input. 759s 759s 759s ---------------------------------------------------------------------- 759s APBS -- Adaptive Poisson-Boltzmann Solver 759s Version APBS 3.4.1 759s 759s Nathan A. Baker (nathan.baker@pnnl.gov) 759s Pacific Northwest National Laboratory 759s 759s Additional contributing authors listed in the code documentation. 759s 759s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 759s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 759s Northwest Division for the U.S. Department of Energy. 759s 759s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 759s Portions Copyright (c) 2002-2020, Nathan A. Baker. 759s Portions Copyright (c) 1999-2002, The Regents of the University of California. 759s Portions Copyright (c) 1995, Michael Holst. 759s All rights reserved. 759s 759s Redistribution and use in source and binary forms, with or without 759s modification, are permitted provided that the following conditions are met: 759s 759s * Redistributions of source code must retain the above copyright notice, this 759s list of conditions and the following disclaimer. 759s 759s * Redistributions in binary form must reproduce the above copyright notice, 759s this list of conditions and the following disclaimer in the documentation 759s and/or other materials provided with the distribution. 759s 759s * Neither the name of the developer nor the names of its contributors may be 759s used to endorse or promote products derived from this software without 759s specific prior written permission. 759s 759s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 759s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 759s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 759s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 759s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 759s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 759s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 759s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 759s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 759s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 759s ---------------------------------------------------------------------- 759s APBS uses FETK (the Finite Element ToolKit) to solve the 759s Poisson-Boltzmann equation numerically. FETK is a portable collection 759s of finite element modeling class libraries developed by the Michael Holst 759s research group and written in an object-oriented form of C. FEtk is 759s designed to solve general coupled systems of nonlinear partial differential 759s equations using adaptive finite element methods, inexact Newton methods, 759s and algebraic multilevel methods. More information about FEtk may be found 759s at . 759s ---------------------------------------------------------------------- 759s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 759s Aqua is a modified form of the Holst group PMG library 759s which has been modified by Patrice Koehl 759s for improved efficiency and 759s memory usage when solving the Poisson-Boltzmann equation. 759s ---------------------------------------------------------------------- 759s Please cite your use of APBS as: 759s 759s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 759s nanosystems: application to microtubules and the ribosome. Proc. 759s Natl. Acad. Sci. USA 98, 10037-10041 2001. 759s 759s 759s This executable compiled on Jan 3 2025 at 11:01:42 759s 759s Parsing input file apbs-smol.in... 759s rank 0 size 1... 759s Parsed input file. 759s Got paths for 3 molecules 759s Reading PQR-format atom data from acetic-acid.pqr. 759s asc_getToken: Error occurred (bailing out). 759s Vio_scanf: Format problem with input. 759s 8 atoms 759s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 759s Net charge -1.67e-16 e 759s Reading PQR-format atom data from acetate.pqr. 759s asc_getToken: Error occurred (bailing out). 759s Vio_scanf: Format problem with input. 759s 8 atoms 759s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 759s Net charge -1.00e+00 e 759s Reading PQR-format atom data from proton.pqr. 759s 1 atoms 759s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 759s Net charge 1.00e+00 e 759s Preparing to run 12 PBE calculations. 759s ---------------------------------------- 759s CALCULATION #1 (acetic-solv): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 7.76163 A 759s Current memory usage: 61.581 MB total, 61.581 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.188 x 0.188 x 0.188 759s Grid lengths: 12.000 x 12.000 x 12.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 1 759s Linearized traditional PBE 759s Multiple Debye-Huckel sphere boundary conditions 759s 2 ion species (0.150 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 78.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 5.824172730822E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #2 (acetic-solv): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 7.76163 A 759s Current memory usage: 61.581 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.094 x 0.094 x 0.094 759s Grid lengths: 6.000 x 6.000 x 6.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 1 759s Linearized traditional PBE 759s Boundary conditions from focusing 759s 2 ion species (0.150 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 78.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 9.793622759239E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #3 (acetic-ref): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 0 A 759s Current memory usage: 61.405 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.188 x 0.188 x 0.188 759s Grid lengths: 12.000 x 12.000 x 12.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 1 759s Linearized traditional PBE 759s Multiple Debye-Huckel sphere boundary conditions 759s 2 ion species (0.000 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 2.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 5.846917564309E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #4 (acetic-ref): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 0 A 759s Current memory usage: 61.405 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.094 x 0.094 x 0.094 759s Grid lengths: 6.000 x 6.000 x 6.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 1 759s Linearized traditional PBE 759s Boundary conditions from focusing 759s 2 ion species (0.000 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 2.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 9.815953282539E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #5 (acetate-solv): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 7.76163 A 759s Current memory usage: 61.581 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.188 x 0.188 x 0.188 759s Grid lengths: 12.000 x 12.000 x 12.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 2 759s Linearized traditional PBE 759s Multiple Debye-Huckel sphere boundary conditions 759s 2 ion species (0.150 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 78.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 8.221328580569E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #6 (acetate-solv): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 7.76163 A 759s Current memory usage: 61.581 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.094 x 0.094 x 0.094 759s Grid lengths: 6.000 x 6.000 x 6.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 2 759s Linearized traditional PBE 759s Boundary conditions from focusing 759s 2 ion species (0.150 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 78.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 1.392867783119E+04 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #7 (acetate-ref): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 0 A 759s Current memory usage: 61.405 MB total, 122.371 MB high water 759s UsTesting computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 759s *** PASSED *** 759s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 759s *** PASSED *** 759s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 759s *** PASSED *** 759s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 759s *** PASSED *** 759s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 759s *** PASSED *** 759s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 759s *** PASSED *** 759s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 759s *** PASSED *** 759s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 759s *** PASSED *** 759s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 759s *** PASSED *** 759s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 759s *** PASSED *** 759s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 759s *** PASSED *** 759s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 759s *** PASSED *** 759s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 759s *** PASSED *** 759s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 759s *** PASSED *** 759s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 759s *** PASSED *** 759s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 759s *** PASSED *** 759s Elapsed time: 8.152504 seconds 759s -------------------------------------------------------------------------------- 759s Total elapsed time: 17.242206 seconds 759s Test results have been logged 759s -------------------------------------------------------------------------------- 759s -------------------------------------------------------------------------------- 759s Testing input file ion-pmf.in 759s 759s ing linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.188 x 0.188 x 0.188 759s Grid lengths: 12.000 x 12.000 x 12.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 2 759s Linearized traditional PBE 759s Multiple Debye-Huckel sphere boundary conditions 759s 2 ion species (0.000 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 2.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 8.420373979905E+03 kJ/mol 759s Calculating forces... 759s [focusFillBound()]: WARNING: 759s Unusually large potential values 759s detected on the focusing boundary! 759s Convergence not guaranteed for NPBE/NRPBE calculations! 759s 759s ---------------------------------------- 759s CALCULATION #8 (acetate-ref): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 0 A 759s Current memory usage: 61.405 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.094 x 0.094 x 0.094 759s Grid lengths: 6.000 x 6.000 x 6.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 2 759s Linearized traditional PBE 759s Boundary conditions from focusing 759s 2 ion species (0.000 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 2.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 1.412716615065E+04 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #9 (proton-solv): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 7.76163 A 759s Current memory usage: 61.410 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.188 x 0.188 x 0.188 759s Grid lengths: 12.000 x 12.000 x 12.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 3 759s Linearized traditional PBE 759s Multiple Debye-Huckel sphere boundary conditions 759s 2 ion species (0.150 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 78.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 3.863066835285E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #10 (proton-solv): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 7.76163 A 759s Current memory usage: 61.410 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.094 x 0.094 x 0.094 759s Grid lengths: 6.000 x 6.000 x 6.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 3 759s Linearized traditional PBE 759s Boundary conditions from focusing 759s 2 ion species (0.150 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 78.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 6.289649216644E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s CALCULATION #11 (proton-ref): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 0 A 759s Current memory usage: 61.371 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.188 x 0.188 x 0.188 759s Grid lengths: 12.000 x 12.000 x 12.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 3 759s Linearized traditional PBE 759s Multiple Debye-Huckel sphere boundary conditions 759s 2 ion species (0.000 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 2.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 4.162533113906E+03 kJ/mol 759s Calculating forces... 759s [focusFillBound()]: WARNING: 759s Unusually large potential values 759s detected on the focusing boundary! 759s Convergence not guaranteed for NPBE/NRPBE calculations! 759s 759s ---------------------------------------- 759s CALCULATION #12 (proton-ref): MULTIGRID 759s Setting up problem... 759s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 759s Debye length: 0 A 759s Current memory usage: 61.371 MB total, 122.371 MB high water 759s Using linear spline charge discretization. 759s Grid dimensions: 65 x 65 x 65 759s Grid spacings: 0.094 x 0.094 x 0.094 759s Grid lengths: 6.000 x 6.000 x 6.000 759s Grid center: (0.000, -0.154, 1.287) 759s Multigrid levels: 5 759s Molecule ID: 3 759s Linearized traditional PBE 759s Boundary conditions from focusing 759s 2 ion species (0.000 M ionic strength): 759s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 759s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 759s Solute dielectric: 2.000 759s Solvent dielectric: 2.000 759s Using "molecular" surface definition;harmonic average smoothing 759s Solvent probe radius: 0.000 A 759s Temperature: 293.000 K 759s Electrostatic energies will be calculated 759s Total electrostatic energy = 6.585616091973E+03 kJ/mol 759s Calculating forces... 759s ---------------------------------------- 759s PRINT STATEMENTS 759s 759s print energy 1 (acetic-solv) - 2 (acetic-ref) end 759s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 759s Global net ELEC energy = -2.233052329981E+01 kJ/mol 759s 759s print energy 3 (acetate-solv) - 4 (acetate-ref) end 759s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 759s Global net ELEC energy = -1.984883194538E+02 kJ/mol 759s 759s print energy 5 (proton-solv) - 6 (proton-ref) end 759s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 759s Global net ELEC energy = -2.959668753288E+02 kJ/mol 759s 759s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 759s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 759s Global net ELEC energy = -4.721246714828E+02 kJ/mol 759s ---------------------------------------- 759s CLEANING UP AND SHUTTING DOWN... 759s Destroying force arrays. 759s No energy arrays to destroy. 759s Destroying multigrid structures. 759s Destroying finite element structures. 759s Destroying 3 molecules 759s Final memory usage: 0.001 MB total, 122.371 MB high water 759s 759s 759s Thanks for using APBS! 759s 767s Checking for intermediate energies in input file apbs-smol.out 767s EXPECTED COMPUTED: 16 767s EXPECTED EXPECTED: 16 767s 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] 767s 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'] 767s COMPUTED RESULT 5824.172730822 767s COMPUTED RESULT 9793.622759239 767s COMPUTED RESULT 5846.917564309 767s COMPUTED RESULT 9815.953282539 767s COMPUTED RESULT 8221.328580569 767s COMPUTED RESULT 13928.67783119 767s COMPUTED RESULT 8420.373979905 767s COMPUTED RESULT 14127.16615065 767s COMPUTED RESULT 3863.066835285 767s COMPUTED RESULT 6289.649216644 767s COMPUTED RESULT 4162.533113906 767s COMPUTED RESULT 6585.616091973 767s COMPUTED RESULT -22.33052329981 767s COMPUTED RESULT -198.4883194538 767s COMPUTED RESULT -295.9668753288 767s COMPUTED RESULT -472.1246714828 767s Running tests for ion-pmf section 767s BINARY: /usr/bin/apbs 767s INPUT: ion-pmf.in 767s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 767s asc_getToken: Error occurred (bailing out). 767s Vio_scanf: Format problem with input. 767s asc_getToken: Error occurred (bailing out). 767s Vio_scanf: Format problem with input. 767s 767s 767s ---------------------------------------------------------------------- 767s APBS -- Adaptive Poisson-Boltzmann Solver 767s Version APBS 3.4.1 767s 767s Nathan A. Baker (nathan.baker@pnnl.gov) 767s Pacific Northwest National Laboratory 767s 767s Additional contributing authors listed in the code documentation. 767s 767s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 767s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 767s Northwest Division for the U.S. Department of Energy. 