0s autopkgtest [00:45:15]: starting date and time: 2025-10-20 00:45:15+0000 0s autopkgtest [00:45:15]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [00:45:15]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zww890p5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-3.secgroup --name adt-resolute-s390x-apbs-20251020-004514-juju-7f2275-prod-proposed-migration-environment-2-8acb8ec3-de80-4f86-9eba-7ea486ff9d9f --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-apbs-20251020-004514-juju-7f2275-prod-proposed-migration-environment-2-8acb8ec3-de80-4f86-9eba-7ea486ff9d9f from image adt/ubuntu-resolute-s390x-server-20251019.img (UUID 7a83b4ca-2eb3-4cb0-b8d6-be2f16efcb4e)... 51s autopkgtest [00:46:06]: testbed dpkg architecture: s390x 51s autopkgtest [00:46:06]: testbed apt version: 3.1.8ubuntu1 52s autopkgtest [00:46:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [00:46:07]: testbed release detected to be: None 53s autopkgtest [00:46:08]: updating testbed package index (apt update) 53s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [47.8 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [396 kB] 54s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.8 kB] 54s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 54s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [102 kB] 54s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 54s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [259 kB] 54s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [6184 B] 54s Fetched 917 kB in 1s (1003 kB/s) 54s Reading package lists... 55s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s The following packages will be upgraded: 56s distro-info-data dpkg dpkg-dev libaudit-common libaudit1 libdpkg-perl 56s libseccomp2 python-apt-common python3-apt 57s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 3003 kB of archives. 57s After this operation, 427 kB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x dpkg s390x 1.22.21ubuntu4 [1287 kB] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libaudit-common all 1:4.0.5-1build2 [6596 B] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libaudit1 s390x 1:4.0.5-1build2 [57.0 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x distro-info-data all 0.68 [7378 B] 57s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libseccomp2 s390x 2.6.0-2ubuntu3 [57.5 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python-apt-common all 3.0.0ubuntu2 [21.7 kB] 57s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3-apt s390x 3.0.0ubuntu2 [198 kB] 57s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x dpkg-dev all 1.22.21ubuntu4 [1088 kB] 57s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x libdpkg-perl all 1.22.21ubuntu4 [280 kB] 58s dpkg-preconfigure: unable to re-open stdin: No such file or directory 58s Fetched 3003 kB in 1s (3019 kB/s) 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56852 files and directories currently installed.) 58s Preparing to unpack .../dpkg_1.22.21ubuntu4_s390x.deb ... 58s Unpacking dpkg (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 58s Setting up dpkg (1.22.21ubuntu4) ... 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56852 files and directories currently installed.) 58s Preparing to unpack .../libaudit-common_1%3a4.0.5-1build2_all.deb ... 58s Unpacking libaudit-common (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 58s Setting up libaudit-common (1:4.0.5-1build2) ... 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56852 files and directories currently installed.) 58s Preparing to unpack .../libaudit1_1%3a4.0.5-1build2_s390x.deb ... 58s Unpacking libaudit1:s390x (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 58s Setting up libaudit1:s390x (1:4.0.5-1build2) ... 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56852 files and directories currently installed.) 58s Preparing to unpack .../0-distro-info-data_0.68_all.deb ... 58s Unpacking distro-info-data (0.68) over (0.67~ubuntu1) ... 58s Preparing to unpack .../1-libseccomp2_2.6.0-2ubuntu3_s390x.deb ... 58s Unpacking libseccomp2:s390x (2.6.0-2ubuntu3) over (2.6.0-2ubuntu2) ... 58s Preparing to unpack .../2-python-apt-common_3.0.0ubuntu2_all.deb ... 58s Unpacking python-apt-common (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 58s Preparing to unpack .../3-python3-apt_3.0.0ubuntu2_s390x.deb ... 58s Unpacking python3-apt (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 58s Preparing to unpack .../4-dpkg-dev_1.22.21ubuntu4_all.deb ... 58s Unpacking dpkg-dev (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 58s Preparing to unpack .../5-libdpkg-perl_1.22.21ubuntu4_all.deb ... 58s Unpacking libdpkg-perl (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 59s Setting up distro-info-data (0.68) ... 59s Setting up libseccomp2:s390x (2.6.0-2ubuntu3) ... 59s Setting up libdpkg-perl (1.22.21ubuntu4) ... 59s Setting up python-apt-common (3.0.0ubuntu2) ... 59s Setting up python3-apt (3.0.0ubuntu2) ... 59s Setting up dpkg-dev (1.22.21ubuntu4) ... 59s Processing triggers for man-db (2.13.1-1) ... 60s Processing triggers for libc-bin (2.42-0ubuntu3) ... 60s autopkgtest [00:46:15]: upgrading testbed (apt dist-upgrade and autopurge) 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 61s Calculating upgrade... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Solving dependencies... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [00:46:16]: rebooting testbed after setup commands that affected boot 75s autopkgtest [00:46:30]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 78s autopkgtest [00:46:33]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 91s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 91s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 91s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 91s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 91s gpgv: Can't check signature: No public key 91s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 93s autopkgtest [00:46:48]: testing package apbs version 3.4.1-6build2 99s autopkgtest [00:46:54]: build not needed 110s autopkgtest [00:47:05]: test test-apbs: preparing testbed 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Solving dependencies... 110s The following NEW packages will be installed: 110s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax libamd3 110s libapbs-dev libapbs3t64 libarpack2t64 libblas3 libcamd3 libccolamd3 110s libcholmod5 libcolamd3 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 110s libfabric1 libfetk-dev libfetk1.9t64 libgfortran5 libgomp1 libhwloc-plugins 110s libhwloc15 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore 110s liblapack3 libmaloc-dev libmaloc1 libopenmpi40 libpciaccess0 librdmacm1t64 110s libspqr4 libsuitesparseconfig7 libsuperlu7 libumfpack6 libxnvctrl0 110s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 111s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 32.7 MB of archives. 111s After this operation, 127 MB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1 [2781 kB] 113s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x apbs-data all 3.4.1-6build2 [1769 kB] 114s Get:3 http://ftpmaster.internal/ubuntu resolute/universe s390x libmaloc1 s390x 1.5-2 [102 kB] 114s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 114s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x libsuperlu7 s390x 7.0.1+dfsg1-2 [233 kB] 114s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-5ubuntu1 [154 kB] 114s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libsuitesparseconfig7 s390x 1:7.10.1+dfsg-1 [21.3 kB] 114s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x libamd3 s390x 1:7.10.1+dfsg-1 [43.3 kB] 114s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x libcamd3 s390x 1:7.10.1+dfsg-1 [37.8 kB] 114s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x libccolamd3 s390x 1:7.10.1+dfsg-1 [40.8 kB] 114s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libcolamd3 s390x 1:7.10.1+dfsg-1 [31.2 kB] 114s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 114s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 116s Get:14 http://ftpmaster.internal/ubuntu resolute/universe s390x libcholmod5 s390x 1:7.10.1+dfsg-1 [927 kB] 117s Get:15 http://ftpmaster.internal/ubuntu resolute/universe s390x libumfpack6 s390x 1:7.10.1+dfsg-1 [378 kB] 117s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x libfetk1.9t64 s390x 3.4.1-6build2 [666 kB] 117s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x libapbs3t64 s390x 3.4.1-6build2 [292 kB] 117s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 118s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 120s Get:20 http://ftpmaster.internal/ubuntu resolute/universe s390x libarpack2t64 s390x 3.9.1-6 [110 kB] 120s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libevent-core-2.1-7t64 s390x 2.1.12-stable-10build1 [93.1 kB] 120s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10build1 [8060 B] 120s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x librdmacm1t64 s390x 56.1-1ubuntu1 [73.6 kB] 120s Get:24 http://ftpmaster.internal/ubuntu resolute/universe s390x libfabric1 s390x 2.1.0-1.1 [640 kB] 120s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x libhwloc15 s390x 2.12.2-1 [175 kB] 121s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x libpciaccess0 s390x 0.18.1-1ubuntu2 [19.1 kB] 121s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 121s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x ocl-icd-libopencl1 s390x 2.3.3-1 [44.9 kB] 121s Get:29 http://ftpmaster.internal/ubuntu resolute/universe s390x libhwloc-plugins s390x 2.12.2-1 [15.9 kB] 121s Get:30 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmpi40 s390x 5.0.8-8ubuntu1 [2907 kB] 121s Get:31 http://ftpmaster.internal/ubuntu resolute/universe s390x libspqr4 s390x 1:7.10.1+dfsg-1 [179 kB] 121s Get:32 http://ftpmaster.internal/ubuntu resolute/universe s390x apbs s390x 3.4.1-6build2 [75.2 kB] 121s Get:33 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 121s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 121s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 121s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 121s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 121s Get:38 http://ftpmaster.internal/ubuntu resolute/universe s390x apbs-doc all 3.4.1-6build2 [5850 kB] 122s Get:39 http://ftpmaster.internal/ubuntu resolute/universe s390x libapbs-dev s390x 3.4.1-6build2 [99.5 kB] 122s Get:40 http://ftpmaster.internal/ubuntu resolute/universe s390x libmaloc-dev s390x 1.5-2 [903 kB] 122s Get:41 http://ftpmaster.internal/ubuntu resolute/universe s390x libfetk-dev s390x 3.4.1-6build2 [144 kB] 122s Get:42 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-apbslib s390x 3.4.1-6build2 [213 kB] 122s Fetched 32.7 MB in 12s (2795 kB/s) 122s Selecting previously unselected package fonts-lato. 123s (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 ... 56856 files and directories currently installed.) 123s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 123s Unpacking fonts-lato (2.015-1) ... 123s Selecting previously unselected package apbs-data. 123s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 123s Unpacking apbs-data (3.4.1-6build2) ... 123s Selecting previously unselected package libmaloc1:s390x. 123s Preparing to unpack .../02-libmaloc1_1.5-2_s390x.deb ... 123s Unpacking libmaloc1:s390x (1.5-2) ... 123s Selecting previously unselected package libblas3:s390x. 123s Preparing to unpack .../03-libblas3_3.12.1-6build1_s390x.deb ... 123s Unpacking libblas3:s390x (3.12.1-6build1) ... 123s Selecting previously unselected package libsuperlu7:s390x. 123s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_s390x.deb ... 123s Unpacking libsuperlu7:s390x (7.0.1+dfsg1-2) ... 123s Selecting previously unselected package libgomp1:s390x. 123s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_s390x.deb ... 123s Unpacking libgomp1:s390x (15.2.0-5ubuntu1) ... 123s Selecting previously unselected package libsuitesparseconfig7:s390x. 123s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_s390x.deb ... 123s Unpacking libsuitesparseconfig7:s390x (1:7.10.1+dfsg-1) ... 