767s 767s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 767s Portions Copyright (c) 2002-2020, Nathan A. Baker. 767s Portions Copyright (c) 1999-2002, The Regents of the University of California. 767s Portions Copyright (c) 1995, Michael Holst. 767s All rights reserved. 767s 767s Redistribution and use in source and binary forms, with or without 767s modification, are permitted provided that the following conditions are met: 767s 767s * Redistributions of source code must retain the above copyright notice, this 767s list of conditions and the following disclaimer. 767s 767s * Redistributions in binary form must reproduce the above copyright notice, 767s this list of conditions and the following disclaimer in the documentation 767s and/or other materials provided with the distribution. 767s 767s * Neither the name of the developer nor the names of its contributors may be 767s used to endorse or promote products derived from this software without 767s specific prior written permission. 767s 767s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 767s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 767s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 767s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 767s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 767s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 767s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 767s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 767s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 767s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 767s ---------------------------------------------------------------------- 767s APBS uses FETK (the Finite Element ToolKit) to solve the 767s Poisson-Boltzmann equation numerically. FETK is a portable collection 767s of finite element modeling class libraries developed by the Michael Holst 767s research group and written in an object-oriented form of C. FEtk is 767s designed to solve general coupled systems of nonlinear partial differential 767s equations using adaptive finite element methods, inexact Newton methods, 767s and algebraic multilevel methods. More information about FEtk may be found 767s at . 767s ---------------------------------------------------------------------- 767s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 767s Aqua is a modified form of the Holst group PMG library 767s which has been modified by Patrice Koehl 767s for improved efficiency and 767s memory usage when solving the Poisson-Boltzmann equation. 767s ---------------------------------------------------------------------- 767s Please cite your use of APBS as: 767s 767s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 767s nanosystems: application to microtubules and the ribosome. Proc. 767s Natl. Acad. Sci. USA 98, 10037-10041 2001. 767s 767s 767s This executable compiled on Jan 3 2025 at 11:01:42 767s 767s Parsing input file ion-pmf.in... 767s rank 0 size 1... 767s Parsed input file. 767s Reading parameter data from parm.dat. 767s Got paths for 1 molecules 767s Reading PDB-format atom data from ion-pmf.pdb. 767s Vpmg_ibForce: No force for zero ionic strength! 767s Vpmg_ibForce: No force for zero ionic strength! 767s 2 atoms 767s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 767s Net charge 2.00e+00 e 767s Preparing to run 3 PBE calculations. 767s ---------------------------------------- 767s CALCULATION #1 (solv): MULTIGRID 767s Setting up problem... 767s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 767s Debye length: 0 A 767s Current memory usage: 61.094 MB total, 61.094 MB high water 767s Using cubic spline charge discretization. 767s Grid dimensions: 65 x 65 x 65 767s Grid spacings: 0.210 x 0.210 x 0.210 767s Grid lengths: 13.440 x 13.440 x 13.440 767s Grid center: (0.000, 0.000, 0.000) 767s Multigrid levels: 5 767s Molecule ID: 1 767s Linearized traditional PBE 767s Multiple Debye-Huckel sphere boundary conditions 767s 0 ion species (0.000 M ionic strength): 767s Solute dielectric: 1.000 767s Solvent dielectric: 78.540 767s Using spline-based surface definition;window = 0.300 767s Temperature: 298.150 K 767s Electrostatic energies will be calculated 767s All-atom solvent forces will be calculated 767s Total electrostatic energy = 7.839535983197E+03 kJ/mol 767s Calculating forces... 767s Printing per-atom forces for molecule 1 (kJ/mol/A) 767s Legend: 767s tot n -- total force for atom n 767s qf n -- fixed charge force for atom n 767s db n -- dielectric boundary force for atom n 767s ib n -- ionic boundary force for atom n 767s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 767s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 767s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 767s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 767s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 767s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 767s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 767s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 767s Vpmg_ibForce: No force for zero ionic strength! 767s Vpmg_ibForce: No force for zero ionic strength! 767s ---------------------------------------- 767s CALCULATION #2 (ref): MULTIGRID 767s Setting up problem... 767s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 767s Debye length: 0 A 767s Current memory usage: 61.095 MB total, 61.134 MB high water 767s Using cubic spline charge discretization. 767s Grid dimensions: 65 x 65 x 65 767s Grid spacings: 0.210 x 0.210 x 0.210 767s Grid lengths: 13.440 x 13.440 x 13.440 767s Grid center: (0.000, 0.000, 0.000) 767s Multigrid levels: 5 767s Molecule ID: 1 767s Linearized traditional PBE 767s Multiple Debye-Huckel sphere boundary conditions 767s 0 ion species (0.000 M ionic strength): 767s Solute dielectric: 1.000 767s Solvent dielectric: 1.000 767s Using spline-based surface definition;window = 0.300 767s Temperature: 298.150 K 767s Electrostatic energies will be calculated 767s All-atom solvent forces will be calculated 767s Total electrostatic energy = 8.964727588811E+03 kJ/mol 767s Calculating forces... 767s Printing per-atom forces for molecule 1 (kJ/mol/A) 767s Legend: 767s tot n -- total force for atom n 767s qf n -- fixed charge force for atom n 767s db n -- dielectric boundary force for atom n 767s ib n -- ionic boundary force for atom n 767s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 767s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 767s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 767s mgF db 0 0.000e+00 0.000e+00 0.000e+00 767s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 767s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 767s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 767s mgF db 1 0.000e+00 0.000e+00 0.000e+00 767s ---------------------------------------- 767s CALCULATION #3 (asolv): APOLAR 767s Printing per atom forces (kJ/mol/A) 767s Legend: 767s tot n -- Total force for atom n 767s sasa n -- SASA force for atom n 767s sav n -- SAV force for atom n 767s wca n -- WCA force for atom n 767s 767s gamma 0.000720 767s pressure 0.000000 767s bconc 0.033000 767s 767s tot 0 2.715e-02 9.130e-07 9.130e-07 767s sasa 0 -1.100e+01 0.000e+00 0.000e+00 767s sav 0 0.000e+00 0.000e+00 0.000e+00 767s wca 0 -5.827e-01 -2.767e-05 -2.767e-05 767s tot 1 -2.723e-02 9.133e-07 9.133e-07 767s sasa 1 1.112e+01 0.000e+00 0.000e+00 767s sav 1 0.000e+00 0.000e+00 0.000e+00 767s wca 1 5.827e-01 -2.767e-05 -2.767e-05 767s 767s 767s Solvent Accessible Surface Area (SASA) for each atom: 767s SASA for atom 0: 1.153275282828E+02 767s SASA for atom 1: 1.153114143344E+02 767s 767s Total solvent accessible surface area: 230.639 A^2 767s 767s Surface tension*area energies (gamma * SASA) for each atom: 767s Surface tension*area energy for atom 0: 8.303582036361E-02 767s Surface tension*area energy for atom 1: 8.302421832080E-02 767s 767s Total surface tension energy: 0.16606 kJ/mol 767s 767s Total solvent accessible volume: 0 A^3 767s 767s Total pressure*volume energy: 0 kJ/mol 767s 767s WCA dispersion Energies for each atom: 767s WCA energy for atom 0: -6.909718359932E+00 767s WCA energy for atom 1: -6.909422551724E+00 767s 767s Total WCA energy: -13.8191 kJ/mol 767s 767s Total non-polar energy = -1.365308087297E+01 kJ/mol 767s ---------------------------------------- 767s PRINT STATEMENTS 767s 767s print energy 1 (solv) - 2 (ref) end 767s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 767s Global net ELEC energy = -1.125191605614E+03 kJ/mol 767s print force 1 (solv) - 2 (ref) end 767s Printing per-atom forces (kJ/mol/A). 767s Legend: 767s tot n -- Total force for atom n 767s qf n -- Fixed charge force for atom n 767s db n -- Dielectric boundary force for atom n 767s ib n -- Ionic boundary force for atom n 767s tot all -- Total force for system 767s qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 767s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 767s db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 767s tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 767s qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 767s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 767s db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 767s tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 767s tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 767s 767s print APOL energy 1 (asolv) end 767s Global net APOL energy = -1.365308087297E+01 kJ/mol 767s 767s print APOL force 1 (asolv) end 767s Printing per atom forces (kJ/mol/A) 767s Legend: 767s tot n -- Total force for atom n 767s sasa n -- SASA force for atom n 767s sav n -- SAV force for atom n 767s wca n -- WCA force for atom n 767s tot all -- Total force for system 767s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 767s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 767s wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 767s tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 767s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 767s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 767s wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 767s tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 767s tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 767s ---------------------------------------- 767s CLEANING UP AND SHUTTING DOWN... 767s Destroying force arrays. 767s No energy arrays to destroy. 767s Destroying multigrid structures. 767s Destroying finite element structures. 767s Destroying 1 molecules 767s Final memory usage: 60.711 MB total, 62.228 MB high water 767s 767s 767s Thanks for using APBS! 767s 767s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 767s *** PASSED *** 767s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 767s *** PASSED *** 767s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 767s *** PASSED *** 767s Elapsed time: 8.336969 seconds 767s -------------------------------------------------------------------------------- 767s Total elapsed time: 8.336969 seconds 767s Test results have been logged 767s -------------------------------------------------------------------------------- 767s -------------------------------------------------------------------------------- 767s Testing input file apbs-mol-vdw.in 767s 802s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 802s *** PASSED *** 802s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 802s *** PASSED *** 802s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 802s *** PASSED *** 802s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 802s *** PASSED *** 802s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 802s *** PASSED *** 802s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 802s *** PASSED *** 802s Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) 802s *** PASSED *** 802s Elapsed time: 35.071953 seconds 802s -------------------------------------------------------------------------------- 802s -------------------------------------------------------------------------------- 802s Testing input file apbs-smol-vdw.in 802s 802s Checking for intermediate energies in input file ion-pmf.out 802s EXPECTED COMPUTED: 4 802s EXPECTED EXPECTED: 4 802s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] 802s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 802s COMPUTED RESULT 7839.535983197 802s COMPUTED RESULT 8964.727588811 802s COMPUTED RESULT -1125.191605614 802s COMPUTED RESULT -13.65308087297 802s Running tests for pka-lig section 802s BINARY: /usr/bin/apbs 802s INPUT: apbs-mol-vdw.in 802s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 802s asc_getToken: Error occurred (bailing out). 802s Vio_scanf: Format problem with input. 802s 802s 802s ---------------------------------------------------------------------- 802s APBS -- Adaptive Poisson-Boltzmann Solver 802s Version APBS 3.4.1 802s 802s Nathan A. Baker (nathan.baker@pnnl.gov) 802s Pacific Northwest National Laboratory 802s 802s Additional contributing authors listed in the code documentation. 802s 802s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 802s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 802s Northwest Division for the U.S. Department of Energy. 802s 802s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 802s Portions Copyright (c) 2002-2020, Nathan A. Baker. 802s Portions Copyright (c) 1999-2002, The Regents of the University of California. 802s Portions Copyright (c) 1995, Michael Holst. 802s All rights reserved. 802s 802s Redistribution and use in source and binary forms, with or without 802s modification, are permitted provided that the following conditions are met: 802s 802s * Redistributions of source code must retain the above copyright notice, this 802s list of conditions and the following disclaimer. 802s 802s * Redistributions in binary form must reproduce the above copyright notice, 802s this list of conditions and the following disclaimer in the documentation 802s and/or other materials provided with the distribution. 802s 802s * Neither the name of the developer nor the names of its contributors may be 802s used to endorse or promote products derived from this software without 802s specific prior written permission. 802s 802s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 802s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 802s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 802s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 802s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 802s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 802s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 802s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 802s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 802s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 802s ---------------------------------------------------------------------- 802s APBS uses FETK (the Finite Element ToolKit) to solve the 802s Poisson-Boltzmann equation numerically. FETK is a portable collection 802s of finite element modeling class libraries developed by the Michael Holst 802s research group and written in an object-oriented form of C. FEtk is 802s designed to solve general coupled systems of nonlinear partial differential 802s equations using adaptive finite element methods, inexact Newton methods, 802s and algebraic multilevel methods. More information about FEtk may be found 802s at . 802s ---------------------------------------------------------------------- 802s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 802s Aqua is a modified form of the Holst group PMG library 802s which has been modified by Patrice Koehl 802s for improved efficiency and 802s memory usage when solving the Poisson-Boltzmann equation. 802s ---------------------------------------------------------------------- 802s Please cite your use of APBS as: 802s 802s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 802s nanosystems: application to microtubules and the ribosome. Proc. 802s Natl. Acad. Sci. USA 98, 10037-10041 2001. 802s 802s 802s This executable compiled on Jan 3 2025 at 11:01:42 802s 802s Parsing input file apbs-mol-vdw.in... 802s rank 0 size 1... 802s Parsed input file. 802s Got paths for 3 molecules 802s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 802s asc_getToken: Error occurred (bailing out). 802s Vio_scanf: Format problem with input. 802s 47 atoms 802s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 802s Net charge 1.11e-16 e 802s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 802s asc_getToken: Error occurred (bailing out). 802s Vio_scanf: Format problem with input. 802s 3423 atoms 802s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 802s Net charge 1.00e+00 e 802s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 802s 3470 atoms 802s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 802s Net charge 1.00e+00 e 802s Preparing to run 6 PBE calculations. 802s ---------------------------------------- 802s CALCULATION #1 (lig-coarse): MULTIGRID 802s Setting up problem... 802s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 802s Debye length: 0 A 802s Current memory usage: 203.811 MB total, 203.811 MB high water 802s Using linear spline charge discretization. 802s Grid dimensions: 97 x 97 x 97 802s Grid spacings: 0.729 x 0.729 x 0.729 802s Grid lengths: 70.000 x 70.000 x 70.000 802s Grid center: (28.969, -32.507, 27.022) 802s Multigrid levels: 4 802s Molecule ID: 1 802s Linearized traditional PBE 802s Single Debye-Huckel sphere boundary conditions 802s 2 ion species (0.000 M ionic strength): 802s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 802s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 802s Solute dielectric: 2.000 802s Solvent dielectric: 78.000 802s Using "molecular" surface definition; no smoothing 802s Solvent probe radius: 0.000 A 802s Temperature: 298.150 K 802s Electrostatic energies will be calculated 802s Total electrostatic energy = 2.224988750664E+03 kJ/mol 802s Calculating forces... 802s ---------------------------------------- 802s CALCULATION #2 (lig-fine): MULTIGRID 802s Setting up problem... 802s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 802s Debye length: 0 A 802s Current memory usage: 203.811 MB total, 405.040 MB high water 802s Using linear spline charge discretization. 802s Grid dimensions: 97 x 97 x 97 802s Grid spacings: 0.250 x 0.250 x 0.250 802s Grid lengths: 24.000 x 24.000 x 24.000 802s Grid center: (24.822, -33.153, 21.545) 802s Multigrid levels: 4 802s Molecule ID: 1 802s Linearized traditional PBE 802s Boundary conditions from focusing 802s 2 ion species (0.000 M ionic strength): 802s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 802s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 802s Solute dielectric: 2.000 802s Solvent dielectric: 78.000 802s Using "molecular" surface definition; no smoothing 802s Solvent probe radius: 0.000 A 802s Temperature: 298.150 K 802s Electrostatic energies will be calculated 802s Total electrostatic energy = 1.049695084686E+04 kJ/mol 802s Calculating forces... 802s ---------------------------------------- 802s CALCULATION #3 (pka-coarse): MULTIGRID 802s Setting up problem... 802s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 802s Debye length: 0 A 802s Current memory usage: 270.381 MB total, 405.040 MB high water 802s Using linear spline charge discretization. 802s Grid dimensions: 97 x 97 x 97 802s Grid spacings: 0.729 x 0.729 x 0.729 802s Grid lengths: 70.000 x 70.000 x 70.000 802s Grid center: (28.969, -32.507, 27.022) 802s Multigrid levels: 4 802s Molecule ID: 2 802s Linearized traditional PBE 802s Single Debye-Huckel sphere boundary conditions 802s 2 ion species (0.000 M ionic strength): 802s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 802s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 802s Solute dielectric: 2.000 802s Solvent dielectric: 78.000 802s Using "molecular" surface definition; no smoothing 802s Solvent probe radius: 0.000 A 802s Temperature: 298.150 K 802s Electrostatic energies will be calculated 802s Total electrostatic energy = 1.818450789522E+05 kJ/mol 802s Calculating forces... 802s [focusFillBound()]: WARNING: 802s Unusually large potential values 802s detected on the focusing boundary! 802s Convergence not guaranteed for NPBE/NRPBE calculations! 802s 802s ---------------------------------------- 802s CALCULATION #4 (pka-fine): MULTIGRID 802s Setting up problem... 802s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 802s Debye length: 0 A 802s Current memory usage: 270.381 MB total, 491.899 MB high water 802s Using linear spline charge discretization. 802s Grid dimensions: 97 x 97 x 97 802s Grid spacings: 0.250 x 0.250 x 0.250 802s Grid lengths: 24.000 x 24.000 x 24.000 802s Grid center: (24.822, -33.153, 21.545) 802s Multigrid levels: 4 802s Molecule ID: 2 802s Linearized traditional PBE 802s Boundary conditions from focusing 802s 2 ion species (0.000 M ionic strength): 802s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 802s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 802s Solute dielectric: 2.000 802s Solvent dielectric: 78.000 802s Using "molecular" surface definition; no smoothing 802s Solvent probe radius: 0.000 A 802s Temperature: 298.150 K 802s Electrostatic energies will be calculated 802s Total electrostatic energy = 3.008254338259E+05 kJ/mol 802s Calculating forces... 802s ---------------------------------------- 802s CALCULATION #5 (complex-coarse): MULTIGRID 802s Setting up problem... 802s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 802s Debye length: 0 A 802s Current memory usage: 271.059 MB total, 491.899 MB high water 802s Using linear spline charge discretization. 802s Grid dimensions: 97 x 97 x 97 802s Grid spacings: 0.729 x 0.729 x 0.729 802s Grid lengths: 70.000 x 70.000 x 70.000 802s Grid center: (28.969, -32.507, 27.022) 802s Multigrid levels: 4 802s Molecule ID: 3 802s Linearized traditional PBE 802s Single Debye-Huckel sphere boundary conditions 802s 2 ion species (0.000 M ionic strength): 802s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 802s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 802s Solute dielectric: 2.000 802s Solvent dielectric: 78.000 802s Using "molecular" surface definition; no smoothing 802s Solvent probe radius: 0.000 A 802s Temperature: 298.150 K 802s Electrostatic energies will be calculated 802s Total electrostatic energy = 1.840918409896E+05 kJ/mol 802s Calculating forces... 802s [focusFillBound()]: WARNING: 802s Unusually large potential values 802s detected on the focusing boundary! 802s Convergence not guaranteed for NPBE/NRPBE calculations! 802s 802s ---------------------------------------- 802s CALCULATION #6 (complex-fine): MULTIGRID 802s Setting up problem... 802s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 802s Debye length: 0 A 802s Current memory usage: 271.059 MB total, 492.811 MB high water 802s Using linear spline charge discretization. 802s Grid dimensions: 97 x 97 x 97 802s Grid spacings: 0.250 x 0.250 x 0.250 802s Grid lengths: 24.000 x 24.000 x 24.000 802s Grid center: (24.822, -33.153, 21.545) 802s Multigrid levels: 4 802s Molecule ID: 3 802s Linearized traditional PBE 802s Boundary conditions from focusing 802s 2 ion species (0.000 M ionic strength): 802s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 802s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 802s Solute dielectric: 2.000 802s Solvent dielectric: 78.000 802s Using "molecular" surface definition; no smoothing 802s Solvent probe radius: 0.000 A 802s Temperature: 298.150 K 802s Electrostatic energies will be calculated 802s Total electrostatic energy = 3.113304681884E+05 kJ/mol 802s Calculating forces... 802s ---------------------------------------- 802s PRINT STATEMENTS 802s 802s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 802s Local net energy (PE 0) = 8.083515648730E+00 kJ/mol 802s Global net ELEC energy = 8.083515648730E+00 kJ/mol 802s ---------------------------------------- 802s CLEANING UP AND SHUTTING DOWN... 802s Destroying force arrays. 802s No energy arrays to destroy. 802s Destroying multigrid structures. 802s Destroying finite element structures. 802s Destroying 3 molecules 802s Final memory usage: 0.001 MB total, 492.811 MB high water 802s 802s 802s Thanks for using APBS! 802s 825s Checking for intermediate energies in input file apbs-mol-vdw.out 825s EXPECTED COMPUTED: 7 825s EXPECTED EXPECTED: 7 825s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] 825s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 825s COMPUTED RESULT 2224.988750664 825s COMPUTED RESULT 10496.95084686 825s COMPUTED RESULT 181845.0789522 825s COMPUTED RESULT 300825.4338259 825s COMPUTED RESULT 184091.8409896 825s COMPUTED RESULT 311330.4681884 825s COMPUTED RESULT 8.08351564873 825s BINARY: /usr/bin/apbs 825s INPUT: apbs-smol-vdw.in 825s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 825s asc_getToken: Error occurred (bailing out). 825s Vio_scanf: Format problem with input. 825s 825s 825s ---------------------------------------------------------------------- 825s APBS -- Adaptive Poisson-Boltzmann Solver 825s Version APBS 3.4.1 825s 825s Nathan A. Baker (nathan.baker@pnnl.gov) 825s Pacific Northwest National Laboratory 825s 825s Additional contributing authors listed in the code documentation. 825s 825s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 825s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 825s Northwest Division for the U.S. Department of Energy. 825s 825s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 825s Portions Copyright (c) 2002-2020, Nathan A. Baker. 825s Portions Copyright (c) 1999-2002, The Regents of the University of California. 825s Portions Copyright (c) 1995, Michael Holst. 825s All rights reserved. 825s 825s Redistribution and use in source and binary forms, with or without 825s modification, are permitted provided that the following conditions are met: 825s 825s * Redistributions of source code must retain the above copyright notice, this 825s list of conditions and the following disclaimer. 825s 825s * Redistributions in binary form must reproduce the above copyright notice, 825s this list of conditions and the following disclaimer in the documentation 825s and/or other materials provided with the distribution. 825s 825s * Neither the name of the developer nor the names of its contributors may be 825s used to endorse or promote products derived from this software without 825s specific prior written permission. 825s 825s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 825s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 825s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 825s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 825s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 825s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 825s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 825s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 825s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 825s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 825s ---------------------------------------------------------------------- 825s APBS uses FETK (the Finite Element ToolKit) to solve the 825s Poisson-Boltzmann equation numerically. FETK is a portable collection 825s of finite element modeling class libraries developed by the Michael Holst 825s research group and written in an object-oriented form of C. FEtk is 825s designed to solve general coupled systems of nonlinear partial differential 825s equations using adaptive finite element methods, inexact Newton methods, 825s and algebraic multilevel methods. More information about FEtk may be found 825s at . 825s ---------------------------------------------------------------------- 825s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 825s Aqua is a modified form of the Holst group PMG library 826s which has been modified by Patrice Koehl 826s for improved efficiency and 826s memory usage when solving the Poisson-Boltzmann equation. 826s ---------------------------------------------------------------------- 826s Please cite your use of APBS as: 826s 826s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 826s nanosystems: application to microtubules and the ribosome. Proc. 826s Natl. Acad. Sci. USA 98, 10037-10041 2001. 826s 826s 826s This executable compiled on Jan 3 2025 at 11:01:42 826s 826s Parsing input file apbs-smol-vdw.in... 826s rank 0 size 1... 826s Parsed input file. 826s Got paths for 3 molecules 826s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 826s asc_getToken: Error occurred (bailing out). 826s Vio_scanf: Format problem with input. 826s 47 atoms 826s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 826s Net charge 1.11e-16 e 826s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 826s asc_getToken: Error occurred (bailing out). 826s Vio_scanf: Format problem with input. 826s 3423 atoms 826s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 826s Net charge 1.00e+00 e 826s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 826s 3470 atoms 826s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 826s Net charge 1.00e+00 e 826s Preparing to run 6 PBE calculations. 826s ---------------------------------------- 826s CALCULATION #1 (lig-coarse): MULTIGRID 826s Setting up problem... 826s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 826s Debye length: 0 A 826s Current memory usage: 203.811 MB total, 203.811 MB high water 826s Using linear spline charge discretization. 826s Grid dimensions: 97 x 97 x 97 826s Grid spacings: 0.729 x 0.729 x 0.729 826s Grid lengths: 70.000 x 70.000 x 70.000 826s Grid center: (28.969, -32.507, 27.022) 826s Multigrid levels: 4 826s Molecule ID: 1 826s Linearized traditional PBE 826s Single Debye-Huckel sphere boundary conditions 826s 2 ion species (0.000 M ionic strength): 826s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 826s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 826s Solute dielectric: 2.000 826s Solvent dielectric: 78.000 826s Using "molecular" surface definition;harmonic average smoothing 826s Solvent probe radius: 0.000 A 826s Temperature: 298.150 K 826s Electrostatic energies will be calculated 826s Total electrostatic energy = 2.226793167046E+03 kJ/mol 826s Calculating forces... 826s ---------------------------------------- 826s CALCULATION #2 (lig-fine): MULTIGRID 826s Setting up problem... 826s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 826s Debye length: 0 A 826s Current memory usage: 203.811 MB total, 405.040 MB high water 826s Using linear spline charge discretization. 826s Grid dimensions: 97 x 97 x 97 826s Grid spacings: 0.250 x 0.250 x 0.250 826s Grid lengths: 24.000 x 24.000 x 24.000 826s Grid center: (24.822, -33.153, 21.545) 826s Multigrid levels: 4 826s Molecule ID: 1 826s Linearized traditional PBE 826s Boundary conditions from focusing 826s 2 ion species (0.000 M ionic strength): 826s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 826s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 826s Solute dielectric: 2.000 826s Solvent dielectric: 78.000 826s Using "molecular" surface definition;harmonic average smoothing 826s Solvent probe radius: 0.000 A 826s Temperature: 298.150 K 826s Electrostatic energies will be calculated 826s Total electrostatic energy = 1.050504485887E+04 kJ/mol 826s Calculating forces... 826s ---------------------------------------- 826s CALCULATION #3 (pka-coarse): MULTIGRID 826s Setting up problem... 826s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 826s Debye length: 0 A 826s Current memory usage: 270.381 MB total, 405.040 MB high water 826s Using linear spline charge discretization. 826s Grid dimensions: 97 x 97 x 97 826s Grid spacings: 0.729 x 0.729 x 0.729 826s Grid lengths: 70.000 x 70.000 x 70.000 826s Grid center: (28.969, -32.507, 27.022) 826s Multigrid levels: 4 826s Molecule ID: 2 826s Linearized traditional PBE 826s Single Debye-Huckel sphere boundary conditions 826s 2 ion species (0.000 M ionic strength): 826s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 826s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 826s Solute dielectric: 2.000 826s Solvent dielectric: 78.000 826s Using "molecular" surface definition;harmonic average smoothing 826s Solvent probe radius: 0.000 A 826s Temperature: 298.150 K 826s Electrostatic energies will be calculated 826s Total electrostatic energy = 1.827976621645E+05 kJ/mol 826s Calculating forces... 826s [focusFillBound()]: WARNING: 826s Unusually large potential values 826s detected on the focusing boundary! 826s Convergence not guaranteed for NPBE/NRPBE calculations! 826s 826s ---------------------------------------- 826s CALCULATION #4 (pka-fine): MULTIGRID 826s Setting up problem... 826s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 826s Debye length: 0 A 826s Current memory usage: 270.381 MB total, 491.899 MB high water 826s Using linear spline charge discretization. 