123s Selecting previously unselected package libamd3:s390x. 123s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 123s Unpacking libamd3:s390x (1:7.10.1+dfsg-1) ... 123s Selecting previously unselected package libcamd3:s390x. 123s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 123s Unpacking libcamd3:s390x (1:7.10.1+dfsg-1) ... 123s Selecting previously unselected package libccolamd3:s390x. 123s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 123s Unpacking libccolamd3:s390x (1:7.10.1+dfsg-1) ... 123s Selecting previously unselected package libcolamd3:s390x. 123s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 123s Unpacking libcolamd3:s390x (1:7.10.1+dfsg-1) ... 123s Selecting previously unselected package libgfortran5:s390x. 123s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 123s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 123s Selecting previously unselected package liblapack3:s390x. 123s Preparing to unpack .../12-liblapack3_3.12.1-6build1_s390x.deb ... 123s Unpacking liblapack3:s390x (3.12.1-6build1) ... 123s Selecting previously unselected package libcholmod5:s390x. 123s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_s390x.deb ... 123s Unpacking libcholmod5:s390x (1:7.10.1+dfsg-1) ... 123s Selecting previously unselected package libumfpack6:s390x. 123s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_s390x.deb ... 123s Unpacking libumfpack6:s390x (1:7.10.1+dfsg-1) ... 123s Selecting previously unselected package libfetk1.9t64:s390x. 123s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_s390x.deb ... 123s Unpacking libfetk1.9t64:s390x (3.4.1-6build2) ... 123s Selecting previously unselected package libapbs3t64:s390x. 123s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_s390x.deb ... 123s Unpacking libapbs3t64:s390x (3.4.1-6build2) ... 123s Selecting previously unselected package fonts-mathjax. 123s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 123s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 123s Selecting previously unselected package libjs-mathjax. 123s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 123s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 124s Selecting previously unselected package libarpack2t64:s390x. 124s Preparing to unpack .../19-libarpack2t64_3.9.1-6_s390x.deb ... 124s Unpacking libarpack2t64:s390x (3.9.1-6) ... 124s Selecting previously unselected package libevent-core-2.1-7t64:s390x. 124s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_s390x.deb ... 124s Unpacking libevent-core-2.1-7t64:s390x (2.1.12-stable-10build1) ... 124s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 124s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_s390x.deb ... 124s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10build1) ... 124s Selecting previously unselected package librdmacm1t64:s390x. 124s Preparing to unpack .../22-librdmacm1t64_56.1-1ubuntu1_s390x.deb ... 124s Unpacking librdmacm1t64:s390x (56.1-1ubuntu1) ... 124s Selecting previously unselected package libfabric1:s390x. 124s Preparing to unpack .../23-libfabric1_2.1.0-1.1_s390x.deb ... 124s Unpacking libfabric1:s390x (2.1.0-1.1) ... 124s Selecting previously unselected package libhwloc15:s390x. 124s Preparing to unpack .../24-libhwloc15_2.12.2-1_s390x.deb ... 124s Unpacking libhwloc15:s390x (2.12.2-1) ... 124s Selecting previously unselected package libpciaccess0:s390x. 124s Preparing to unpack .../25-libpciaccess0_0.18.1-1ubuntu2_s390x.deb ... 124s Unpacking libpciaccess0:s390x (0.18.1-1ubuntu2) ... 124s Selecting previously unselected package libxnvctrl0:s390x. 124s Preparing to unpack .../26-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 124s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 124s Selecting previously unselected package ocl-icd-libopencl1:s390x. 124s Preparing to unpack .../27-ocl-icd-libopencl1_2.3.3-1_s390x.deb ... 124s Unpacking ocl-icd-libopencl1:s390x (2.3.3-1) ... 124s Selecting previously unselected package libhwloc-plugins:s390x. 124s Preparing to unpack .../28-libhwloc-plugins_2.12.2-1_s390x.deb ... 124s Unpacking libhwloc-plugins:s390x (2.12.2-1) ... 124s Selecting previously unselected package libopenmpi40:s390x. 124s Preparing to unpack .../29-libopenmpi40_5.0.8-8ubuntu1_s390x.deb ... 124s Unpacking libopenmpi40:s390x (5.0.8-8ubuntu1) ... 124s Selecting previously unselected package libspqr4:s390x. 124s Preparing to unpack .../30-libspqr4_1%3a7.10.1+dfsg-1_s390x.deb ... 124s Unpacking libspqr4:s390x (1:7.10.1+dfsg-1) ... 124s Selecting previously unselected package apbs. 124s Preparing to unpack .../31-apbs_3.4.1-6build2_s390x.deb ... 124s Unpacking apbs (3.4.1-6build2) ... 124s Selecting previously unselected package libjs-jquery. 124s Preparing to unpack .../32-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 124s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 124s Selecting previously unselected package libjs-underscore. 124s Preparing to unpack .../33-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 124s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 124s Selecting previously unselected package libjs-sphinxdoc. 124s Preparing to unpack .../34-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 124s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 124s Selecting previously unselected package fonts-font-awesome. 124s Preparing to unpack .../35-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 124s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 124s Selecting previously unselected package sphinx-rtd-theme-common. 124s Preparing to unpack .../36-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 124s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 124s Selecting previously unselected package apbs-doc. 124s Preparing to unpack .../37-apbs-doc_3.4.1-6build2_all.deb ... 124s Unpacking apbs-doc (3.4.1-6build2) ... 124s Selecting previously unselected package libapbs-dev:s390x. 124s Preparing to unpack .../38-libapbs-dev_3.4.1-6build2_s390x.deb ... 124s Unpacking libapbs-dev:s390x (3.4.1-6build2) ... 124s Selecting previously unselected package libmaloc-dev. 124s Preparing to unpack .../39-libmaloc-dev_1.5-2_s390x.deb ... 124s Unpacking libmaloc-dev (1.5-2) ... 124s Selecting previously unselected package libfetk-dev:s390x. 124s Preparing to unpack .../40-libfetk-dev_3.4.1-6build2_s390x.deb ... 124s Unpacking libfetk-dev:s390x (3.4.1-6build2) ... 124s Selecting previously unselected package python3-apbslib. 124s Preparing to unpack .../41-python3-apbslib_3.4.1-6build2_s390x.deb ... 124s Unpacking python3-apbslib (3.4.1-6build2) ... 124s Setting up libmaloc1:s390x (1.5-2) ... 124s Setting up libpciaccess0:s390x (0.18.1-1ubuntu2) ... 124s Setting up fonts-lato (2.015-1) ... 124s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 124s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 124s Setting up apbs-data (3.4.1-6build2) ... 124s Setting up libgomp1:s390x (15.2.0-5ubuntu1) ... 124s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 124s Setting up libblas3:s390x (3.12.1-6build1) ... 124s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 124s Setting up libhwloc15:s390x (2.12.2-1) ... 124s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 124s Setting up ocl-icd-libopencl1:s390x (2.3.3-1) ... 124s Setting up libsuitesparseconfig7:s390x (1:7.10.1+dfsg-1) ... 124s Setting up librdmacm1t64:s390x (56.1-1ubuntu1) ... 124s Setting up libevent-core-2.1-7t64:s390x (2.1.12-stable-10build1) ... 124s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 124s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 124s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 124s Setting up libmaloc-dev (1.5-2) ... 124s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 124s Setting up libfabric1:s390x (2.1.0-1.1) ... 124s Setting up liblapack3:s390x (3.12.1-6build1) ... 124s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 124s Setting up libarpack2t64:s390x (3.9.1-6) ... 124s Setting up libamd3:s390x (1:7.10.1+dfsg-1) ... 124s Setting up libcolamd3:s390x (1:7.10.1+dfsg-1) ... 124s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10build1) ... 124s Setting up libhwloc-plugins:s390x (2.12.2-1) ... 124s Setting up libcamd3:s390x (1:7.10.1+dfsg-1) ... 124s Setting up libsuperlu7:s390x (7.0.1+dfsg1-2) ... 124s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 124s Setting up libccolamd3:s390x (1:7.10.1+dfsg-1) ... 124s Setting up libopenmpi40:s390x (5.0.8-8ubuntu1) ... 124s Setting up libcholmod5:s390x (1:7.10.1+dfsg-1) ... 124s Setting up libspqr4:s390x (1:7.10.1+dfsg-1) ... 124s Setting up apbs-doc (3.4.1-6build2) ... 124s Setting up libumfpack6:s390x (1:7.10.1+dfsg-1) ... 124s Setting up libfetk1.9t64:s390x (3.4.1-6build2) ... 124s Setting up libapbs3t64:s390x (3.4.1-6build2) ... 124s Setting up libfetk-dev:s390x (3.4.1-6build2) ... 124s Setting up libapbs-dev:s390x (3.4.1-6build2) ... 124s Setting up apbs (3.4.1-6build2) ... 124s Setting up python3-apbslib (3.4.1-6build2) ... 124s Processing triggers for man-db (2.13.1-1) ... 125s Processing triggers for libc-bin (2.42-0ubuntu3) ... 128s autopkgtest [00:47:23]: test test-apbs: [----------------------- 128s TESTING WITH BINARY_NAME:apbs 128s START_DIR:/tmp/autopkgtest.mRye7P/autopkgtest_tmp/build 128s -------------------------------------------------------------------------------- 128s Testing forces from apbs-forces.in 128s 128s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000531 seconds 128s -------------------------------------------------------------------------------- 128s -------------------------------------------------------------------------------- 128s Testing input file apbs-mol-auto.in 128s 129s CHECKING:/usr/local/sbin/apbs 129s CHECKING:/usr/local/bin/apbs 129s CHECKING:/usr/sbin/apbs 129s CHECKING:/usr/bin/apbs 129s NOTE: Using apbs binary:/usr/bin/apbs 129s Testing all sections 129s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 129s ================================================================================ 129s Running tests for born section 129s BINARY: /usr/bin/apbs 129s INPUT: apbs-mol-auto.in 129s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 129s asc_getToken: Error occurred (bailing out). 129s Vio_scanf: Format problem with input. 129s 129s 129s ---------------------------------------------------------------------- 129s APBS -- Adaptive Poisson-Boltzmann Solver 129s Version APBS 3.4.1 129s 129s Nathan A. Baker (nathan.baker@pnnl.gov) 129s Pacific Northwest National Laboratory 129s 129s Additional contributing authors listed in the code documentation. 129s 129s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 129s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 129s Northwest Division for the U.S. Department of Energy. 129s 129s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 129s Portions Copyright (c) 2002-2020, Nathan A. Baker. 129s Portions Copyright (c) 1999-2002, The Regents of the University of California. 129s Portions Copyright (c) 1995, Michael Holst. 129s All rights reserved. 129s 129s Redistribution and use in source and binary forms, with or without 129s modification, are permitted provided that the following conditions are met: 129s 129s * Redistributions of source code must retain the above copyright notice, this 129s list of conditions and the following disclaimer. 129s 129s * Redistributions in binary form must reproduce the above copyright notice, 129s this list of conditions and the following disclaimer in the documentation 129s and/or other materials provided with the distribution. 129s 129s * Neither the name of the developer nor the names of its contributors may be 129s used to endorse or promote products derived from this software without 129s specific prior written permission. 