826s Grid dimensions: 97 x 97 x 97 826s Grid spacings: 0.250 x 0.250 x 0.250 826s Grid lengths: 24.000 x 24.000 x 24.000 826s Grid center: (24.822, -33.153, 21.545) 826s Multigrid levels: 4 826s Molecule ID: 2 826s Linearized traditional PBE 826s Boundary conditions from focusing 826s 2 ion species (0.000 M ionic strength): 826s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 826s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 826s Solute dielectric: 2.000 826s Solvent dielectric: 78.000 826s Using "molecular" surface definition;harmonic average smoothing 826s Solvent probe radius: 0.000 A 826s Temperature: 298.150 K 826s Electrostatic energies will be calculated 826s Total electrostatic energy = 3.017228546773E+05 kJ/mol 826s Calculating forces... 826s ---------------------------------------- 826s CALCULATION #5 (complex-coarse): MULTIGRID 826s Setting up problem... 826s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 826s Debye length: 0 A 826s Current memory usage: 271.059 MB total, 491.899 MB high water 826s Using linear spline charge discretization. 826s Grid dimensions: 97 x 97 x 97 826s Grid spacings: 0.729 x 0.729 x 0.729 826s Grid lengths: 70.000 x 70.000 x 70.000 826s Grid center: (28.969, -32.507, 27.022) 826s Multigrid levels: 4 826s Molecule ID: 3 826s Linearized traditional PBE 826s Single Debye-Huckel sphere boundary conditions 826s 2 ion species (0.000 M ionic strength): 826s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 826s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 826s Solute dielectric: 2.000 826s Solvent dielectric: 78.000 826s Using "molecular" surface definition;harmonic average smoothing 826s Solvent probe radius: 0.000 A 826s Temperature: 298.150 K 826s Electrostatic energies will be calculated 826s Total electrostatic energy = 1.850819075387E+05 kJ/mol 826s Calculating forces... 826s [focusFillBound()]: WARNING: 826s Unusually large potential values 826s detected on the focusing boundary! 826s Convergence not guaranteed for NPBE/NRPBE calculations! 826s 826s ---------------------------------------- 826s CALCULATION #6 (complex-fine): MULTIGRID 826s Setting up problem... 826s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 826s Debye length: 0 A 826s Current memory usage: 271.059 MB total, 492.811 MB high water 826s Using linear spline charge discretization. 826s Grid dimensions: 97 x 97 x 97 826s Grid spacings: 0.250 x 0.250 x 0.250 826s Grid lengths: 24.000 x 24.000 x 24.000 826s Grid center: (24.822, -33.153, 21.545) 826s Multigrid levels: 4 826s Molecule ID: 3 826s Linearized traditional PBE 826s Boundary conditions from focusing 826s 2 ion species (0.000 M ionic strength): 826s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 826s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 826s Solute dielectric: 2.000 826s Solvent dielectric: 78.000 826s Using "molecular" surface definition;harmonic average smoothing 826s Solvent probe radius: 0.000 A 826s Temperature: 298.150 K 826s Electrostatic energies will be calculated 826s Total electrostatic energy = 3.122488625388E+05 kJ/mol 826s Calculating forces... 826s ---------------------------------------- 826s PRINT STATEMENTS 826s 826s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 826s Local net energy (PE 0) = 2.096300255723E+01 kJ/mol 826s Global net ELEC energy = 2.096300255723E+01 kJ/mol 826s ---------------------------------------- 826s CLEANING UP AND SHUTTING DOWN... 826s Destroying force arrays. 826s No energy arrays to destroy. 826s Destroying multigrid structures. 826s Destroying finite element structures. 826s Destroying 3 molecules 826s Final memory usage: 0.001 MB total, 492.811 MB high water 826s 826s 826s Thanks for using APBS! 826s 853s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 853s *** PASSED *** 853s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 853s *** PASSED *** 853s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 853s *** PASSED *** 853s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 853s *** PASSED *** 853s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 853s *** PASSED *** 853s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 853s *** PASSED *** 853s Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) 853s *** PASSED *** 853s Elapsed time: 27.168482 seconds 853s -------------------------------------------------------------------------------- 853s -------------------------------------------------------------------------------- 853s Testing input file apbs-smol-surf.in 853s 853s Checking for intermediate energies in input file apbs-smol-vdw.out 853s EXPECTED COMPUTED: 7 853s EXPECTED EXPECTED: 7 853s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] 853s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 853s COMPUTED RESULT 2226.793167046 853s COMPUTED RESULT 10505.04485887 853s COMPUTED RESULT 182797.6621645 853s COMPUTED RESULT 301722.8546773 853s COMPUTED RESULT 185081.9075387 853s COMPUTED RESULT 312248.8625388 853s COMPUTED RESULT 20.96300255723 853s BINARY: /usr/bin/apbs 853s INPUT: apbs-mol-surf.in 853s COMMAND: ['/usr/bin/apbs', 'apbs-mol-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-mol-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; no smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 2.244350164274E+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; no smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 1.052149475373E+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; no smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 1.862615690066E+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; no smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 3.051810884053E+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; no smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 1.886625455219E+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; no smoothing 853s Solvent probe radius: 1.400 A 853s Temperature: 298.150 K 853s Electrostatic energies will be calculated 853s Total electrostatic energy = 3.158218439277E+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) = 1.192607686581E+02 kJ/mol 853s Global net ELEC energy = 1.192607686581E+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 875s Checking for intermediate energies in input file apbs-mol-surf.out 875s EXPECTED COMPUTED: 7 875s EXPECTED EXPECTED: 7 875s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] 875s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 875s COMPUTED RESULT 2244.350164274 875s COMPUTED RESULT 10521.49475373 875s COMPUTED RESULT 186261.5690066 875s COMPUTED RESULT 305181.0884053 875s COMPUTED RESULT 188662.5455219 875s COMPUTED RESULT 315821.8439277 875s COMPUTED RESULT 119.2607686581 875s BINARY: /usr/bin/apbs 875s INPUT: apbs-smol-surf.in 875s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 875s asc_getToken: Error occurred (bailing out). 875s Vio_scanf: Format problem with input. 875s 875s 875s ---------------------------------------------------------------------- 875s APBS -- Adaptive Poisson-Boltzmann Solver 875s Version APBS 3.4.1 875s 875s Nathan A. Baker (nathan.baker@pnnl.gov) 875s Pacific Northwest National Laboratory 875s 875s Additional contributing authors listed in the code documentation. 875s 875s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 875s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 875s Northwest Division for the U.S. Department of Energy. 875s 875s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 875s Portions Copyright (c) 2002-2020, Nathan A. Baker. 875s Portions Copyright (c) 1999-2002, The Regents of the University of California. 875s Portions Copyright (c) 1995, Michael Holst. 875s All rights reserved. 875s 875s Redistribution and use in source and binary forms, with or without 875s modification, are permitted provided that the following conditions are met: 875s 875s * Redistributions of source code must retain the above copyright notice, this 875s list of conditions and the following disclaimer. 875s 875s * Redistributions in binary form must reproduce the above copyright notice, 875s this list of conditions and the following disclaimer in the documentation 875s and/or other materials provided with the distribution. 875s 875s * Neither the name of the developer nor the names of its contributors may be 875s used to endorse or promote products derived from this software without 875s specific prior written permission. 875s 875s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 875s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 875s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 875s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 875s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 875s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 875s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 875s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 875s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 875s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 875s ---------------------------------------------------------------------- 875s APBS uses FETK (the Finite Element ToolKit) to solve the 875s Poisson-Boltzmann equation numerically. FETK is a portable collection 875s of finite element modeling class libraries developed by the Michael Holst 875s research group and written in an object-oriented form of C. FEtk is 875s designed to solve general coupled systems of nonlinear partial differential 875s equations using adaptive finite element methods, inexact Newton methods, 875s and algebraic multilevel methods. More information about FEtk may be found 875s at . 875s ---------------------------------------------------------------------- 875s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 875s Aqua is a modified form of the Holst group PMG library 875s which has been modified by Patrice Koehl 875s for improved efficiency and 875s memory usage when solving the Poisson-Boltzmann equation. 875s ---------------------------------------------------------------------- 875s Please cite your use of APBS as: 875s 875s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 875s nanosystems: application to microtubules and the ribosome. Proc. 875s Natl. Acad. Sci. USA 98, 10037-10041 2001. 875s 875s 875s This executable compiled on Jan 3 2025 at 11:01:42 875s 875s Parsing input file apbs-smol-surf.in... 875s rank 0 size 1... 875s Parsed input file. 875s Got paths for 3 molecules 875s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 875s asc_getToken: Error occurred (bailing out). 875s Vio_scanf: Format problem with input. 875s 47 atoms 875s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 875s Net charge 1.11e-16 e 875s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 875s asc_getToken: Error occurred (bailing out). 875s Vio_scanf: Format problem with input. 875s 3423 atoms 875s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 875s Net charge 1.00e+00 e 875s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 875s 3470 atoms 875s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 875s Net charge 1.00e+00 e 875s Preparing to run 6 PBE calculations. 875s ---------------------------------------- 875s CALCULATION #1 (lig-coarse): MULTIGRID 875s Setting up problem... 875s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 875s Debye length: 0 A 875s Current memory usage: 203.396 MB total, 203.396 MB high water 875s Using linear spline charge discretization. 875s Grid dimensions: 97 x 97 x 97 875s Grid spacings: 0.729 x 0.729 x 0.729 875s Grid lengths: 70.000 x 70.000 x 70.000 875s Grid center: (28.969, -32.507, 27.022) 875s Multigrid levels: 4 875s Molecule ID: 1 875s Linearized traditional PBE 875s Single Debye-Huckel sphere boundary conditions 875s 2 ion species (0.000 M ionic strength): 875s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 875s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 875s Solute dielectric: 2.000 875s Solvent dielectric: 78.000 875s Using "molecular" surface definition;harmonic average smoothing 875s Solvent probe radius: 1.400 A 875s Temperature: 298.150 K 875s Electrostatic energies will be calculated 875s Total electrostatic energy = 2.251466789420E+03 kJ/mol 875s Calculating forces... 875s ---------------------------------------- 875s CALCULATION #2 (lig-fine): MULTIGRID 875s Setting up problem... 875s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 875s Debye length: 0 A 875s Current memory usage: 203.396 MB total, 404.625 MB high water 875s Using linear spline charge discretization. 875s Grid dimensions: 97 x 97 x 97 875s Grid spacings: 0.250 x 0.250 x 0.250 875s Grid lengths: 24.000 x 24.000 x 24.000 875s Grid center: (24.822, -33.153, 21.545) 875s Multigrid levels: 4 875s Molecule ID: 1 875s Linearized traditional PBE 875s Boundary conditions from focusing 875s 2 ion species (0.000 M ionic strength): 875s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 875s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 875s Solute dielectric: 2.000 875s Solvent dielectric: 78.000 875s Using "molecular" surface definition;harmonic average smoothing 875s Solvent probe radius: 1.400 A 875s Temperature: 298.150 K 875s Electrostatic energies will be calculated 875s Total electrostatic energy = 1.052814502873E+04 kJ/mol 875s Calculating forces... 875s ---------------------------------------- 875s CALCULATION #3 (pka-coarse): MULTIGRID 875s Setting up problem... 875s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 875s Debye length: 0 A 875s Current memory usage: 230.750 MB total, 404.625 MB high water 875s Using linear spline charge discretization. 875s Grid dimensions: 97 x 97 x 97 875s Grid spacings: 0.729 x 0.729 x 0.729 875s Grid lengths: 70.000 x 70.000 x 70.000 875s Grid center: (28.969, -32.507, 27.022) 875s Multigrid levels: 4 875s Molecule ID: 2 875s Linearized traditional PBE 875s Single Debye-Huckel sphere boundary conditions 875s 2 ion species (0.000 M ionic strength): 875s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 875s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 875s Solute dielectric: 2.000 875s Solvent dielectric: 78.000 875s Using "molecular" surface definition;harmonic average smoothing 875s Solvent probe radius: 1.400 A 875s Temperature: 298.150 K 875s Electrostatic energies will be calculated 875s Total electrostatic energy = 1.864071689626E+05 kJ/mol 875s Calculating forces... 875s [focusFillBound()]: WARNING: 875s Unusually large potential values 875s detected on the focusing boundary! 875s Convergence not guaranteed for NPBE/NRPBE calculations! 875s 875s ---------------------------------------- 875s CALCULATION #4 (pka-fine): MULTIGRID 875s Setting up problem... 875s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 875s Debye length: 0 A 875s Current memory usage: 230.750 MB total, 452.268 MB high water 875s Using linear spline charge discretization. 875s Grid dimensions: 97 x 97 x 97 875s Grid spacings: 0.250 x 0.250 x 0.250 875s Grid lengths: 24.000 x 24.000 x 24.000 875s Grid center: (24.822, -33.153, 21.545) 875s Multigrid levels: 4 875s Molecule ID: 2 875s Linearized traditional PBE 875s Boundary conditions from focusing 875s 2 ion species (0.000 M ionic strength): 875s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 875s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 875s Solute dielectric: 2.000 875s Solvent dielectric: 78.000 875s Using "molecular" surface definition;harmonic average smoothing 875s Solvent probe radius: 1.400 A 875s Temperature: 298.150 K 875s Electrostatic energies will be calculated 875s Total electrostatic energy = 3.053319953673E+05 kJ/mol 875s Calculating forces... 875s ---------------------------------------- 875s CALCULATION #5 (complex-coarse): MULTIGRID 875s Setting up problem... 875s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 875s Debye length: 0 A 875s Current memory usage: 230.854 MB total, 452.268 MB high water 875s Using linear spline charge discretization. 875s Grid dimensions: 97 x 97 x 97 875s Grid spacings: 0.729 x 0.729 x 0.729 875s Grid lengths: 70.000 x 70.000 x 70.000 875s Grid center: (28.969, -32.507, 27.022) 875s Multigrid levels: 4 875s Molecule ID: 3 875s Linearized traditional PBE 875s Single Debye-Huckel sphere boundary conditions 875s 2 ion species (0.000 M ionic strength): 875s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 875s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 875s Solute dielectric: 2.000 875s Solvent dielectric: 78.000 875s Using "molecular" surface definition;harmonic average smoothing 875s Solvent probe radius: 1.400 A 875s Temperature: 298.150 K 875s Electrostatic energies will be calculated 875s Total electrostatic energy = 1.888027142979E+05 kJ/mol 875s Calculating forces... 875s [focusFillBound()]: WARNING: 875s Unusually large potential values 875s detected on the focusing boundary! 875s Convergence not guaranteed for NPBE/NRPBE calculations! 875s 875s ---------------------------------------- 875s CALCULATION #6 (complex-fine): MULTIGRID 875s Setting up problem... 875s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 875s Debye length: 0 A 875s Current memory usage: 230.854 MB total, 452.606 MB high water 875s Using linear spline charge discretization. 875s Grid dimensions: 97 x 97 x 97 875s Grid spacings: 0.250 x 0.250 x 0.250 875s Grid lengths: 24.000 x 24.000 x 24.000 875s Grid center: (24.822, -33.153, 21.545) 875s Multigrid levels: 4 875s Molecule ID: 3 875s Linearized traditional PBE 875s Boundary conditions from focusing 875s 2 ion species (0.000 M ionic strength): 875s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 875s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 875s Solute dielectric: 2.000 875s Solvent dielectric: 78.000 875s Using "molecular" surface definition;harmonic average smoothing 875s Solvent probe radius: 1.400 A 875s Temperature: 298.150 K 875s Electrostatic energies will be calculated 875s Total electrostatic energy = 3.159690177241E+05 kJ/mol 875s Calculating forces... 875s ---------------------------------------- 875s PRINT STATEMENTS 875s 875s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 875s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 875s Global net ELEC energy = 1.088773280806E+02 kJ/mol 875s ---------------------------------------- 875s CLEANING UP AND SHUTTING DOWN... 875s Destroying force arrays. 875s No energy arrays to destroy. 875s Destroying multigrid structures. 875s Destroying finite element structures. 875s Destroying 3 molecules 875s Final memory usage: 0.001 MB total, 452.606 MB high water 875s 875s 875s ThTesting computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 875s *** PASSED *** 875s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 875s *** PASSED *** 875s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 875s *** PASSED *** 875s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 875s *** PASSED *** 875s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 875s *** PASSED *** 875s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 875s *** PASSED *** 875s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 875s *** PASSED *** 875s Elapsed time: 22.781247 seconds 875s -------------------------------------------------------------------------------- 875s Total elapsed time: 108.216201 seconds 875s Test results have been logged 875s -------------------------------------------------------------------------------- 875s -------------------------------------------------------------------------------- 875s Testing input file complex-0_1.in 875s 876s anks for using APBS! 876s 878s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 878s *** PASSED *** 878s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 878s *** PASSED *** 878s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 878s *** PASSED *** 878s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 878s *** PASSED *** 878s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 878s *** PASSED *** 878s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 878s *** PASSED *** 878s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 878s *** PASSED *** 878s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 878s *** PASSED *** 878s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 878s *** PASSED *** 878s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 878s *** PASSED *** 878s Elapsed time: 2.118493 seconds 878s -------------------------------------------------------------------------------- 878s -------------------------------------------------------------------------------- 878s Testing input file complex-0_2.in 878s 878s Checking for intermediate energies in input file apbs-smol-surf.out 878s EXPECTED COMPUTED: 7 878s EXPECTED EXPECTED: 7 878s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 878s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 878s COMPUTED RESULT 2251.46678942 878s COMPUTED RESULT 10528.14502873 878s COMPUTED RESULT 186407.1689626 878s COMPUTED RESULT 305331.9953673 878s COMPUTED RESULT 188802.7142979 878s COMPUTED RESULT 315969.0177241 878s COMPUTED RESULT 108.8773280806 878s Running tests for point-pmf section 878s BINARY: /usr/bin/apbs 878s INPUT: complex-0_1.in 878s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 878s asc_getToken: Error occurred (bailing out). 878s Vio_scanf: Format problem with input. 878s 878s 878s ---------------------------------------------------------------------- 878s APBS -- Adaptive Poisson-Boltzmann Solver 878s Version APBS 3.4.1 878s 878s Nathan A. Baker (nathan.baker@pnnl.gov) 878s Pacific Northwest National Laboratory 878s 878s Additional contributing authors listed in the code documentation. 878s 878s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 878s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 878s Northwest Division for the U.S. Department of Energy. 878s 878s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 878s Portions Copyright (c) 2002-2020, Nathan A. Baker. 878s Portions Copyright (c) 1999-2002, The Regents of the University of California. 878s Portions Copyright (c) 1995, Michael Holst. 878s All rights reserved. 878s 878s Redistribution and use in source and binary forms, with or without 878s modification, are permitted provided that the following conditions are met: 878s 878s * Redistributions of source code must retain the above copyright notice, this 878s list of conditions and the following disclaimer. 878s 878s * Redistributions in binary form must reproduce the above copyright notice, 878s this list of conditions and the following disclaimer in the documentation 878s and/or other materials provided with the distribution. 878s 878s * Neither the name of the developer nor the names of its contributors may be 878s used to endorse or promote products derived from this software without 878s specific prior written permission. 878s 878s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 878s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 878s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 878s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 878s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 878s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 878s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 878s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 878s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 878s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 878s ---------------------------------------------------------------------- 878s APBS uses FETK (the Finite Element ToolKit) to solve the 878s Poisson-Boltzmann equation numerically. FETK is a portable collection 878s of finite element modeling class libraries developed by the Michael Holst 878s research group and written in an object-oriented form of C. FEtk is 878s designed to solve general coupled systems of nonlinear partial differential 878s equations using adaptive finite element methods, inexact Newton methods, 878s and algebraic multilevel methods. More information about FEtk may be found 878s at . 878s ---------------------------------------------------------------------- 878s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 878s Aqua is a modified form of the Holst group PMG library 878s which has been modified by Patrice Koehl 878s for improved efficiency and 878s memory usage when solving the Poisson-Boltzmann equation. 878s ---------------------------------------------------------------------- 878s Please cite your use of APBS as: 878s 878s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 878s nanosystems: application to microtubules and the ribosome. Proc. 878s Natl. Acad. Sci. USA 98, 10037-10041 2001. 878s 878s 878s This executable compiled on Jan 3 2025 at 11:01:42 878s 878s Parsing input file complex-0_1.in... 878s rank 0 size 1... 878s Parsed input file. 878s Got paths for 3 molecules 878s Reading PQR-format atom data from mol0.pqr. 878s asc_getToken: Error occurred (bailing out). 878s Vio_scanf: Format problem with input. 878s 1 atoms 878s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 878s Net charge 1.00e+00 e 878s Reading PQR-format atom data from mol1.pqr. 878s asc_getToken: Error occurred (bailing out). 878s Vio_scanf: Format problem with input. 878s 1 atoms 878s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 878s Net charge 1.00e+00 e 878s Reading PQR-format atom data from complex-0_1.pqr. 878s 2 atoms 878s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 878s Net charge 2.00e+00 e 878s Preparing to run 3 PBE calculations. 878s ---------------------------------------- 878s CALCULATION #1 (point1): MULTIGRID 878s Setting up problem... 878s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 878s Debye length: 0 A 878s Current memory usage: 61.059 MB total, 61.059 MB high water 878s Using linear spline charge discretization. 878s Grid dimensions: 65 x 65 x 65 878s Grid spacings: 0.210 x 0.210 x 0.210 878s Grid lengths: 13.440 x 13.440 x 13.440 878s Grid center: (0.000, 0.000, 0.000) 878s Multigrid levels: 5 878s Molecule ID: 1 878s Linearized traditional PBE 878s Multiple Debye-Huckel sphere boundary conditions 878s 0 ion species (0.000 M ionic strength): 878s Solute dielectric: 78.540 878s Solvent dielectric: 78.540 878s Using spline-based surface definition;window = 0.300 878s Temperature: 298.150 K 878s Electrostatic energies will be calculated 878s Total electrostatic energy = 9.776035707281E+01 kJ/mol 878s Fixed charge energy = 97.7604 kJ/mol 878s Mobile charge energy = 0 kJ/mol 878s Dielectric energy = 96.5336 kJ/mol 878s Per-atom energies: 878s Atom 0: 9.776035707281E+01 kJ/mol 878s Calculating forces... 878s ---------------------------------------- 878s CALCULATION #2 (point2): MULTIGRID 878s Setting up problem... 878s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 878s Debye length: 0 A 878s Current memory usage: 61.059 MB total, 61.066 MB high water 878s Using linear spline charge discretization. 878s Grid dimensions: 65 x 65 x 65 878s Grid spacings: 0.210 x 0.210 x 0.210 878s Grid lengths: 13.440 x 13.440 x 13.440 878s Grid center: (0.000, 0.000, 0.000) 878s Multigrid levels: 5 878s Molecule ID: 2 878s Linearized traditional PBE 878s Multiple Debye-Huckel sphere boundary conditions 878s 0 ion species (0.000 M ionic strength): 878s Solute dielectric: 78.540 878s Solvent dielectric: 78.540 878s Using spline-based surface definition;window = 0.300 878s Temperature: 298.150 K 878s Electrostatic energies will be calculated 878s Total electrostatic energy = 8.975920687031E+01 kJ/mol 878s Fixed charge energy = 89.7592 kJ/mol 878s Mobile charge energy = 0 kJ/mol 878s Dielectric energy = 88.6151 kJ/mol 878s Per-atom energies: 878s Atom 0: 8.975920687031E+01 kJ/mol 878s Calculating forces... 878s ---------------------------------------- 878s CALCULATION #3 (complex): MULTIGRID 878s Setting up problem... 878s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 878s Debye length: 0 A 878s Current memory usage: 61.059 MB total, 61.066 MB high water 878s Using linear spline charge discretization. 878s Grid dimensions: 65 x 65 x 65 878s Grid spacings: 0.210 x 0.210 x 0.210 878s Grid lengths: 13.440 x 13.440 x 13.440 878s Grid center: (0.000, 0.000, 0.000) 878s Multigrid levels: 5 878s Molecule ID: 3 878s Linearized traditional PBE 878s Multiple Debye-Huckel sphere boundary conditions 878s 0 ion species (0.000 M ionic strength): 878s Solute dielectric: 78.540 878s Solvent dielectric: 78.540 878s Using spline-based surface definition;window = 0.300 878s Temperature: 298.150 K 878s Electrostatic energies will be calculated 878s Total electrostatic energy = 2.058277719334E+02 kJ/mol 878s Fixed charge energy = 205.828 kJ/mol 878s Mobile charge energy = 0 kJ/mol 878s Dielectric energy = 201.106 kJ/mol 878s Per-atom energies: 878s Atom 0: 1.069144350786E+02 kJ/mol 878s Atom 1: 9.891333685475E+01 kJ/mol 878s Calculating forces... 878s ---------------------------------------- 878s PRINT STATEMENTS 878s 878s print energy 3 (complex) - 1 (point1) - 2 (point2) end 878s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 878s Global net ELEC energy = 1.830820799027E+01 kJ/mol 878s ---------------------------------------- 878s CLEANING UP AND SHUTTING DOWN... 878s Destroying force arrays. 878s No energy arrays to destroy. 878s Destroying multigrid structures. 878s Destroying finite element structures. 878s Destroying 3 molecules 878s Final memory usage: 0.001 MB total, 61.066 MB high water 878s 878s 878s Thanks for using APBS! 878s 880s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 880s *** PASSED *** 880s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 880s *** PASSED *** 880s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 880s *** PASSED *** 880s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 880s *** PASSED *** 880s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 880s *** PASSED *** 880s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 880s *** PASSED *** 880s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 880s *** PASSED *** 880s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 880s *** PASSED *** 880s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 880s *** PASSED *** 880s Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) 880s *** PASSED *** 880s Elapsed time: 2.228067 seconds 880s -------------------------------------------------------------------------------- 880s -------------------------------------------------------------------------------- 880s Testing input file complex-0_3.in 880s 880s Checking for intermediate energies in input file complex-0_1.out 880s EXPECTED COMPUTED: 13 880s EXPECTED EXPECTED: 13 880s 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] 880s 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'] 880s COMPUTED RESULT 97.76035707281 880s COMPUTED RESULT 89.75920687031 880s COMPUTED RESULT 205.8277719334 880s COMPUTED RESULT 0.0 880s COMPUTED RESULT 0.0 880s COMPUTED RESULT 0.0 880s COMPUTED RESULT 97.7604 880s COMPUTED RESULT 89.7592 880s COMPUTED RESULT 205.828 880s COMPUTED RESULT 96.5336 880s COMPUTED RESULT 88.6151 880s COMPUTED RESULT 201.106 880s COMPUTED RESULT 18.30820799027 880s BINARY: /usr/bin/apbs 880s INPUT: complex-0_2.in 880s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 880s asc_getToken: Error occurred (bailing out). 880s Vio_scanf: Format problem with input. 880s 880s 880s ---------------------------------------------------------------------- 880s APBS -- Adaptive Poisson-Boltzmann Solver 880s Version APBS 3.4.1 880s 880s Nathan A. Baker (nathan.baker@pnnl.gov) 880s Pacific Northwest National Laboratory 880s 880s Additional contributing authors listed in the code documentation. 880s 880s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 880s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 880s Northwest Division for the U.S. Department of Energy. 880s 880s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 880s Portions Copyright (c) 2002-2020, Nathan A. Baker. 880s Portions Copyright (c) 1999-2002, The Regents of the University of California. 880s Portions Copyright (c) 1995, Michael Holst. 880s All rights reserved. 880s 880s Redistribution and use in source and binary forms, with or without 880s modification, are permitted provided that the following conditions are met: 880s 880s * Redistributions of source code must retain the above copyright notice, this 880s list of conditions and the following disclaimer. 880s 880s * Redistributions in binary form must reproduce the above copyright notice, 880s this list of conditions and the following disclaimer in the documentation 880s and/or other materials provided with the distribution. 880s 880s * Neither the name of the developer nor the names of its contributors may be 880s used to endorse or promote products derived from this software without 880s specific prior written permission. 