129s 129s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 129s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 129s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 129s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 129s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 129s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 129s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 129s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 129s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 129s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 129s ---------------------------------------------------------------------- 129s APBS uses FETK (the Finite Element ToolKit) to solve the 129s Poisson-Boltzmann equation numerically. FETK is a portable collection 129s of finite element modeling class libraries developed by the Michael Holst 129s research group and written in an object-oriented form of C. FEtk is 129s designed to solve general coupled systems of nonlinear partial differential 129s equations using adaptive finite element methods, inexact Newton methods, 129s and algebraic multilevel methods. More information about FEtk may be found 129s at . 129s ---------------------------------------------------------------------- 129s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 129s Aqua is a modified form of the Holst group PMG library 129s which has been modified by Patrice Koehl 129s for improved efficiency and 129s memory usage when solving the Poisson-Boltzmann equation. 129s ---------------------------------------------------------------------- 129s Please cite your use of APBS as: 129s 129s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 129s nanosystems: application to microtubules and the ribosome. Proc. 129s Natl. Acad. Sci. USA 98, 10037-10041 2001. 129s 129s 129s This executable compiled on Jan 3 2025 at 11:01:42 129s 129s Parsing input file apbs-mol-auto.in... 129s rank 0 size 1... 129s Parsed input file. 129s Got paths for 1 molecules 129s Reading PQR-format atom data from ion.pqr. 129s 1 atoms 129s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 129s Net charge 1.00e+00 e 129s Preparing to run 6 PBE calculations. 129s ---------------------------------------- 129s CALCULATION #1 (solvated): MULTIGRID 129s Setting up problem... 129s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 129s Debye length: 0 A 129s Current memory usage: 61.280 MB total, 61.280 MB high water 129s Using cubic spline charge discretization. 129s Grid dimensions: 65 x 65 x 65 129s Grid spacings: 0.781 x 0.781 x 0.781 129s Grid lengths: 50.000 x 50.000 x 50.000 129s Grid center: (0.000, 0.000, 0.000) 129s Multigrid levels: 5 129s Molecule ID: 1 129s Linearized traditional PBE 129s Multiple Debye-Huckel sphere boundary conditions 129s 0 ion species (0.000 M ionic strength): 129s Solute dielectric: 1.000 129s Solvent dielectric: 78.540 129s Using "molecular" surface definition; no smoothing 129s Solvent probe radius: 1.400 A 129s Temperature: 298.150 K 129s Electrostatic energies will be calculated 129s Total electrostatic energy = 9.607073836227E+02 kJ/mol 129s Calculating forces... 129s ---------------------------------------- 129s CALCULATION #2 (solvated): MULTIGRID 129s Setting up problem... 129s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 129s Debye length: 0 A 129s Current memory usage: 61.280 MB total, 122.102 MB high water 129s Using cubic spline charge discretization. 129s Grid dimensions: 65 x 65 x 65 129s Grid spacings: 0.383 x 0.383 x 0.383 129s Grid lengths: 24.495 x 24.495 x 24.495 129s Grid center: (0.000, 0.000, 0.000) 129s Multigrid levels: 5 129s Molecule ID: 1 129s Linearized traditional PBE 129s Boundary conditions from focusing 129s 0 ion species (0.000 M ionic strength): 129s Solute dielectric: 1.000 129s Solvent dielectric: 78.540 129s Using "molecular" surface definition; no smoothing 129s Solvent probe radius: 1.400 A 129s Temperature: 298.150 K 129s Electrostatic energies will be calculated 129s Total electrostatic energy = 2.200266567971E+03 kJ/mol 129s Calculating forces... 129s ---------------------------------------- 129s CALCULATION #3 (solvated): MULTIGRID 129s Setting up problem... 129s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 129s Debye length: 0 A 129s Current memory usage: 61.280 MB total, 122.102 MB high water 129s Using cubic spline charge discretization. 129s Grid dimensions: 65 x 65 x 65 129s Grid spacings: 0.188 x 0.188 x 0.188 129s Grid lengths: 12.000 x 12.000 x 12.000 129s Grid center: (0.000, 0.000, 0.000) 129s Multigrid levels: 5 129s Molecule ID: 1 129s Linearized traditional PBE 129s Boundary conditions from focusing 129s 0 ion species (0.000 M ionic strength): 129s Solute dielectric: 1.000 129s Solvent dielectric: 78.540 129s Using "molecular" surface definition; no smoothing 129s Solvent probe radius: 1.400 A 129s Temperature: 298.150 K 129s Electrostatic energies will be calculated 129s Potential to be written to potential.dx.gz 129s Total electrostatic energy = 4.732245131587E+03 kJ/mol 129s Calculating forces... 129s Writing potential to potential-PE0.dx.gz 129s ---------------------------------------- 129s CALCULATION #4 (reference): MULTIGRID 129s Setting up problem... 129s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 129s Debye length: 0 A 129s Current memory usage: 61.207 MB total, 122.102 MB high water 129s Using cubic spline charge discretization. 129s Grid dimensions: 65 x 65 x 65 129s Grid spacings: 0.781 x 0.781 x 0.781 129s Grid lengths: 50.000 x 50.000 x 50.000 129s Grid center: (0.000, 0.000, 0.000) 129s Multigrid levels: 5 129s Molecule ID: 1 129s Linearized traditional PBE 129s Multiple Debye-Huckel sphere boundary conditions 129s 0 ion species (0.000 M ionic strength): 129s Solute dielectric: 1.000 129s Solvent dielectric: 1.000 129s Using "molecular" surface definition; no smoothing 129s Solvent probe radius: 1.400 A 129s Temperature: 298.150 K 129s Electrostatic energies will be calculated 129s Total electrostatic energy = 1.190871482831E+03 kJ/mol 129s Calculating forces... 129s ---------------------------------------- 129s CALCULATION #5 (reference): MULTIGRID 129s Setting up problem... 129s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 129s Debye length: 0 A 129s Current memory usage: 61.207 MB total, 122.102 MB high water 129s Using cubic spline charge discretization. 129s Grid dimensions: 65 x 65 x 65 129s Grid spacings: 0.383 x 0.383 x 0.383 129s Grid lengths: 24.495 x 24.495 x 24.495 129s Grid center: (0.000, 0.000, 0.000) 129s Multigrid levels: 5 129s Molecule ID: 1 129s Linearized traditional PBE 129s Boundary conditions from focusing 129s 0 ion species (0.000 M ionic strength): 129s Solute dielectric: 1.000 129s Solvent dielectric: 1.000 129s Using "molecular" surface definition; no smoothing 129s Solvent probe radius: 1.400 A 129s Temperature: 298.150 K 129s Electrostatic energies will be calculated 129s Total electrostatic energy = 2.430874049735E+03 kJ/mol 129s Calculating forces... 129s [focusFillBound()]: WARNING: 129s Unusually large potential values 129s detected on the focusing boundary! 129s Convergence not guaranteed for NPBE/NRPBE calculations! 129s 129s ---------------------------------------- 129s CALCULATION #6 (reference): MULTIGRID 129s Setting up problem... 129s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 129s Debye length: 0 A 129s Current memory usage: 61.207 MB total, 122.102 MB high water 129s Using cubic spline charge discretization. 129s Grid dimensions: 65 x 65 x 65 129s Grid spacings: 0.188 x 0.188 x 0.188 129s Grid lengths: 12.000 x 12.000 x 12.000 129s Grid center: (0.000, 0.000, 0.000) 129s Multigrid levels: 5 129s Molecule ID: 1 129s Linearized traditional PBE 129s Boundary conditions from focusing 129s 0 ion species (0.000 M ionic strength): 129s Solute dielectric: 1.000 129s Solvent dielectric: 1.000 129s Using "molecular" surface definition; no smoothing 129s Solvent probe radius: 1.400 A 129s Temperature: 298.150 K 129s Electrostatic energies will be calculated 129s Total electrostatic energy = 4.962018684215E+03 kJ/mol 129s Calculating forces... 129s ---------------------------------------- 129s PRINT STATEMENTS 129s 129s print energy 1 (solvated) - 2 (reference) end 129s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 129s Global net ELEC energy = -2.297735526282E+02 kJ/mol 129s ---------------------------------------- 129s CLEANING UP AND SHUTTING DOWN... 129s Destroying force arrays. 129s No energy arrays to destroy. 129s Destroying multigrid structures. 129s Destroying finite element structures. 129s Destroying 1 molecules 129s Final memory usage: 0.001 MB total, 122.102 MB high water 129s 129s 129s Thanks for using APBS! 129s 129s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 129s *** PASSED *** 129s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 129s *** PASSED *** 129s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 129s *** PASSED *** 129s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 129s *** PASSED *** 129s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 129s *** PASSED *** 129s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 129s *** PASSED *** 129s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 129s *** PASSED *** 129s Elapsed time: 1.043925 seconds 129s -------------------------------------------------------------------------------- 129s -------------------------------------------------------------------------------- 129s Testing input file apbs-smol-auto.in 129s 130s Checking for intermediate energies in input file apbs-mol-auto.out 130s EXPECTED COMPUTED: 7 130s EXPECTED EXPECTED: 7 130s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 130s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 130s COMPUTED RESULT 960.7073836227 130s COMPUTED RESULT 2200.266567971 130s COMPUTED RESULT 4732.245131587 130s COMPUTED RESULT 1190.871482831 130s COMPUTED RESULT 2430.874049735 130s COMPUTED RESULT 4962.018684215 130s COMPUTED RESULT -229.7735526282 130s BINARY: /usr/bin/apbs 130s INPUT: apbs-smol-auto.in 130s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 130s asc_getToken: Error occurred (bailing out). 130s Vio_scanf: Format problem with input. 130s 130s 130s ---------------------------------------------------------------------- 130s APBS -- Adaptive Poisson-Boltzmann Solver 130s Version APBS 3.4.1 130s 130s Nathan A. Baker (nathan.baker@pnnl.gov) 130s Pacific Northwest National Laboratory 130s 130s Additional contributing authors listed in the code documentation. 130s 130s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 130s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 130s Northwest Division for the U.S. Department of Energy. 130s 130s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 130s Portions Copyright (c) 2002-2020, Nathan A. Baker. 130s Portions Copyright (c) 1999-2002, The Regents of the University of California. 130s Portions Copyright (c) 1995, Michael Holst. 130s All rights reserved. 130s 130s Redistribution and use in source and binary forms, with or without 130s modification, are permitted provided that the following conditions are met: 130s 130s * Redistributions of source code must retain the above copyright notice, this 130s list of conditions and the following disclaimer. 130s 130s * Redistributions in binary form must reproduce the above copyright notice, 130s this list of conditions and the following disclaimer in the documentation 130s and/or other materials provided with the distribution. 130s 130s * Neither the name of the developer nor the names of its contributors may be 130s used to endorse or promote products derived from this software without 130s specific prior written permission. 130s 130s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 130s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 130s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 130s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 130s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 130s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 130s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 130s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 130s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 130s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 130s ---------------------------------------------------------------------- 130s APBS uses FETK (the Finite Element ToolKit) to solve the 130s Poisson-Boltzmann equation numerically. FETK is a portable collection 130s of finite element modeling class libraries developed by the Michael Holst 130s research group and written in an object-oriented form of C. FEtk is 130s designed to solve general coupled systems of nonlinear partial differential 130s equations using adaptive finite element methods, inexact Newton methods, 130s and algebraic multilevel methods. More information about FEtk may be found 130s at . 