880s 880s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 880s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 880s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 880s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 880s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 880s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 880s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 880s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 880s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 880s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 880s ---------------------------------------------------------------------- 880s APBS uses FETK (the Finite Element ToolKit) to solve the 880s Poisson-Boltzmann equation numerically. FETK is a portable collection 880s of finite element modeling class libraries developed by the Michael Holst 880s research group and written in an object-oriented form of C. FEtk is 880s designed to solve general coupled systems of nonlinear partial differential 880s equations using adaptive finite element methods, inexact Newton methods, 880s and algebraic multilevel methods. More information about FEtk may be found 880s at . 880s ---------------------------------------------------------------------- 880s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 880s Aqua is a modified form of the Holst group PMG library 880s which has been modified by Patrice Koehl 880s for improved efficiency and 880s memory usage when solving the Poisson-Boltzmann equation. 880s ---------------------------------------------------------------------- 880s Please cite your use of APBS as: 880s 880s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 880s nanosystems: application to microtubules and the ribosome. Proc. 880s Natl. Acad. Sci. USA 98, 10037-10041 2001. 880s 880s 880s This executable compiled on Jan 3 2025 at 11:01:42 880s 880s Parsing input file complex-0_2.in... 880s rank 0 size 1... 880s Parsed input file. 880s Got paths for 3 molecules 880s Reading PQR-format atom data from mol0.pqr. 880s asc_getToken: Error occurred (bailing out). 880s Vio_scanf: Format problem with input. 880s 1 atoms 880s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 880s Net charge 1.00e+00 e 880s Reading PQR-format atom data from mol2.pqr. 880s asc_getToken: Error occurred (bailing out). 880s Vio_scanf: Format problem with input. 880s 1 atoms 880s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 880s Net charge 1.00e+00 e 880s Reading PQR-format atom data from complex-0_2.pqr. 880s 2 atoms 880s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 880s Net charge 2.00e+00 e 880s Preparing to run 3 PBE calculations. 880s ---------------------------------------- 880s CALCULATION #1 (point1): MULTIGRID 880s Setting up problem... 880s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 880s Debye length: 0 A 880s Current memory usage: 61.059 MB total, 61.059 MB high water 880s Using linear spline charge discretization. 880s Grid dimensions: 65 x 65 x 65 880s Grid spacings: 0.210 x 0.210 x 0.210 880s Grid lengths: 13.440 x 13.440 x 13.440 880s Grid center: (0.000, 0.000, 0.000) 880s Multigrid levels: 5 880s Molecule ID: 1 880s Linearized traditional PBE 880s Multiple Debye-Huckel sphere boundary conditions 880s 0 ion species (0.000 M ionic strength): 880s Solute dielectric: 78.540 880s Solvent dielectric: 78.540 880s Using spline-based surface definition;window = 0.300 880s Temperature: 298.150 K 880s Electrostatic energies will be calculated 880s Total electrostatic energy = 9.776035707281E+01 kJ/mol 880s Fixed charge energy = 97.7604 kJ/mol 880s Mobile charge energy = 0 kJ/mol 880s Dielectric energy = 96.5336 kJ/mol 880s Per-atom energies: 880s Atom 0: 9.776035707281E+01 kJ/mol 880s Calculating forces... 880s ---------------------------------------- 880s CALCULATION #2 (point2): MULTIGRID 880s Setting up problem... 880s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 880s Debye length: 0 A 880s Current memory usage: 61.059 MB total, 61.066 MB high water 880s Using linear spline charge discretization. 880s Grid dimensions: 65 x 65 x 65 880s Grid spacings: 0.210 x 0.210 x 0.210 880s Grid lengths: 13.440 x 13.440 x 13.440 880s Grid center: (0.000, 0.000, 0.000) 880s Multigrid levels: 5 880s Molecule ID: 2 880s Linearized traditional PBE 880s Multiple Debye-Huckel sphere boundary conditions 880s 0 ion species (0.000 M ionic strength): 880s Solute dielectric: 78.540 880s Solvent dielectric: 78.540 880s Using spline-based surface definition;window = 0.300 880s Temperature: 298.150 K 880s Electrostatic energies will be calculated 880s Total electrostatic energy = 1.017611498797E+02 kJ/mol 880s Fixed charge energy = 101.761 kJ/mol 880s Mobile charge energy = 0 kJ/mol 880s Dielectric energy = 100.656 kJ/mol 880s Per-atom energies: 880s Atom 0: 1.017611498797E+02 kJ/mol 880s Calculating forces... 880s ---------------------------------------- 880s CALCULATION #3 (complex): MULTIGRID 880s Setting up problem... 880s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 880s Debye length: 0 A 880s Current memory usage: 61.059 MB total, 61.066 MB high water 880s Using linear spline charge discretization. 880s Grid dimensions: 65 x 65 x 65 880s Grid spacings: 0.210 x 0.210 x 0.210 880s Grid lengths: 13.440 x 13.440 x 13.440 880s Grid center: (0.000, 0.000, 0.000) 880s Multigrid levels: 5 880s Molecule ID: 3 880s Linearized traditional PBE 880s Multiple Debye-Huckel sphere boundary conditions 880s 0 ion species (0.000 M ionic strength): 880s Solute dielectric: 78.540 880s Solvent dielectric: 78.540 880s Using spline-based surface definition;window = 0.300 880s Temperature: 298.150 K 880s Electrostatic energies will be calculated 880s Total electrostatic energy = 2.084282010393E+02 kJ/mol 880s Fixed charge energy = 208.428 kJ/mol 880s Mobile charge energy = 0 kJ/mol 880s Dielectric energy = 203.83 kJ/mol 880s Per-atom energies: 880s Atom 0: 1.022136878480E+02 kJ/mol 880s Atom 1: 1.062145131913E+02 kJ/mol 880s Calculating forces... 880s ---------------------------------------- 880s PRINT STATEMENTS 880s 880s print energy 3 (complex) - 1 (point1) - 2 (point2) end 880s Local net energy (PE 0) = 8.906694086750E+00 kJ/mol 880s Global net ELEC energy = 8.906694086750E+00 kJ/mol 880s ---------------------------------------- 880s CLEANING UP AND SHUTTING DOWN... 880s Destroying force arrays. 880s No energy arrays to destroy. 880s Destroying multigrid structures. 880s Destroying finite element structures. 880s Destroying 3 molecules 880s Final memory usage: 0.001 MB total, 61.066 MB high water 880s 880s 880s Thanks for using APBS! 880s 882s Checking for intermediate energies in input file complex-0_2.out 882s EXPECTED COMPUTED: 13 882s EXPECTED EXPECTED: 13 882s 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] 882s 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'] 882s COMPUTED RESULT 97.76035707281 882s COMPUTED RESULT 101.7611498797 882s COMPUTED RESULT 208.4282010393 882s COMPUTED RESULT 0.0 882s COMPUTED RESULT 0.0 882s COMPUTED RESULT 0.0 882s COMPUTED RESULT 97.7604 882s COMPUTED RESULT 101.761 882s COMPUTED RESULT 208.428 882s COMPUTED RESULT 96.5336 882s COMPUTED RESULT 100.656 882s COMPUTED RESULT 203.83 882s COMPUTED RESULT 8.90669408675 882s BINARY: /usr/bin/apbs 882s INPUT: complex-0_3.in 882s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 882s asc_getToken: Error occurred (bailing out). 882s Vio_scanf: Format problem with input. 882s 882s 882s ---------------------------------------------------------------------- 882s APBS -- Adaptive Poisson-Boltzmann Solver 882s Version APBS 3.4.1 882s 882s Nathan A. Baker (nathan.baker@pnnl.gov) 882s Pacific Northwest National Laboratory 882s 882s Additional contributing authors listed in the code documentation. 882s 882s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 882s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 882s Northwest Division for the U.S. Department of Energy. 882s 882s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 882s Portions Copyright (c) 2002-2020, Nathan A. Baker. 882s Portions Copyright (c) 1999-2002, The Regents of the University of California. 882s Portions Copyright (c) 1995, Michael Holst. 882s All rights reserved. 882s 882s Redistribution and use in source and binary forms, with or without 882s modification, are permitted provided that the following conditions are met: 882s 882s * Redistributions of source code must retain the above copyright notice, this 882s list of conditions and the following disclaimer. 882s 882s * Redistributions in binary form must reproduce the above copyright notice, 882s this list of conditions and the following disclaimer in the documentation 882s and/or other materials provided with the distribution. 882s 882s * Neither the name of the developer nor the names of its contributors may be 882s used to endorse or promote products derived from this software without 882s specific prior written permission. 882s 882s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 882s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 882s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 882s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 882s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 882s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 882s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 882s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 882s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 882s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 882s ---------------------------------------------------------------------- 882s APBS uses FETK (the Finite Element ToolKit) to solve the 882s Poisson-Boltzmann equation numerically. FETK is a portable collection 882s of finite element modeling class libraries developed by the Michael Holst 882s research group and written in an object-oriented form of C. FEtk is 882s designed to solve general coupled systems of nonlinear partial differential 882s equations using adaptive finite element methods, inexact Newton methods, 882s and algebraic multilevel methods. More information about FEtk may be found 882s at . 882s ---------------------------------------------------------------------- 882s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 882s Aqua is a modified form of the Holst group PMG library 882s which has been modified by Patrice Koehl 882s for improved efficiency and 882s memory usage when solving the Poisson-Boltzmann equation. 882s ---------------------------------------------------------------------- 882s Please cite your use of APBS as: 882s 882s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 882s nanosystems: application to microtubules and the ribosome. Proc. 882s Natl. Acad. Sci. USA 98, 10037-10041 2001. 882s 882s 882s This executable compiled on Jan 3 2025 at 11:01:42 882s 882s Parsing input file complex-0_3.in... 882s rank 0 size 1... 882s Parsed input file. 882s Got paths for 3 molecules 882s Reading PQR-format atom data from mol0.pqr. 882s asc_getToken: Error occurred (bailing out). 882s Vio_scanf: Format problem with input. 882s 1 atoms 882s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 882s Net charge 1.00e+00 e 882s Reading PQR-format atom data from mol3.pqr. 882s asc_getToken: Error occurred (bailing out). 882s Vio_scanf: Format problem with input. 882s 1 atoms 882s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 882s Net charge 1.00e+00 e 882s Reading PQR-format atom data from complex-0_3.pqr. 882s 2 atoms 882s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 882s Net charge 2.00e+00 e 882s Preparing to run 3 PBE calculations. 882s ---------------------------------------- 882s CALCULATION #1 (point1): MULTIGRID 882s Setting up problem... 882s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 882s Debye length: 0 A 882s Current memory usage: 61.059 MB total, 61.059 MB high water 882s Using linear spline charge discretization. 882s Grid dimensions: 65 x 65 x 65 882s Grid spacings: 0.210 x 0.210 x 0.210 882s Grid lengths: 13.440 x 13.440 x 13.440 882s Grid center: (0.000, 0.000, 0.000) 882s Multigrid levels: 5 882s Molecule ID: 1 882s Linearized traditional PBE 882s Multiple Debye-Huckel sphere boundary conditions 882s 0 ion species (0.000 M ionic strength): 882s Solute dielectric: 78.540 882s Solvent dielectric: 78.540 882s Using spline-based surface definition;window = 0.300 882s Temperature: 298.150 K 882s Electrostatic energies will be calculated 882s Total electrostatic energy = 9.776035707281E+01 kJ/mol 882s Fixed charge energy = 97.7604 kJ/mol 882s Mobile charge energy = 0 kJ/mol 882s Dielectric energy = 96.5336 kJ/mol 882s Per-atom energies: 882s Atom 0: 9.776035707281E+01 kJ/mol 882s Calculating forces... 882s ---------------------------------------- 882s CALCULATION #2 (point2): MULTIGRID 882s Setting up problem... 882s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 882s Debye length: 0 A 882s Current memory usage: 61.059 MB total, 61.066 MB high water 882s Using linear spline charge discretization. 882s Grid dimensions: 65 x 65 x 65 882s Grid spacings: 0.210 x 0.210 x 0.210 882s Grid lengths: 13.440 x 13.440 x 13.440 882s Grid center: (0.000, 0.000, 0.000) 882s Multigrid levels: 5 882s Molecule ID: 2 882s Linearized traditional PBE 882s Multiple Debye-Huckel sphere boundary conditions 882s 0 ion species (0.000 M ionic strength): 882s Solute dielectric: 78.540 882s Solvent dielectric: 78.540 882s Using spline-based surface definition;window = 0.300 882s Temperature: 298.150 K 882s Electrostatic energies will be calculated 882s Total electrostatic energy = 1.337661883222E+02 kJ/mol 882s Fixed charge energy = 133.766 kJ/mol 882s Mobile charge energy = 0 kJ/mol 882s Dielectric energy = 132.672 kJ/mol 882s Per-atom energies: 882s Atom 0: 1.337661883222E+02 kJ/mol 882s Calculating forces... 882s ---------------------------------------- 882s CALCULATION #3 (complex): MULTIGRID 882s Setting up problem... 882s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 882s Debye length: 0 A 882s Current memory usage: 61.059 MB total, 61.066 MB high water 882s Using linear spline charge discretization. 882s Grid dimensions: 65 x 65 x 65 882s Grid spacings: 0.210 x 0.210 x 0.210 882s Grid lengths: 13.440 x 13.440 x 13.440 882s Grid center: (0.000, 0.000, 0.000) 882s Multigrid levels: 5 882s Molecule ID: 3 882s Linearized traditional PBE 882s Multiple Debye-Huckel sphere boundary conditions 882s 0 ion species (0.000 M ionic strength): 882s Solute dielectric: 78.540 882s Solvent dielectric: 78.540 882s Using spline-based surface definition;window = 0.300 882s Temperature: 298.150 K 882s Electrostatic energies will be calculated 882s Total electrostatic energy = 2.374361452120E+02 kJ/mol 882s Fixed charge energy = 237.436 kJ/mol 882s Mobile charge energy = 0 kJ/mol 882s Dielectric energy = 232.924 kJ/mol 882s Per-atom energies: 882s Atom 0: 1.007151570480E+02 kJ/mol 882s Atom 1: 1.367209881640E+02 kJ/mol 882s Calculating forces... 882s ---------------------------------------- 882s PRINT STATEMENTS 882s 882s print energy 3 (complex) - 1 (point1) - 2 (point2) end 882s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 882s Global net ELEC energy = 5.909599816984E+00 kJ/mol 882s ---------------------------------------- 882s CLEANING UP AND SHUTTING DOWN... 882s Destroying force arrays. 882s No energy arrays to destroy. 882s Destroying multigrid structures. 882s Destroying finite element structures. 882s Destroying 3 molecules 882s Final memory usage: 0.001 MB total, 61.066 MB high water 882s 882s 882s Thanks for using APBS! 882s 882s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 882s *** PASSED *** 882s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 882s *** PASSED *** 882s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 882s *** PASSED *** 882s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 882s *** PASSED *** 882s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 882s *** PASSED *** 882s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 882s *** PASSED *** 882s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 882s *** PASSED *** 882s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 882s *** PASSED *** 882s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 882s *** PASSED *** 882s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 882s *** PASSED *** 882s Elapsed time: 2.123685 seconds 882s -------------------------------------------------------------------------------- 882s -------------------------------------------------------------------------------- 882s Testing input file complex-0_4.in 882s 884s Checking for intermediate energies in input file complex-0_3.out 884s EXPECTED COMPUTED: 13 884s EXPECTED EXPECTED: 13 884s 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] 884s 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'] 884s COMPUTED RESULT 97.76035707281 884s COMPUTED RESULT 133.7661883222 884s COMPUTED RESULT 237.436145212 884s COMPUTED RESULT 0.0 884s COMPUTED RESULT 0.0 884s COMPUTED RESULT 0.0 884s COMPUTED RESULT 97.7604 884s COMPUTED RESULT 133.766 884s COMPUTED RESULT 237.436 884s COMPUTED RESULT 96.5336 884s COMPUTED RESULT 132.672 884s COMPUTED RESULT 232.924 884s COMPUTED RESULT 5.909599816984 884s BINARY: /usr/bin/apbs 884s INPUT: complex-0_4.in 884s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 884s asc_getToken: Error occurred (bailing out). 884s Vio_scanf: Format problem with input. 884s 884s 884s ---------------------------------------------------------------------- 884s APBS -- Adaptive Poisson-Boltzmann Solver 884s Version APBS 3.4.1 884s 884s Nathan A. Baker (nathan.baker@pnnl.gov) 884s Pacific Northwest National Laboratory 884s 884s Additional contributing authors listed in the code documentation. 884s 884s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 884s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 884s Northwest Division for the U.S. Department of Energy. 884s 884s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 884s Portions Copyright (c) 2002-2020, Nathan A. Baker. 884s Portions Copyright (c) 1999-2002, The Regents of the University of California. 884s Portions Copyright (c) 1995, Michael Holst. 884s All rights reserved. 884s 884s Redistribution and use in source and binary forms, with or without 884s modification, are permitted provided that the following conditions are met: 884s 884s * Redistributions of source code must retain the above copyright notice, this 884s list of conditions and the following disclaimer. 884s 884s * Redistributions in binary form must reproduce the above copyright notice, 884s this list of conditions and the following disclaimer in the documentation 884s and/or other materials provided with the distribution. 884s 884s * Neither the name of the developer nor the names of its contributors may be 884s used to endorse or promote products derived from this software without 884s specific prior written permission. 884s 884s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 884s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 884s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 884s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 884s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 884s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 884s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 884s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 884s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 884s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 884s ---------------------------------------------------------------------- 884s APBS uses FETK (the Finite Element ToolKit) to solve the 884s Poisson-Boltzmann equation numerically. FETK is a portable collection 884s of finite element modeling class libraries developed by the Michael Holst 884s research group and written in an object-oriented form of C. FEtk is 884s designed to solve general coupled systems of nonlinear partial differential 884s equations using adaptive finite element methods, inexact Newton methods, 884s and algebraic multilevel methods. More information about FEtk may be found 884s at . 884s ---------------------------------------------------------------------- 884s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 884s Aqua is a modified form of the Holst group PMG library 884s which has been modified by Patrice Koehl 884s for improved efficiency and 884s memory usage when solving the Poisson-Boltzmann equation. 884s ---------------------------------------------------------------------- 884s Please cite your use of APBS as: 884s 884s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 884s nanosystems: application to microtubules and the ribosome. Proc. 884s Natl. Acad. Sci. USA 98, 10037-10041 2001. 884s 884s 884s This executable compiled on Jan 3 2025 at 11:01:42 884s 884s Parsing input file complex-0_4.in... 884s rank 0 size 1... 884s Parsed input file. 884s Got paths for 3 molecules 884s Reading PQR-format atom data from mol0.pqr. 884s asc_getToken: Error occurred (bailing out). 884s Vio_scanf: Format problem with input. 884s 1 atoms 884s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 884s Net charge 1.00e+00 e 884s Reading PQR-format atom data from mol4.pqr. 884s asc_getToken: Error occurred (bailing out). 884s Vio_scanf: Format problem with input. 884s 1 atoms 884s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 884s Net charge 1.00e+00 e 884s Reading PQR-format atom data from complex-0_4.pqr. 884s 2 atoms 884s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 884s Net charge 2.00e+00 e 884s Preparing to run 3 PBE calculations. 884s ---------------------------------------- 884s CALCULATION #1 (point1): MULTIGRID 884s Setting up problem... 884s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 884s Debye length: 0 A 884s Current memory usage: 61.059 MB total, 61.059 MB high water 884s Using linear spline charge discretization. 884s Grid dimensions: 65 x 65 x 65 884s Grid spacings: 0.210 x 0.210 x 0.210 884s Grid lengths: 13.440 x 13.440 x 13.440 884s Grid center: (0.000, 0.000, 0.000) 884s Multigrid levels: 5 884s Molecule ID: 1 884s Linearized traditional PBE 884s Multiple Debye-Huckel sphere boundary conditions 884s 0 ion species (0.000 M ionic strength): 884s Solute dielectric: 78.540 884s Solvent dielectric: 78.540 884s Using spline-based surface definition;window = 0.300 884s Temperature: 298.150 K 884s Electrostatic energies will be calculated 884s Total electrostatic energy = 9.776035707281E+01 kJ/mol 884s Fixed charge energy = 97.7604 kJ/mol 884s Mobile charge energy = 0 kJ/mol 884s Dielectric energy = 96.5336 kJ/mol 884s Per-atom energies: 884s Atom 0: 9.776035707281E+01 kJ/mol 884s Calculating forces... 884s ---------------------------------------- 884s CALCULATION #2 (point2): MULTIGRID 884s Setting up problem... 884s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 884s Debye length: 0 A 884s Current memory usage: 61.059 MB total, 61.066 MB high water 884s Using linear spline charge discretization. 884s Grid dimensions: 65 x 65 x 65 884s Grid spacings: 0.210 x 0.210 x 0.210 884s Grid lengths: 13.440 x 13.440 x 13.440 884s Grid center: (0.000, 0.000, 0.000) 884s Multigrid levels: 5 884s Molecule ID: 2 884s Linearized traditional PBE 884s Multiple Debye-Huckel sphere boundary conditions 884s 0 ion species (0.000 M ionic strength): 884s Solute dielectric: 78.540 884s Solvent dielectric: 78.540 884s Using spline-based surface definition;window = 0.300 884s Temperature: 298.150 K 884s Electrostatic energies will be calculated 884s Total electrostatic energy = 1.017611498797E+02 kJ/mol 884s Fixed charge energy = 101.761 kJ/mol 884s Mobile charge energy = 0 kJ/mol 884s Dielectric energy = 100.654 kJ/mol 884s Per-atom energies: 884s Atom 0: 1.017611498797E+02 kJ/mol 884s Calculating forces... 884s ---------------------------------------- 884s CALCULATION #3 (complex): MULTIGRID 884s Setting up problem... 884s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 884s Debye length: 0 A 884s Current memory usage: 61.059 MB total, 61.066 MB high water 884s Using linear spline charge discretization. 884s Grid dimensions: 65 x 65 x 65 884s Grid spacings: 0.210 x 0.210 x 0.210 884s Grid lengths: 13.440 x 13.440 x 13.440 884s Grid center: (0.000, 0.000, 0.000) 884s Multigrid levels: 5 884s Molecule ID: 3 884s Linearized traditional PBE 884s Multiple Debye-Huckel sphere boundary conditions 884s 0 ion species (0.000 M ionic strength): 884s Solute dielectric: 78.540 884s Solvent dielectric: 78.540 884s Using spline-based surface definition;window = 0.300 884s Temperature: 298.150 K 884s Electrostatic energies will be calculated 884s Total electrostatic energy = 2.039516519000E+02 kJ/mol 884s Fixed charge energy = 203.952 kJ/mol 884s Mobile charge energy = 0 kJ/mol 884s Dielectric energy = 199.493 kJ/mol 884s Per-atom energies: 884s Atom 0: 9.997541697022E+01 kJ/mol 884s Atom 1: 1.039762349297E+02 kJ/mol 884s Calculating forces... 884s ---------------------------------------- 884s PRINT STATEMENTS 884s 884s print energy 3 (complex) - 1 (point1) - 2 (point2) end 884s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 884s Global net ELEC energy = 4.430144947418E+00 kJ/mol 884s ---------------------------------------- 884s CLEANING UP AND SHUTTING DOWN... 884s Destroying force arrays. 884s No energy arrays to destroy. 884s Destroying multigrid structures. 884s Destroying finite element structures. 884s Destroying 3 molecules 884s Final memory usage: 0.001 MB total, 61.066 MB high water 884s 884s 884s Thanks for using APBS! 884s 884s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 884s *** PASSED *** 884s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 884s *** PASSED *** 884s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 884s *** PASSED *** 884s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 884s *** PASSED *** 884s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 884s *** PASSED *** 884s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 884s *** PASSED *** 884s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 884s *** PASSED *** 884s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 884s *** PASSED *** 884s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 884s *** PASSED *** 884s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 884s *** PASSED *** 884s Elapsed time: 2.145669 seconds 884s -------------------------------------------------------------------------------- 884s Total elapsed time: 8.615914 seconds 884s Test results have been logged 884s -------------------------------------------------------------------------------- 884s -------------------------------------------------------------------------------- 884s Testing input file apbs-mol.in 884s 887s Checking for intermediate energies in input file complex-0_4.out 887s EXPECTED COMPUTED: 13 887s EXPECTED EXPECTED: 13 887s 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] 887s 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'] 887s COMPUTED RESULT 97.76035707281 887s COMPUTED RESULT 101.7611498797 887s COMPUTED RESULT 203.9516519 887s COMPUTED RESULT 0.0 887s COMPUTED RESULT 0.0 887s COMPUTED RESULT 0.0 887s COMPUTED RESULT 97.7604 887s COMPUTED RESULT 101.761 887s COMPUTED RESULT 203.952 887s COMPUTED RESULT 96.5336 887s COMPUTED RESULT 100.654 887s COMPUTED RESULT 199.493 887s COMPUTED RESULT 4.430144947418 887s Running tests for solv section 887s BINARY: /usr/bin/apbs 887s INPUT: apbs-mol.in 887s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 887s asc_getToken: Error occurred (bailing out). 887s Vio_scanf: Format problem with input. 887s 887s 887s ---------------------------------------------------------------------- 887s APBS -- Adaptive Poisson-Boltzmann Solver 887s Version APBS 3.4.1 887s 887s Nathan A. Baker (nathan.baker@pnnl.gov) 887s Pacific Northwest National Laboratory 887s 887s Additional contributing authors listed in the code documentation. 887s 887s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 887s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 887s Northwest Division for the U.S. Department of Energy. 887s 887s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 887s Portions Copyright (c) 2002-2020, Nathan A. Baker. 887s Portions Copyright (c) 1999-2002, The Regents of the University of California. 887s Portions Copyright (c) 1995, Michael Holst. 887s All rights reserved. 887s 887s Redistribution and use in source and binary forms, with or without 887s modification, are permitted provided that the following conditions are met: 887s 887s * Redistributions of source code must retain the above copyright notice, this 887s list of conditions and the following disclaimer. 887s 887s * Redistributions in binary form must reproduce the above copyright notice, 887s this list of conditions and the following disclaimer in the documentation 887s and/or other materials provided with the distribution. 887s 887s * Neither the name of the developer nor the names of its contributors may be 887s used to endorse or promote products derived from this software without 887s specific prior written permission. 887s 887s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 887s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 887s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 887s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 887s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 887s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 887s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 887s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 887s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 887s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 887s ---------------------------------------------------------------------- 887s APBS uses FETK (the Finite Element ToolKit) to solve the 887s Poisson-Boltzmann equation numerically. FETK is a portable collection 887s of finite element modeling class libraries developed by the Michael Holst 887s research group and written in an object-oriented form of C. FEtk is 887s designed to solve general coupled systems of nonlinear partial differential 887s equations using adaptive finite element methods, inexact Newton methods, 887s and algebraic multilevel methods. More information about FEtk may be found 887s at . 887s ---------------------------------------------------------------------- 887s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 887s Aqua is a modified form of the Holst group PMG library 887s which has been modified by Patrice Koehl 887s for improved efficiency and 887s memory usage when solving the Poisson-Boltzmann equation. 887s ---------------------------------------------------------------------- 887s Please cite your use of APBS as: 887s 887s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 887s nanosystems: application to microtubules and the ribosome. Proc. 887s Natl. Acad. Sci. USA 98, 10037-10041 2001. 887s 887s 887s This executable compiled on Jan 3 2025 at 11:01:42 887s 887s Parsing input file apbs-mol.in... 887s rank 0 size 1... 887s Parsed input file. 887s Got paths for 2 molecules 887s Reading PQR-format atom data from methanol.pqr. 887s asc_getToken: Error occurred (bailing out). 887s Vio_scanf: Format problem with input. 887s 3 atoms 887s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 887s Net charge 5.55e-17 e 887s Reading PQR-format atom data from methoxide.pqr. 887s 2 atoms 887s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 887s Net charge -1.00e+00 e 887s Preparing to run 4 PBE calculations. 887s ---------------------------------------- 887s CALCULATION #1 (methanol-solv): MULTIGRID 887s Setting up problem... 887s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 887s Debye length: 0 A 887s Current memory usage: 61.247 MB total, 61.247 MB high water 887s Using linear spline charge discretization. 887s Grid dimensions: 65 x 65 x 65 887s Grid spacings: 0.250 x 0.250 x 0.250 887s Grid lengths: 16.000 x 16.000 x 16.000 887s Grid center: (0.309, 0.000, -0.242) 887s Multigrid levels: 5 887s Molecule ID: 1 887s Linearized traditional PBE 887s Multiple Debye-Huckel sphere boundary conditions 887s 2 ion species (0.000 M ionic strength): 887s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 887s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 887s Solute dielectric: 2.000 887s Solvent dielectric: 78.000 887s Using "molecular" surface definition; no smoothing 887s Solvent probe radius: 0.000 A 887s Temperature: 300.000 K 887s Electrostatic energies will be calculated 887s Total electrostatic energy = 1.847663548071E+03 kJ/mol 887s Calculating forces... 887s ---------------------------------------- 887s CALCULATION #2 (methanol-ref): MULTIGRID 887s Setting up problem... 