130s ---------------------------------------------------------------------- 130s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 130s Aqua is a modified form of the Holst group PMG library 130s which has been modified by Patrice Koehl 130s for improved efficiency and 130s memory usage when solving the Poisson-Boltzmann equation. 130s ---------------------------------------------------------------------- 130s Please cite your use of APBS as: 130s 130s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 130s nanosystems: application to microtubules and the ribosome. Proc. 130s Natl. Acad. Sci. USA 98, 10037-10041 2001. 130s 130s 130s This executable compiled on Jan 3 2025 at 11:01:42 130s 130s Parsing input file apbs-smol-auto.in... 130s rank 0 size 1... 130s Parsed input file. 130s Got paths for 1 molecules 130s Reading PQR-format atom data from ion.pqr. 130s 1 atoms 130s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 130s Net charge 1.00e+00 e 130s Preparing to run 6 PBE calculations. 130s ---------------------------------------- 130s CALCULATION #1 (solvated): MULTIGRID 130s Setting up problem... 130s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 130s Debye length: 0 A 130s Current memory usage: 61.280 MB total, 61.280 MB high water 130s Using cubic spline charge discretization. 130s Grid dimensions: 65 x 65 x 65 130s Grid spacings: 0.781 x 0.781 x 0.781 130s Grid lengths: 50.000 x 50.000 x 50.000 130s Grid center: (0.000, 0.000, 0.000) 130s Multigrid levels: 5 130s Molecule ID: 1 130s Linearized traditional PBE 130s Multiple Debye-Huckel sphere boundary conditions 130s 0 ion species (0.000 M ionic strength): 130s Solute dielectric: 1.000 130s Solvent dielectric: 78.540 130s Using "molecular" surface definition;harmonic average smoothing 130s Solvent probe radius: 1.400 A 130s Temperature: 298.150 K 130s Electrostatic energies will be calculated 130s Total electrostatic energy = 9.532928767450E+02 kJ/mol 130s Calculating forces... 130s ---------------------------------------- 130s CALCULATION #2 (solvated): MULTIGRID 130s Setting up problem... 130s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 130s Debye length: 0 A 130s Current memory usage: 61.280 MB total, 122.102 MB high water 130s Using cubic spline charge discretization. 130s Grid dimensions: 65 x 65 x 65 130s Grid spacings: 0.383 x 0.383 x 0.383 130s Grid lengths: 24.495 x 24.495 x 24.495 130s Grid center: (0.000, 0.000, 0.000) 130s Multigrid levels: 5 130s Molecule ID: 1 130s Linearized traditional PBE 130s Boundary conditions from focusing 130s 0 ion species (0.000 M ionic strength): 130s Solute dielectric: 1.000 130s Solvent dielectric: 78.540 130s Using "molecular" surface definition;harmonic average smoothing 130s Solvent probe radius: 1.400 A 130s Temperature: 298.150 K 130s Electrostatic energies will be calculated 130s Total electrostatic energy = 2.201243880085E+03 kJ/mol 130s Calculating forces... 130s ---------------------------------------- 130s CALCULATION #3 (solvated): MULTIGRID 130s Setting up problem... 130s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 130s Debye length: 0 A 130s Current memory usage: 61.280 MB total, 122.102 MB high water 130s Using cubic spline charge discretization. 130s Grid dimensions: 65 x 65 x 65 130s Grid spacings: 0.188 x 0.188 x 0.188 130s Grid lengths: 12.000 x 12.000 x 12.000 130s Grid center: (0.000, 0.000, 0.000) 130s Multigrid levels: 5 130s Molecule ID: 1 130s Linearized traditional PBE 130s Boundary conditions from focusing 130s 0 ion species (0.000 M ionic strength): 130s Solute dielectric: 1.000 130s Solvent dielectric: 78.540 130s Using "molecular" surface definition;harmonic average smoothing 130s Solvent probe radius: 1.400 A 130s Temperature: 298.150 K 130s Electrostatic energies will be calculated 130s Total electrostatic energy = 4.733006258977E+03 kJ/mol 130s Calculating forces... 130s ---------------------------------------- 130s CALCULATION #4 (reference): MULTIGRID 130s Setting up problem... 130s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 130s Debye length: 0 A 130s Current memory usage: 61.207 MB total, 122.102 MB high water 130s Using cubic spline charge discretization. 130s Grid dimensions: 65 x 65 x 65 130s Grid spacings: 0.781 x 0.781 x 0.781 130s Grid lengths: 50.000 x 50.000 x 50.000 130s Grid center: (0.000, 0.000, 0.000) 130s Multigrid levels: 5 130s Molecule ID: 1 130s Linearized traditional PBE 130s Multiple Debye-Huckel sphere boundary conditions 130s 0 ion species (0.000 M ionic strength): 130s Solute dielectric: 1.000 130s Solvent dielectric: 1.000 130s Using "molecular" surface definition;harmonic average smoothing 130s Solvent probe radius: 1.400 A 130s Temperature: 298.150 K 130s Electrostatic energies will be calculated 130s Total electrostatic energy = 1.190871482831E+03 kJ/mol 130s Calculating forces... 130s ---------------------------------------- 130s CALCULATION #5 (reference): MULTIGRID 130s Setting up problem... 130s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 130s Debye length: 0 A 130s Current memory usage: 61.207 MB total, 122.102 MB high water 130s Using cubic spline charge discretization. 130s Grid dimensions: 65 x 65 x 65 130s Grid spacings: 0.383 x 0.383 x 0.383 130s Grid lengths: 24.495 x 24.495 x 24.495 130s Grid center: (0.000, 0.000, 0.000) 130s Multigrid levels: 5 130s Molecule ID: 1 130s Linearized traditional PBE 130s Boundary conditions from focusing 130s 0 ion species (0.000 M ionic strength): 130s Solute dielectric: 1.000 130s Solvent dielectric: 1.000 130s Using "molecular" surface definition;harmonic average smoothing 130s Solvent probe radius: 1.400 A 130s Temperature: 298.150 K 130s Electrostatic energies will be calculated 130s Total electrostatic energy = 2.430874049735E+03 kJ/mol 130s Calculating forces... 130s [focusFillBound()]: WARNING: 130s Unusually large potential values 130s detected on the focusing boundary! 130s Convergence not guaranteed for NPBE/NRPBE calculations! 130s 130s ---------------------------------------- 130s CALCULATION #6 (reference): MULTIGRID 130s Setting up problem... 130s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 130s Debye length: 0 A 130s Current memory usage: 61.207 MB total, 122.102 MB high water 130s Using cubic spline charge discretization. 130s Grid dimensions: 65 x 65 x 65 130s Grid spacings: 0.188 x 0.188 x 0.188 130s Grid lengths: 12.000 x 12.000 x 12.000 130s Grid center: (0.000, 0.000, 0.000) 130s Multigrid levels: 5 130s Molecule ID: 1 130s Linearized traditional PBE 130s Boundary conditions from focusing 130s 0 ion species (0.000 M ionic strength): 130s Solute dielectric: 1.000 130s Solvent dielectric: 1.000 130s Using "molecular" surface definition;harmonic average smoothing 130s Solvent probe radius: 1.400 A 130s Temperature: 298.150 K 130s Electrostatic energies will be calculated 130s Total electrostatic energy = 4.962018684215E+03 kJ/mol 130s Calculating forces... 130s ---------------------------------------- 130s PRINT STATEMENTS 130s 130s print energy 1 (solvated) - 2 (reference) end 130s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 130s Global net ELEC energy = -2.290124252387E+02 kJ/mol 130s ---------------------------------------- 130s CLEANING UP AND SHUTTING DOWN... 130s Destroying force arrays. 130s No energy arrays to destroy. 130s Destroying multigrid structures. 130s Destroying finite element structures. 130s Destroying 1 molecules 130s Final memory usage: 0.001 MB total, 122.102 MB high water 130s 130s 130s Thanks for using APBS! 130s 130s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 130s *** PASSED *** 130s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 130s *** PASSED *** 130s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 130s *** PASSED *** 130s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 130s *** PASSED *** 130s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 130s *** PASSED *** 130s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 130s *** PASSED *** 130s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 130s *** PASSED *** 130s Elapsed time: 1.192752 seconds 130s -------------------------------------------------------------------------------- 130s -------------------------------------------------------------------------------- 130s Testing input file apbs-mol-parallel.in 130s 130s Splitting the input file into 4 separate files using the inputgen utility 130s 132s Checking for intermediate energies in input file apbs-smol-auto.out 132s EXPECTED COMPUTED: 7 132s EXPECTED EXPECTED: 7 132s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 132s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 132s COMPUTED RESULT 953.292876745 132s COMPUTED RESULT 2201.243880085 132s COMPUTED RESULT 4733.006258977 132s COMPUTED RESULT 1190.871482831 132s COMPUTED RESULT 2430.874049735 132s COMPUTED RESULT 4962.018684215 132s COMPUTED RESULT -229.0124252387 132s BINARY: /usr/bin/apbs 132s INPUT: apbs-mol-parallel-PE0.in 132s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 132s Processor 0 results: 132s 2.401768459022e+02 132s 8.142935592471e+02 132s 1.485255308186e+03 132s 2.977178707009e+02 132s 8.799304557588e+02 132s 1.542873949131e+03 132s -5.761864094552e+01 132s 132s asc_getToken: Error occurred (bailing out). 132s Vio_scanf: Format problem with input. 132s 132s 132s ---------------------------------------------------------------------- 132s APBS -- Adaptive Poisson-Boltzmann Solver 132s Version APBS 3.4.1 132s 132s Nathan A. Baker (nathan.baker@pnnl.gov) 132s Pacific Northwest National Laboratory 132s 132s Additional contributing authors listed in the code documentation. 132s 132s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 132s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 132s Northwest Division for the U.S. Department of Energy. 132s 132s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 132s Portions Copyright (c) 2002-2020, Nathan A. Baker. 132s Portions Copyright (c) 1999-2002, The Regents of the University of California. 132s Portions Copyright (c) 1995, Michael Holst. 132s All rights reserved. 132s 132s Redistribution and use in source and binary forms, with or without 132s modification, are permitted provided that the following conditions are met: 132s 132s * Redistributions of source code must retain the above copyright notice, this 132s list of conditions and the following disclaimer. 132s 132s * Redistributions in binary form must reproduce the above copyright notice, 132s this list of conditions and the following disclaimer in the documentation 132s and/or other materials provided with the distribution. 132s 132s * Neither the name of the developer nor the names of its contributors may be 132s used to endorse or promote products derived from this software without 132s specific prior written permission. 132s 132s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 132s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 132s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 132s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 132s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 132s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 132s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 132s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 132s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 132s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 132s ---------------------------------------------------------------------- 132s APBS uses FETK (the Finite Element ToolKit) to solve the 132s Poisson-Boltzmann equation numerically. FETK is a portable collection 132s of finite element modeling class libraries developed by the Michael Holst 132s research group and written in an object-oriented form of C. FEtk is 132s designed to solve general coupled systems of nonlinear partial differential 132s equations using adaptive finite element methods, inexact Newton methods, 132s and algebraic multilevel methods. More information about FEtk may be found 132s at . 