887s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 887s Debye length: 0 A 887s Current memory usage: 61.247 MB total, 61.316 MB high water 887s Using linear spline charge discretization. 887s Grid dimensions: 65 x 65 x 65 887s Grid spacings: 0.250 x 0.250 x 0.250 887s Grid lengths: 16.000 x 16.000 x 16.000 887s Grid center: (0.309, 0.000, -0.242) 887s Multigrid levels: 5 887s Molecule ID: 1 887s Linearized traditional PBE 887s Multiple Debye-Huckel sphere boundary conditions 887s 2 ion species (0.000 M ionic strength): 887s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 887s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 887s Solute dielectric: 2.000 887s Solvent dielectric: 1.000 887s Using "molecular" surface definition; no smoothing 887s Solvent probe radius: 0.000 A 887s Temperature: 300.000 K 887s Electrostatic energies will be calculated 887s Total electrostatic energy = 1.883912182952E+03 kJ/mol 887s Calculating forces... 887s ---------------------------------------- 887s CALCULATION #3 (methoxide-solv): MULTIGRID 887s Setting up problem... 887s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 887s Debye length: 0 A 887s Current memory usage: 61.243 MB total, 61.316 MB high water 887s Using linear spline charge discretization. 887s Grid dimensions: 65 x 65 x 65 887s Grid spacings: 0.250 x 0.250 x 0.250 887s Grid lengths: 16.000 x 16.000 x 16.000 887s Grid center: (0.000, 0.000, -0.128) 887s Multigrid levels: 5 887s Molecule ID: 2 887s Linearized traditional PBE 887s Multiple Debye-Huckel sphere boundary conditions 887s 2 ion species (0.000 M ionic strength): 887s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 887s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 887s Solute dielectric: 2.000 887s Solvent dielectric: 78.000 887s Using "molecular" surface definition; no smoothing 887s Solvent probe radius: 0.000 A 887s Temperature: 300.000 K 887s Electrostatic energies will be calculated 887s Total electrostatic energy = 2.732623683321E+03 kJ/mol 887s Calculating forces... 887s ---------------------------------------- 887s CALCULATION #4 (methoxide-ref): MULTIGRID 887s Setting up problem... 887s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 887s Debye length: 0 A 887s Current memory usage: 61.243 MB total, 61.316 MB high water 887s Using linear spline charge discretization. 887s Grid dimensions: 65 x 65 x 65 887s Grid spacings: 0.250 x 0.250 x 0.250 887s Grid lengths: 16.000 x 16.000 x 16.000 887s Grid center: (0.000, 0.000, -0.128) 887s Multigrid levels: 5 887s Molecule ID: 2 887s Linearized traditional PBE 887s Multiple Debye-Huckel sphere boundary conditions 887s 2 ion species (0.000 M ionic strength): 887s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 887s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 887s Solute dielectric: 2.000 887s Solvent dielectric: 1.000 887s Using "molecular" surface definition; no smoothing 887s Solvent probe radius: 0.000 A 887s Temperature: 300.000 K 887s Electrostatic energies will be calculated 887s Total electrostatic energy = 3.123035854133E+03 kJ/mol 887s Calculating forces... 887s ---------------------------------------- 887s PRINT STATEMENTS 887s 887s print energy 1 (methanol-solv) - 2 (methanol-ref) end 887s Local net energy (PE 0) = -3.624863488074E+01 kJ/mol 887s Global net ELEC energy = -3.624863488074E+01 kJ/mol 887s 887s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 887s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 887s Global net ELEC energy = -3.904121708125E+02 kJ/mol 887s 887s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 887s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 887s Global net ELEC energy = -3.541635359318E+02 kJ/mol 887s ---------------------------------------- 887s CLEANING UP AND SHUTTING DOWN... 887s Destroying force arrays. 887s No energy arrays to destroy. 887s Destroying multigrid structures. 887s Destroying finite element structures. 887s Destroying 2 molecules 887s Final memory usage: 0.001 MB total, 61.316 MB high water 887s 887s 887s Thanks for using APBS! 887s 887s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 887s *** PASSED *** 887s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 887s *** PASSED *** 887s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 887s *** PASSED *** 887s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 887s *** PASSED *** 887s Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) 887s *** PASSED *** 887s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 887s *** PASSED *** 887s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 887s *** PASSED *** 887s Elapsed time: 3.405273 seconds 887s -------------------------------------------------------------------------------- 887s -------------------------------------------------------------------------------- 887s Testing input file apbs-smol.in 887s 890s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 890s *** PASSED *** 890s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 890s *** PASSED *** 890s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 890s *** PASSED *** 890s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 890s *** PASSED *** 890s Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) 890s *** PASSED *** 890s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 890s *** PASSED *** 890s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 890s *** PASSED *** 890s Elapsed time: 2.909294 seconds 890s -------------------------------------------------------------------------------- 890s Total elapsed time: 6.314567 seconds 890s Test results have been logged 890s -------------------------------------------------------------------------------- 890s Checking for intermediate energies in input file apbs-mol.out 890s EXPECTED COMPUTED: 7 890s EXPECTED EXPECTED: 7 890s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] 890s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 890s COMPUTED RESULT 1847.663548071 890s COMPUTED RESULT 1883.912182952 890s COMPUTED RESULT 2732.623683321 890s COMPUTED RESULT 3123.035854133 890s COMPUTED RESULT -36.24863488074 890s COMPUTED RESULT -390.4121708125 890s COMPUTED RESULT -354.1635359318 890s BINARY: /usr/bin/apbs 890s INPUT: apbs-smol.in 890s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 890s asc_getToken: Error occurred (bailing out). 890s Vio_scanf: Format problem with input. 890s 890s 890s ---------------------------------------------------------------------- 890s APBS -- Adaptive Poisson-Boltzmann Solver 890s Version APBS 3.4.1 890s 890s Nathan A. Baker (nathan.baker@pnnl.gov) 890s Pacific Northwest National Laboratory 890s 890s Additional contributing authors listed in the code documentation. 890s 890s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 890s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 890s Northwest Division for the U.S. Department of Energy. 890s 890s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 890s Portions Copyright (c) 2002-2020, Nathan A. Baker. 890s Portions Copyright (c) 1999-2002, The Regents of the University of California. 890s Portions Copyright (c) 1995, Michael Holst. 890s All rights reserved. 890s 890s Redistribution and use in source and binary forms, with or without 890s modification, are permitted provided that the following conditions are met: 890s 890s * Redistributions of source code must retain the above copyright notice, this 890s list of conditions and the following disclaimer. 890s 890s * Redistributions in binary form must reproduce the above copyright notice, 890s this list of conditions and the following disclaimer in the documentation 890s and/or other materials provided with the distribution. 890s 890s * Neither the name of the developer nor the names of its contributors may be 890s used to endorse or promote products derived from this software without 890s specific prior written permission. 890s 890s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 890s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 890s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 890s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 890s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 890s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 890s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 890s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 890s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 890s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 890s ---------------------------------------------------------------------- 890s APBS uses FETK (the Finite Element ToolKit) to solve the 890s Poisson-Boltzmann equation numerically. FETK is a portable collection 890s of finite element modeling class libraries developed by the Michael Holst 890s research group and written in an object-oriented form of C. FEtk is 890s designed to solve general coupled systems of nonlinear partial differential 890s equations using adaptive finite element methods, inexact Newton methods, 890s and algebraic multilevel methods. More information about FEtk may be found 890s at . 890s ---------------------------------------------------------------------- 890s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 890s Aqua is a modified form of the Holst group PMG library 890s which has been modified by Patrice Koehl 890s for improved efficiency and 890s memory usage when solving the Poisson-Boltzmann equation. 890s ---------------------------------------------------------------------- 890s Please cite your use of APBS as: 890s 890s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 890s nanosystems: application to microtubules and the ribosome. Proc. 890s Natl. Acad. Sci. USA 98, 10037-10041 2001. 890s 890s 890s This executable compiled on Jan 3 2025 at 11:01:42 890s 890s Parsing input file apbs-smol.in... 890s rank 0 size 1... 890s Parsed input file. 890s Got paths for 2 molecules 890s Reading PQR-format atom data from methanol.pqr. 890s asc_getToken: Error occurred (bailing out). 890s Vio_scanf: Format problem with input. 890s 3 atoms 890s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 890s Net charge 5.55e-17 e 890s Reading PQR-format atom data from methoxide.pqr. 890s 2 atoms 890s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 890s Net charge -1.00e+00 e 890s Preparing to run 4 PBE calculations. 890s ---------------------------------------- 890s CALCULATION #1 (methanol-solv): MULTIGRID 890s Setting up problem... 890s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 890s Debye length: 0 A 890s Current memory usage: 61.247 MB total, 61.247 MB high water 890s Using linear spline charge discretization. 890s Grid dimensions: 65 x 65 x 65 890s Grid spacings: 0.250 x 0.250 x 0.250 890s Grid lengths: 16.000 x 16.000 x 16.000 890s Grid center: (0.309, 0.000, -0.242) 890s Multigrid levels: 5 890s Molecule ID: 1 890s Linearized traditional PBE 890s Multiple Debye-Huckel sphere boundary conditions 890s 2 ion species (0.000 M ionic strength): 890s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 890s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 890s Solute dielectric: 2.000 890s Solvent dielectric: 78.000 890s Using "molecular" surface definition;harmonic average smoothing 890s Solvent probe radius: 0.000 A 890s Temperature: 300.000 K 890s Electrostatic energies will be calculated 890s Total electrostatic energy = 1.847860440020E+03 kJ/mol 890s Calculating forces... 890s ---------------------------------------- 890s CALCULATION #2 (methanol-ref): MULTIGRID 890s Setting up problem... 890s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 890s Debye length: 0 A 890s Current memory usage: 61.247 MB total, 61.316 MB high water 890s Using linear spline charge discretization. 890s Grid dimensions: 65 x 65 x 65 890s Grid spacings: 0.250 x 0.250 x 0.250 890s Grid lengths: 16.000 x 16.000 x 16.000 890s Grid center: (0.309, 0.000, -0.242) 890s Multigrid levels: 5 890s Molecule ID: 1 890s Linearized traditional PBE 890s Multiple Debye-Huckel sphere boundary conditions 890s 2 ion species (0.000 M ionic strength): 890s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 890s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 890s Solute dielectric: 2.000 890s Solvent dielectric: 1.000 890s Using "molecular" surface definition;harmonic average smoothing 890s Solvent probe radius: 0.000 A 890s Temperature: 300.000 K 890s Electrostatic energies will be calculated 890s Total electrostatic energy = 1.885436377745E+03 kJ/mol 890s Calculating forces... 890s ---------------------------------------- 890s CALCULATION #3 (methoxide-solv): MULTIGRID 890s Setting up problem... 890s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 890s Debye length: 0 A 890s Current memory usage: 61.243 MB total, 61.316 MB high water 890s Using linear spline charge discretization. 890s Grid dimensions: 65 x 65 x 65 890s Grid spacings: 0.250 x 0.250 x 0.250 890s Grid lengths: 16.000 x 16.000 x 16.000 890s Grid center: (0.000, 0.000, -0.128) 890s Multigrid levels: 5 890s Molecule ID: 2 890s Linearized traditional PBE 890s Multiple Debye-Huckel sphere boundary conditions 890s 2 ion species (0.000 M ionic strength): 890s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 890s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 890s Solute dielectric: 2.000 890s Solvent dielectric: 78.000 890s Using "molecular" surface definition;harmonic average smoothing 890s Solvent probe radius: 0.000 A 890s Temperature: 300.000 K 890s Electrostatic energies will be calculated 890s Total electrostatic energy = 2.734040568569E+03 kJ/mol 890s Calculating forces... 890s ---------------------------------------- 890s CALCULATION #4 (methoxide-ref): MULTIGRID 890s Setting up problem... 890s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 890s Debye length: 0 A 890s Current memory usage: 61.243 MB total, 61.316 MB high water 890s Using linear spline charge discretization. 890s Grid dimensions: 65 x 65 x 65 890s Grid spacings: 0.250 x 0.250 x 0.250 890s Grid lengths: 16.000 x 16.000 x 16.000 890s Grid center: (0.000, 0.000, -0.128) 890s Multigrid levels: 5 890s Molecule ID: 2 890s Linearized traditional PBE 890s Multiple Debye-Huckel sphere boundary conditions 890s 2 ion species (0.000 M ionic strength): 890s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 890s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 890s Solute dielectric: 2.000 890s Solvent dielectric: 1.000 890s Using "molecular" surface definition;harmonic average smoothing 890s Solvent probe radius: 0.000 A 890s Temperature: 300.000 K 890s Electrostatic energies will be calculated 890s Total electrostatic energy = 3.125279428954E+03 kJ/mol 890s Calculating forces... 890s ---------------------------------------- 890s PRINT STATEMENTS 890s 890s print energy 1 (methanol-solv) - 2 (methanol-ref) end 890s Local net energy (PE 0) = -3.757593772493E+01 kJ/mol 890s Global net ELEC energy = -3.757593772493E+01 kJ/mol 890s 890s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 890s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 890s Global net ELEC energy = -3.912388603848E+02 kJ/mol 890s 890s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 890s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 890s Global net ELEC energy = -3.536629226599E+02 kJ/mol 890s ---------------------------------------- 890s CLEANING UP AND SHUTTING DOWN... 890s Destroying force arrays. 890s No energy arrays to destroy. 890s Destroying multigrid structures. 890s Destroying finite element structures. 890s Destroying 2 molecules 890s Final memory usage: 0.001 MB total, 61.316 MB high water 890s 890s 890s Thanks for using APBS! 890s 890s Checking for intermediate energies in input file apbs-smol.out 890s EXPECTED COMPUTED: 7 890s EXPECTED EXPECTED: 7 890s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] 890s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 890s COMPUTED RESULT 1847.86044002 890s COMPUTED RESULT 1885.436377745 890s COMPUTED RESULT 2734.040568569 890s COMPUTED RESULT 3125.279428954 890s COMPUTED RESULT -37.57593772493 890s COMPUTED RESULT -391.2388603848 890s COMPUTED RESULT -353.6629226599 891s autopkgtest [00:49:56]: test test-apbs: -----------------------] 895s autopkgtest [00:50:00]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 895s test-apbs PASS 899s autopkgtest [00:50:04]: @@@@@@@@@@@@@@@@@@@@ summary 899s test-apbs PASS