132s ---------------------------------------------------------------------- 132s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 132s Aqua is a modified form of the Holst group PMG library 132s which has been modified by Patrice Koehl 132s for improved efficiency and 132s memory usage when solving the Poisson-Boltzmann equation. 132s ---------------------------------------------------------------------- 132s Please cite your use of APBS as: 132s 132s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 132s nanosystems: application to microtubules and the ribosome. Proc. 132s Natl. Acad. Sci. USA 98, 10037-10041 2001. 132s 132s 132s This executable compiled on Jan 3 2025 at 11:01:42 132s 132s Parsing input file apbs-mol-parallel-PE0.in... 132s rank 0 size 1... 132s Parsed input file. 132s Got paths for 1 molecules 132s Reading PQR-format atom data from ion.pqr. 132s 1 atoms 132s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 132s Net charge 1.00e+00 e 132s Preparing to run 6 PBE calculations. 132s ---------------------------------------- 132s CALCULATION #1 (solvated): MULTIGRID 132s Setting up problem... 132s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 132s Debye length: 0 A 132s Current memory usage: 61.280 MB total, 61.280 MB high water 132s Using cubic spline charge discretization. 132s Partition overlap fraction = 0.1 132s Processor array = 2 x 2 x 1 132s Grid dimensions: 65 x 65 x 65 132s Grid spacings: 0.781 x 0.781 x 0.781 132s Grid lengths: 50.000 x 50.000 x 50.000 132s Grid center: (0.000, 0.000, 0.000) 132s Multigrid levels: 5 132s Molecule ID: 1 132s Linearized traditional PBE 132s Multiple Debye-Huckel sphere boundary conditions 132s 0 ion species (0.000 M ionic strength): 132s Solute dielectric: 1.000 132s Solvent dielectric: 78.540 132s Using "molecular" surface definition; no smoothing 132s Solvent probe radius: 1.400 A 132s Temperature: 298.150 K 132s Electrostatic energies will be calculated 132s Total electrostatic energy = 2.401768459022E+02 kJ/mol 132s Calculating forces... 132s ---------------------------------------- 132s CALCULATION #2 (solvated): MULTIGRID 132s Setting up problem... 132s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 132s Debye length: 0 A 132s Current memory usage: 61.280 MB total, 122.102 MB high water 132s Using cubic spline charge discretization. 132s Partition overlap fraction = 0.1 132s Processor array = 2 x 2 x 1 132s Grid dimensions: 65 x 65 x 65 132s Grid spacings: 0.296 x 0.296 x 0.383 132s Grid lengths: 18.944 x 18.944 x 24.495 132s Grid center: (-2.411, -2.411, 0.000) 132s Multigrid levels: 5 132s Molecule ID: 1 132s Linearized traditional PBE 132s Boundary conditions from focusing 132s 0 ion species (0.000 M ionic strength): 132s Solute dielectric: 1.000 132s Solvent dielectric: 78.540 132s Using "molecular" surface definition; no smoothing 132s Solvent probe radius: 1.400 A 132s Temperature: 298.150 K 132s Electrostatic energies will be calculated 132s Total electrostatic energy = 8.142935592471E+02 kJ/mol 132s Calculating forces... 132s [focusFillBound()]: WARNING: 132s Unusually large potential values 132s detected on the focusing boundary! 132s Convergence not guaranteed for NPBE/NRPBE calculations! 132s 132s ---------------------------------------- 132s CALCULATION #3 (solvated): MULTIGRID 132s Setting up problem... 132s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 132s Debye length: 0 A 132s Current memory usage: 61.280 MB total, 122.102 MB high water 132s Using cubic spline charge discretization. 132s Partition overlap fraction = 0.1 132s Processor array = 2 x 2 x 1 132s Grid dimensions: 65 x 65 x 65 132s Grid spacings: 0.112 x 0.112 x 0.188 132s Grid lengths: 7.178 x 7.178 x 12.000 132s Grid center: (-2.411, -2.411, 0.000) 132s Multigrid levels: 5 132s Molecule ID: 1 132s Linearized traditional PBE 132s Boundary conditions from focusing 132s 0 ion species (0.000 M ionic strength): 132s Solute dielectric: 1.000 132s Solvent dielectric: 78.540 132s Using "molecular" surface definition; no smoothing 132s Solvent probe radius: 1.400 A 132s Temperature: 298.150 K 132s Electrostatic energies will be calculated 132s Total electrostatic energy = 1.485255308186E+03 kJ/mol 132s Calculating forces... 132s ---------------------------------------- 132s CALCULATION #4 (reference): MULTIGRID 132s Setting up problem... 132s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 132s Debye length: 0 A 132s Current memory usage: 61.207 MB total, 122.102 MB high water 132s Using cubic spline charge discretization. 132s Partition overlap fraction = 0.1 132s Processor array = 2 x 2 x 1 132s Grid dimensions: 65 x 65 x 65 132s Grid spacings: 0.781 x 0.781 x 0.781 132s Grid lengths: 50.000 x 50.000 x 50.000 132s Grid center: (0.000, 0.000, 0.000) 132s Multigrid levels: 5 132s Molecule ID: 1 132s Linearized traditional PBE 132s Multiple Debye-Huckel sphere boundary conditions 132s 0 ion species (0.000 M ionic strength): 132s Solute dielectric: 1.000 132s Solvent dielectric: 1.000 132s Using "molecular" surface definition; no smoothing 132s Solvent probe radius: 1.400 A 132s Temperature: 298.150 K 132s Electrostatic energies will be calculated 132s Total electrostatic energy = 2.977178707009E+02 kJ/mol 132s Calculating forces... 132s ---------------------------------------- 132s CALCULATION #5 (reference): MULTIGRID 132s Setting up problem... 132s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 132s Debye length: 0 A 132s Current memory usage: 61.207 MB total, 122.102 MB high water 132s Using cubic spline charge discretization. 132s Partition overlap fraction = 0.1 132s Processor array = 2 x 2 x 1 132s Grid dimensions: 65 x 65 x 65 132s Grid spacings: 0.296 x 0.296 x 0.383 132s Grid lengths: 18.944 x 18.944 x 24.495 132s Grid center: (-2.411, -2.411, 0.000) 132s Multigrid levels: 5 132s Molecule ID: 1 132s Linearized traditional PBE 132s Boundary conditions from focusing 132s 0 ion species (0.000 M ionic strength): 132s Solute dielectric: 1.000 132s Solvent dielectric: 1.000 132s Using "molecular" surface definition; no smoothing 132s Solvent probe radius: 1.400 A 132s Temperature: 298.150 K 132s Electrostatic energies will be calculated 132s Total electrostatic energy = 8.799304557588E+02 kJ/mol 132s Calculating forces... 132s [focusFillBound()]: WARNING: 132s Unusually large potential values 132s detected on the focusing boundary! 132s Convergence not guaranteed for NPBE/NRPBE calculations! 132s 132s ---------------------------------------- 132s CALCULATION #6 (reference): MULTIGRID 132s Setting up problem... 132s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 132s Debye length: 0 A 132s Current memory usage: 61.207 MB total, 122.102 MB high water 132s Using cubic spline charge discretization. 132s Partition overlap fraction = 0.1 132s Processor array = 2 x 2 x 1 132s Grid dimensions: 65 x 65 x 65 132s Grid spacings: 0.112 x 0.112 x 0.188 132s Grid lengths: 7.178 x 7.178 x 12.000 132s Grid center: (-2.411, -2.411, 0.000) 132s Multigrid levels: 5 132s Molecule ID: 1 132s Linearized traditional PBE 132s Boundary conditions from focusing 132s 0 ion species (0.000 M ionic strength): 132s Solute dielectric: 1.000 132s Solvent dielectric: 1.000 132s Using "molecular" surface definition; no smoothing 132s Solvent probe radius: 1.400 A 132s Temperature: 298.150 K 132s Electrostatic energies will be calculated 132s Total electrostatic energy = 1.542873949131E+03 kJ/mol 132s Calculating forces... 132s ---------------------------------------- 132s PRINT STATEMENTS 132s 132s print energy 1 (solvated) - 2 (reference) end 132s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 132s Global net ELEC energy = -5.761864094552E+01 kJ/mol 132s ---------------------------------------- 132s CLEANING UP AND SHUTTING DOWN... 132s Destroying force arrays. 132s No energy arrays to destroy. 132s Destroying multigrid structures. 132s Destroying finite element structures. 132s Destroying 1 molecules 132s Final memory usage: 0.001 MB total, 122.102 MB high water 132s 132s 132s Thanks for using APBS! 132s 133s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 133s BINARY: /usr/bin/apbs 133s INPUT: apbs-mol-parallel-PE1.in 133s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 133s asc_getToken: Error occurred (bailing out). 133s Vio_scanf: Format problem with input. 133s 133s 133s ---------------------------------------------------------------------- 133s APBS -- Adaptive Poisson-Boltzmann Solver 133s Version APBS 3.4.1 133s 133s Nathan A. Baker (nathan.baker@pnnl.gov) 133s Pacific Northwest National Laboratory 133s 133s Additional contributing authors listed in the code documentation. 133s 133s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 133s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 133s Northwest Division for the U.S. Department of Energy. 133s 133s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 133s Portions Copyright (c) 2002-2020, Nathan A. Baker. 133s Portions Copyright (c) 1999-2002, The Regents of the University of California. 133s Portions Copyright (c) 1995, Michael Holst. 133s All rights reserved. 133s 133s Redistribution and use in source and binary forms, with or without 133s modification, are permitted provided that the following conditions are met: 133s 133s * Redistributions of source code must retain the above copyright notice, this 133s list of conditions and the following disclaimer. 133s 133s * Redistributions in binary form must reproduce the above copyright notice, 133s this list of conditions and the following disclaimer in the documentation 133s and/or other materials provided with the distribution. 133s 133s * Neither the name of the developer nor the names of its contributors may be 133s used to endorse or promote products derived from this software without 133s specific prior written permission. 133s 133s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 133s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 133s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 133s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 133s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 133s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 133s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 133s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 133s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 133s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 133s ---------------------------------------------------------------------- 133s APBS uses FETK (the Finite Element ToolKit) to solve the 133s Poisson-Boltzmann equation numerically. FETK is a portable collection 133s of finite element modeling class libraries developed by the Michael Holst 133s research group and written in an object-oriented form of C. FEtk is 133s designed to solve general coupled systems of nonlinear partial differential 133s equations using adaptive finite element methods, inexact Newton methods, 133s and algebraic multilevel methods. More information about FEtk may be found 133s at . 133s ---------------------------------------------------------------------- 133s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 133s Aqua is a modified form of the Holst group PMG library 133s which has been modified by Patrice Koehl 133s for improved efficiency and 133s memory usage when solving the Poisson-Boltzmann equation. 133s ---------------------------------------------------------------------- 133s Please cite your use of APBS as: 133s 133s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 133s nanosystems: application to microtubules and the ribosome. Proc. 133s Natl. Acad. Sci. USA 98, 10037-10041 2001. 133s 133s 133s This executable compiled on Jan 3 2025 at 11:01:42 133s 133s Parsing input file apbs-mol-parallel-PE1.in... 133s rank 0 size 1... 133s Parsed input file. 133s Got paths for 1 molecules 133s Reading PQR-format atom data from ion.pqr. 133s 1 atoms 133s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 133s Net charge 1.00e+00 e 133s Preparing to run 6 PBE calculations. 133s ---------------------------------------- 133s CALCULATION #1 (solvated): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.280 MB total, 61.280 MB high water 133s Using cubic spline charge discretization. 133s Partition overlap fraction = 0.1 133s Processor array = 2 x 2 x 1 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.781 x 0.781 x 0.781 133s Grid lengths: 50.000 x 50.000 x 50.000 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Multiple Debye-Huckel sphere boundary conditions 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 78.540 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 2.401768459022E+02 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #2 (solvated): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.280 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Partition overlap fraction = 0.1 133s Processor array = 2 x 2 x 1 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.296 x 0.296 x 0.383 133s Grid lengths: 18.944 x 18.944 x 24.495 133s Grid center: (2.411, -2.411, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 78.540 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 8.142778312125E+02 kJ/mol 133s Calculating forces... 133s [focusFillBound()]: WARNING: 133s Unusually large potential values 133s detected on the focusing boundary! 133s Convergence not guaranteed for NPBE/NRPBE calculations! 133s 133s ---------------------------------------- 133s CALCULATION #3 (solvated): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.280 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Partition overlap fraction = 0.1 133s Processor array = 2 x 2 x 1 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.112 x 0.112 x 0.188 133s Grid lengths: 7.178 x 7.178 x 12.000 133s Grid center: (2.411, -2.411, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 78.540 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 1.485246667424E+03 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #4 (reference): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.207 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Partition overlap fraction = 0.1 133s Processor array = 2 x 2 x 1 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.781 x 0.781 x 0.781 133s Grid lengths: 50.000 x 50.000 x 50.000 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Multiple Debye-Huckel sphere boundary conditions 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 1.000 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 2.977178707009E+02 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #5 (reference): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.207 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Partition overlap fraction = 0.1 133s Processor array = 2 x 2 x 1 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.296 x 0.296 x 0.383 133s Grid lengths: 18.944 x 18.944 x 24.495 133s Grid center: (2.411, -2.411, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 1.000 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 8.799304557588E+02 kJ/mol 133s Calculating forces... 133s [focusFillBound()]: WARNING: 133s Unusually large potential values 133s detected on the focusing boundary! 133s Convergence not guaranteed for NPBE/NRPBE calculations! 133s 133s ---------------------------------------- 133s CALCULATION #6 (reference): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.207 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Partition overlap fraction = 0.1 133s Processor array = 2 x 2 x 1 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.112 x 0.112 x 0.188 133s Grid lengths: 7.178 x 7.178 x 12.000 133s Grid center: (2.411, -2.411, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 1.000 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 1.542873949131E+03 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s PRINT STATEMENTS 133s 133s print energy 1 (solvated) - 2 (reference) end 133s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 133s Global net ELEC energy = -5.762728170718E+01 kJ/mol 133s ---------------------------------------- 133s CLEANING UP AND SHUTTING DOWN... 133s Destroying force arrays. 133s No energy arrays to destroy. 133s Destroying multigrid structures. 133s Destroying finite element structures. 133s Destroying 1 molecules 133s Final memory usage: 0.001 MB total, 122.102 MB high water 133s 133s 133s Thanks for using APBS! 133s 133s Processor 1 results: 133s 2.401768459022e+02 133s 8.142778312125e+02 133s 1.485246667424e+03 133s 2.977178707009e+02 133s 8.799304557588e+02 133s 1.542873949131e+03 133s -5.762728170718e+01 133s 134s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 134s BINARY: /usr/bin/apbs 134s INPUT: apbs-mol-parallel-PE2.in 134s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 134s asc_getToken: Error occurred (bailing out). 134s Vio_scanf: Format problem with input. 134s 134s 134s ---------------------------------------------------------------------- 134s APBS -- Adaptive Poisson-Boltzmann Solver 134s Version APBS 3.4.1 134s 134s Nathan A. Baker (nathan.baker@pnnl.gov) 134s Pacific Northwest National Laboratory 134s 134s Additional contributing authors listed in the code documentation. 134s 134s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 134s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 134s Northwest Division for the U.S. Department of Energy. 134s 134s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 134s Portions Copyright (c) 2002-2020, Nathan A. Baker. 134s Portions Copyright (c) 1999-2002, The Regents of the University of California. 134s Portions Copyright (c) 1995, Michael Holst. 134s All rights reserved. 134s 134s Redistribution and use in source and binary forms, with or without 134s modification, are permitted provided that the following conditions are met: 134s 134s * Redistributions of source code must retain the above copyright notice, this 134s list of conditions and the following disclaimer. 134s 134s * Redistributions in binary form must reproduce the above copyright notice, 134s this list of conditions and the following disclaimer in the documentation 134s and/or other materials provided with the distribution. 134s 134s * Neither the name of the developer nor the names of its contributors may be 134s used to endorse or promote products derived from this software without 134s specific prior written permission. 134s 134s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 134s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 134s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 134s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 134s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 134s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 134s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 134s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 134s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 134s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 134s ---------------------------------------------------------------------- 134s APBS uses FETK (the Finite Element ToolKit) to solve the 134s Poisson-Boltzmann equation numerically. FETK is a portable collection 134s of finite element modeling class libraries developed by the Michael Holst 134s research group and written in an object-oriented form of C. FEtk is 134s designed to solve general coupled systems of nonlinear partial differential 134s equations using adaptive finite element methods, inexact Newton methods, 134s and algebraic multilevel methods. More information about FEtk may be found 134s at . 134s ---------------------------------------------------------------------- 134s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 134s Aqua is a modified form of the Holst group PMG library 134s which has been modified by Patrice Koehl 134s for improved efficiency and 134s memory usage when solving the Poisson-Boltzmann equation. 134s ---------------------------------------------------------------------- 134s Please cite your use of APBS as: 134s 134s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 134s nanosystems: application to microtubules and the ribosome. Proc. 134s Natl. Acad. Sci. USA 98, 10037-10041 2001. 134s 134s 134s This executable compiled on Jan 3 2025 at 11:01:42 134s 134s Parsing input file apbs-mol-parallel-PE2.in... 134s rank 0 size 1... 134s Parsed input file. 134s Got paths for 1 molecules 134s Reading PQR-format atom data from ion.pqr. 134s 1 atoms 134s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 134s Net charge 1.00e+00 e 134s Preparing to run 6 PBE calculations. 134s ---------------------------------------- 134s CALCULATION #1 (solvated): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.280 MB total, 61.280 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.781 x 0.781 x 0.781 134s Grid lengths: 50.000 x 50.000 x 50.000 134s Grid center: (0.000, 0.000, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Multiple Debye-Huckel sphere boundary conditions 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 78.540 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 2.401768459091E+02 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s CALCULATION #2 (solvated): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.280 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.296 x 0.296 x 0.383 134s Grid lengths: 18.944 x 18.944 x 24.495 134s Grid center: (-2.411, 2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 78.540 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 8.142935605695E+02 kJ/mol 134s Calculating forces... 134s [focusFillBound()]: WARNING: 134s Unusually large potential values 134s detected on the focusing boundary! 134s Convergence not guaranteed for NPBE/NRPBE calculations! 134s 134s ---------------------------------------- 134s CALCULATION #3 (solvated): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.280 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.112 x 0.112 x 0.188 134s Grid lengths: 7.178 x 7.178 x 12.000 134s Grid center: (-2.411, 2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 78.540 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 1.485255306569E+03 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s CALCULATION #4 (reference): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.207 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.781 x 0.781 x 0.781 134s Grid lengths: 50.000 x 50.000 x 50.000 134s Grid center: (0.000, 0.000, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Multiple Debye-Huckel sphere boundary conditions 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 1.000 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 2.977178707146E+02 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s CALCULATION #5 (reference): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.207 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.296 x 0.296 x 0.383 134s Grid lengths: 18.944 x 18.944 x 24.495 134s Grid center: (-2.411, 2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 1.000 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 8.799304557596E+02 kJ/mol 134s Calculating forces... 134s [focusFillBound()]: WARNING: 134s Unusually large potential values 134s detected on the focusing boundary! 134s Convergence not guaranteed for NPBE/NRPBE calculations! 134s 134s ---------------------------------------- 134s CALCULATION #6 (reference): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.207 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.112 x 0.112 x 0.188 134s Grid lengths: 7.178 x 7.178 x 12.000 134s Grid center: (-2.411, 2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 1.000 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 1.542873949141E+03 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s PRINT STATEMENTS 134s 134s print energy 1 (solvated) - 2 (reference) end 134s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 134s Global net ELEC energy = -5.761864257239E+01 kJ/mol 134s ---------------------------------------- 134s CLEANING UP AND SHUTTING DOWN... 134s Destroying force arrays. 134s No energy arrays to destroy. 134s Destroying multigrid structures. 134s Destroying finite element structures. 134s Destroying 1 molecules 134s Final memory usage: 0.001 MB total, 122.102 MB high water 134s 134s 134s Thanks for using APBS! 134s 134s Processor 2 results: 134s 2.401768459091e+02 134s 8.142935605695e+02 134s 1.485255306569e+03 134s 2.977178707146e+02 134s 8.799304557596e+02 134s 1.542873949141e+03 134s -5.761864257239e+01 134s 136s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 136s BINARY: /usr/bin/apbs 136s INPUT: apbs-mol-parallel-PE3.in 136s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 136s asc_getToken: Error occurred (bailing out). 136s Vio_scanf: Format problem with input. 136s 136s 136s ---------------------------------------------------------------------- 136s APBS -- Adaptive Poisson-Boltzmann Solver 136s Version APBS 3.4.1 136s 136s Nathan A. Baker (nathan.baker@pnnl.gov) 136s Pacific Northwest National Laboratory 136s 136s Additional contributing authors listed in the code documentation. 136s 136s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 136s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 136s Northwest Division for the U.S. Department of Energy. 136s 136s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 136s Portions Copyright (c) 2002-2020, Nathan A. Baker. 136s Portions Copyright (c) 1999-2002, The Regents of the University of California. 136s Portions Copyright (c) 1995, Michael Holst. 136s All rights reserved. 136s 136s Redistribution and use in source and binary forms, with or without 136s modification, are permitted provided that the following conditions are met: 136s 136s * Redistributions of source code must retain the above copyright notice, this 136s list of conditions and the following disclaimer. 136s 136s * Redistributions in binary form must reproduce the above copyright notice, 136s this list of conditions and the following disclaimer in the documentation 136s and/or other materials provided with the distribution. 136s 136s * Neither the name of the developer nor the names of its contributors may be 136s used to endorse or promote products derived from this software without 136s specific prior written permission. 136s 136s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 136s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 136s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 136s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 136s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 136s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 136s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 136s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 136s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 136s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 136s ---------------------------------------------------------------------- 136s APBS uses FETK (the Finite Element ToolKit) to solve the 136s Poisson-Boltzmann equation numerically. FETK is a portable collection 136s of finite element modeling class libraries developed by the Michael Holst 136s research group and written in an object-oriented form of C. FEtk is 136s designed to solve general coupled systems of nonlinear partial differential 136s equations using adaptive finite element methods, inexact Newton methods, 136s and algebraic multilevel methods. More information about FEtk may be found 136s at . 136s ---------------------------------------------------------------------- 136s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 136s Aqua is a modified form of the Holst group PMG library 136s which has been modified by Patrice Koehl 136s for improved efficiency and 136s memory usage when solving the Poisson-Boltzmann equation. 136s ---------------------------------------------------------------------- 136s Please cite your use of APBS as: 136s 136s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 136s nanosystems: application to microtubules and the ribosome. Proc. 136s Natl. Acad. Sci. USA 98, 10037-10041 2001. 136s 136s 136s This executable compiled on Jan 3 2025 at 11:01:42 136s 136s Parsing input file apbs-mol-parallel-PE3.in... 136s rank 0 size 1... 136s Parsed input file. 136s Got paths for 1 molecules 136s Reading PQR-format atom data from ion.pqr. 136s 1 atoms 136s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 136s Net charge 1.00e+00 e 136s Preparing to run 6 PBE calculations. 136s ---------------------------------------- 136s CALCULATION #1 (solvated): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.280 MB total, 61.280 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.781 x 0.781 x 0.781 136s Grid lengths: 50.000 x 50.000 x 50.000 136s Grid center: (0.000, 0.000, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Multiple Debye-Huckel sphere boundary conditions 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 78.540 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 2.401768459091E+02 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s CALCULATION #2 (solvated): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.280 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.296 x 0.296 x 0.383 136s Grid lengths: 18.944 x 18.944 x 24.495 136s Grid center: (2.411, 2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 78.540 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 8.142778325440E+02 kJ/mol 136s Calculating forces... 136s [focusFillBound()]: WARNING: 136s Unusually large potential values 136s detected on the focusing boundary! 136s Convergence not guaranteed for NPBE/NRPBE calculations! 136s 136s ---------------------------------------- 136s CALCULATION #3 (solvated): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.280 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.112 x 0.112 x 0.188 136s Grid lengths: 7.178 x 7.178 x 12.000 136s Grid center: (2.411, 2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 78.540 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 1.485246665692E+03 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s CALCULATION #4 (reference): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.207 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.781 x 0.781 x 0.781 136s Grid lengths: 50.000 x 50.000 x 50.000 136s Grid center: (0.000, 0.000, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Multiple Debye-Huckel sphere boundary conditions 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 1.000 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 2.977178707146E+02 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s CALCULATION #5 (reference): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.207 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.296 x 0.296 x 0.383 136s Grid lengths: 18.944 x 18.944 x 24.495 136s Grid center: (2.411, 2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 1.000 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 8.799304557596E+02 kJ/mol 136s Calculating forces... 136s [focusFillBound()]: WARNING: 136s Unusually large potential values 136s detected on the focusing boundary! 136s Convergence not guaranteed for NPBE/NRPBE calculations! 136s 136s ---------------------------------------- 136s CALCULATION #6 (reference): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.207 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.112 x 0.112 x 0.188 136s Grid lengths: 7.178 x 7.178 x 12.000 136s Grid center: (2.411, 2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 1.000 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 1.542873949141E+03 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s PRINT STATEMENTS 136s 136s print energy 1 (solvated) - 2 (reference) end 136s Local net energy (PE 0) = -5.762728344953E+01 kJ/mol 136s Global net ELEC energy = -5.762728344953E+01 kJ/mol 136s ---------------------------------------- 136s CLEANING UP AND SHUTTING DOWN... 136s Destroying force arrays. 136s No energy arrays to destroy. 136s Destroying multigrid structures. 136s Destroying finite element structures. 136s Destroying 1 molecules 136s Final memory usage: 0.001 MB total, 122.102 MB high water 136s 136s 136s Thanks for using APBS! 136s 136s Processor 3 results: 136s 2.401768459091e+02 136s 8.142778325440e+02 136s 1.485246665692e+03 136s 2.977178707146e+02 136s 8.799304557596e+02 136s 1.542873949141e+03 136s -5.762728344953e+01 136s 136s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 136s *** PASSED *** 136s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 136s *** PASSED *** 136s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 136s *** PASSED *** 136s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 136s *** PASSED *** 136s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 136s *** PASSED *** 136s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 136s *** PASSED *** 136s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 136s *** PASSED *** 136s Elapsed time: 5.505053 seconds 136s -------------------------------------------------------------------------------- 136s -------------------------------------------------------------------------------- 136s Testing input file apbs-smol-parallel.in 136s 136s Splitting the input file into 4 separate files using the inputgen utility 136s 137s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 137s EXPECTED COMPUTED: 7 137s EXPECTED EXPECTED: 7 137s COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 137s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 137s COMPUTED RESULT 960.7073836226 137s COMPUTED RESULT 3257.1427835730997 137s COMPUTED RESULT 5941.0039478710005 137s COMPUTED RESULT 1190.8714828309999 137s COMPUTED RESULT 3519.7218230368003 137s COMPUTED RESULT 6171.495796544 137s COMPUTED RESULT -230.49184867462003 137s BINARY: /usr/bin/apbs 137s INPUT: apbs-smol-parallel-PE0.in 137s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 137s Processor 0 results: 137s asc_getToken: Error occurred (bailing out). 137s Vio_scanf: Format problem with input. 137s 137s 137s ---------------------------------------------------------------------- 137s APBS -- Adaptive Poisson-Boltzmann Solver 137s Version APBS 3.4.1 137s 137s Nathan A. Baker (nathan.baker@pnnl.gov) 137s Pacific Northwest National Laboratory 137s 137s Additional contributing authors listed in the code documentation. 137s 137s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 137s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 137s Northwest Division for the U.S. Department of Energy. 137s 137s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 137s Portions Copyright (c) 2002-2020, Nathan A. Baker. 137s Portions Copyright (c) 1999-2002, The Regents of the University of California. 137s Portions Copyright (c) 1995, Michael Holst. 137s All rights reserved. 137s 137s Redistribution and use in source and binary forms, with or without 137s modification, are permitted provided that the following conditions are met: 137s 137s * Redistributions of source code must retain the above copyright notice, this 137s list of conditions and the following disclaimer. 137s 137s * Redistributions in binary form must reproduce the above copyright notice, 137s this list of conditions and the following disclaimer in the documentation 137s and/or other materials provided with the distribution. 137s 137s * Neither the name of the developer nor the names of its contributors may be 137s used to endorse or promote products derived from this software without 137s specific prior written permission. 137s 137s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 137s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 137s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 137s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 137s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 137s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 137s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 137s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 137s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 137s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 137s ---------------------------------------------------------------------- 137s APBS uses FETK (the Finite Element ToolKit) to solve the 137s Poisson-Boltzmann equation numerically. FETK is a portable collection 137s of finite element modeling class libraries developed by the Michael Holst 137s research group and written in an object-oriented form of C. FEtk is 137s designed to solve general coupled systems of nonlinear partial differential 137s equations using adaptive finite element methods, inexact Newton methods, 137s and algebraic multilevel methods. More information about FEtk may be found 137s at . 137s ---------------------------------------------------------------------- 137s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 137s Aqua is a modified form of the Holst group PMG library 137s which has been modified by Patrice Koehl 137s for improved efficiency and 137s memory usage when solving the Poisson-Boltzmann equation. 137s ---------------------------------------------------------------------- 137s Please cite your use of APBS as: 137s 137s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 137s nanosystems: application to microtubules and the ribosome. Proc. 137s Natl. Acad. Sci. USA 98, 10037-10041 2001. 137s 137s 137s This executable compiled on Jan 3 2025 at 11:01:42 137s 137s Parsing input file apbs-smol-parallel-PE0.in... 137s rank 0 size 1... 137s Parsed input file. 137s Got paths for 1 molecules 137s Reading PQR-format atom data from ion.pqr. 137s 1 atoms 137s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 137s Net charge 1.00e+00 e 137s Preparing to run 6 PBE calculations. 137s ---------------------------------------- 137s CALCULATION #1 (solvated): MULTIGRID 137s Setting up problem... 137s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 137s Debye length: 0 A 137s Current memory usage: 61.280 MB total, 61.280 MB high water 137s Using cubic spline charge discretization. 137s Partition overlap fraction = 0.1 137s Processor array = 2 x 2 x 1 137s Grid dimensions: 65 x 65 x 65 137s Grid spacings: 0.781 x 0.781 x 0.781 137s Grid lengths: 50.000 x 50.000 x 50.000 137s Grid center: (0.000, 0.000, 0.000) 137s Multigrid levels: 5 137s Molecule ID: 1 137s Linearized traditional PBE 137s Multiple Debye-Huckel sphere boundary conditions 137s 0 ion species (0.000 M ionic strength): 137s Solute dielectric: 1.000 137s Solvent dielectric: 78.540 137s Using "molecular" surface definition;harmonic average smoothing 137s Solvent probe radius: 1.400 A 137s Temperature: 298.150 K 137s Electrostatic energies will be calculated 137s Total electrostatic energy = 2.383232191816E+02 kJ/mol 137s Calculating forces... 137s ---------------------------------------- 137s CALCULATION #2 (solvated): MULTIGRID 137s Setting up problem... 137s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 137s Debye length: 0 A 137s Current memory usage: 61.280 MB total, 122.102 MB high water 137s Using cubic spline charge discretization. 137s Partition overlap fraction = 0.1 137s Processor array = 2 x 2 x 1 137s Grid dimensions: 65 x 65 x 65 137s Grid spacings: 0.296 x 0.296 x 0.383 137s Grid lengths: 18.944 x 18.944 x 24.495 137s Grid center: (-2.411, -2.411, 0.000) 137s Multigrid levels: 5 137s Molecule ID: 1 137s Linearized traditional PBE 137s Boundary conditions from focusing 137s 0 ion species (0.000 M ionic strength): 137s Solute dielectric: 1.000 137s Solvent dielectric: 78.540 137s Using "molecular" surface definition;harmonic average smoothing 137s Solvent probe radius: 1.400 A 137s Temperature: 298.150 K 137s Electrostatic energies will be calculated 137s Total electrostatic energy = 8.145369591602E+02 kJ/mol 137s Calculating forces... 137s [focusFillBound()]: WARNING: 137s Unusually large potential values 137s detected on the focusing boundary! 137s Convergence not guaranteed for NPBE/NRPBE calculations! 137s 137s ---------------------------------------- 137s CALCULATION #3 (solvated): MULTIGRID 137s Setting up problem... 137s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 137s Debye length: 0 A 137s Current memory usage: 61.280 MB total, 122.102 MB high water 137s Using cubic spline charge discretization. 137s Partition overlap fraction = 0.1 137s Processor array = 2 x 2 x 1 137s Grid dimensions: 65 x 65 x 65 137s Grid spacings: 0.112 x 0.112 x 0.188 137s Grid lengths: 7.178 x 7.178 x 12.000 137s Grid center: (-2.411, -2.411, 0.000) 137s Multigrid levels: 5 137s Molecule ID: 1 137s Linearized traditional PBE 137s Boundary conditions from focusing 137s 0 ion species (0.000 M ionic strength): 137s Solute dielectric: 1.000 137s Solvent dielectric: 78.540 137s Using "molecular" surface definition;harmonic average smoothing 137s Solvent probe radius: 1.400 A 137s Temperature: 298.150 K 137s Electrostatic energies will be calculated 137s Total electrostatic energy = 1.485524998001E+03 kJ/mol 137s Calculating forces... 137s ---------------------------------------- 137s CALCULATION #4 (reference): MULTIGRID 137s Setting up problem... 137s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 137s Debye length: 0 A 137s Current memory usage: 61.207 MB total, 122.102 MB high water 137s Using cubic spline charge discretization. 137s Partition overlap fraction = 0.1 137s Processor array = 2 x 2 x 1 137s Grid dimensions: 65 x 65 x 65 137s Grid spacings: 0.781 x 0.781 x 0.781 137s Grid lengths: 50.000 x 50.000 x 50.000 137s Grid center: (0.000, 0.000, 0.000) 137s Multigrid levels: 5 137s Molecule ID: 1 137s Linearized traditional PBE 137s Multiple Debye-Huckel sphere boundary conditions 137s 0 ion species (0.000 M ionic strength): 137s Solute dielectric: 1.000 137s Solvent dielectric: 1.000 137s Using "molecular" surface definition;harmonic average smoothing 137s Solvent probe radius: 1.400 A 137s Temperature: 298.150 K 137s Electrostatic energies will be calculated 137s Total electrostatic energy = 2.977178707009E+02 kJ/mol 137s Calculating forces... 137s ---------------------------------------- 137s CALCULATION #5 (reference): MULTIGRID 137s Setting up problem... 137s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 137s Debye length: 0 A 137s Current memory usage: 61.207 MB total, 122.102 MB high water 137s Using cubic spline charge discretization. 137s Partition overlap fraction = 0.1 137s Processor array = 2 x 2 x 1 137s Grid dimensions: 65 x 65 x 65 137s Grid spacings: 0.296 x 0.296 x 0.383 137s Grid lengths: 18.944 x 18.944 x 24.495 137s Grid center: (-2.411, -2.411, 0.000) 137s Multigrid levels: 5 137s Molecule ID: 1 137s Linearized traditional PBE 137s Boundary conditions from focusing 137s 0 ion species (0.000 M ionic strength): 137s Solute dielectric: 1.000 137s Solvent dielectric: 1.000 137s Using "molecular" surface definition;harmonic average smoothing 137s Solvent probe radius: 1.400 A 137s Temperature: 298.150 K 137s Electrostatic energies will be calculated 137s Total electrostatic energy = 8.799304557588E+02 kJ/mol 137s Calculating forces... 137s [focusFillBound()]: WARNING: 137s Unusually large potential values 137s detected on the focusing boundary! 137s Convergence not guaranteed for NPBE/NRPBE calculations! 137s 137s ---------------------------------------- 137s CALCULATION #6 (reference): MULTIGRID 137s Setting up problem... 137s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 137s Debye length: 0 A 137s Current memory usage: 61.207 MB total, 122.102 MB high water 137s Using cubic spline charge discretization. 137s Partition overlap fraction = 0.1 137s Processor array = 2 x 2 x 1 137s Grid dimensions: 65 x 65 x 65 137s Grid spacings: 0.112 x 0.112 x 0.188 137s Grid lengths: 7.178 x 7.178 x 12.000 137s Grid center: (-2.411, -2.411, 0.000) 137s Multigrid levels: 5 137s Molecule ID: 1 137s Linearized traditional PBE 137s Boundary conditions from focusing 137s 0 ion species (0.000 M ionic strength): 137s Solute dielectric: 1.000 137s Solvent dielectric: 1.000 137s Using "molecular" surface definition;harmonic average smoothing 137s Solvent probe radius: 1.400 A 137s Temperature: 298.150 K 137s Electrostatic energies will be calculated 137s Total electrostatic energy = 1.542873949131E+03 kJ/mol 137s Calculating forces... 137s ---------------------------------------- 137s PRINT STATEMENTS 137s 137s print energy 1 (solvated) - 2 (reference) end 137s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 137s Global net ELEC energy = -5.734895113069E+01 kJ/mol 137s ---------------------------------------- 137s CLEANING UP AND SHUTTING DOWN... 137s Destroying force arrays. 137s No energy arrays to destroy. 137s Destroying multigrid structures. 137s Destroying finite element structures. 137s Destroying 1 molecules 137s Final memory usage: 0.001 MB total, 122.102 MB high water 137s 137s 137s Thanks for using APBS! 137s 137s 2.383232191816e+02 137s 8.145369591602e+02 137s 1.485524998001e+03 137s 2.977178707009e+02 137s 8.799304557588e+02 137s 1.542873949131e+03 137s -5.734895113069e+01 137s 139s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 139s BINARY: /usr/bin/apbs 139s INPUT: apbs-smol-parallel-PE1.in 139s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 139s asc_getToken: Error occurred (bailing out). 139s Vio_scanf: Format problem with input. 139s 139s 139s ---------------------------------------------------------------------- 139s APBS -- Adaptive Poisson-Boltzmann Solver 139s Version APBS 3.4.1 139s 139s Nathan A. Baker (nathan.baker@pnnl.gov) 139s Pacific Northwest National Laboratory 139s 139s Additional contributing authors listed in the code documentation. 139s 139s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 139s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 139s Northwest Division for the U.S. Department of Energy. 139s 139s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 139s Portions Copyright (c) 2002-2020, Nathan A. Baker. 139s Portions Copyright (c) 1999-2002, The Regents of the University of California. 139s Portions Copyright (c) 1995, Michael Holst. 139s All rights reserved. 139s 139s Redistribution and use in source and binary forms, with or without 139s modification, are permitted provided that the following conditions are met: 139s 139s * Redistributions of source code must retain the above copyright notice, this 139s list of conditions and the following disclaimer. 139s 139s * Redistributions in binary form must reproduce the above copyright notice, 139s this list of conditions and the following disclaimer in the documentation 139s and/or other materials provided with the distribution. 139s 139s * Neither the name of the developer nor the names of its contributors may be 139s used to endorse or promote products derived from this software without 139s specific prior written permission. 139s 139s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 139s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 139s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 139s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 139s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 139s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 139s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 139s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 139s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 139s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 139s ---------------------------------------------------------------------- 139s APBS uses FETK (the Finite Element ToolKit) to solve the 139s Poisson-Boltzmann equation numerically. FETK is a portable collection 139s of finite element modeling class libraries developed by the Michael Holst 139s research group and written in an object-oriented form of C. FEtk is 139s designed to solve general coupled systems of nonlinear partial differential 139s equations using adaptive finite element methods, inexact Newton methods, 139s and algebraic multilevel methods. More information about FEtk may be found 139s at . 139s ---------------------------------------------------------------------- 139s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 139s Aqua is a modified form of the Holst group PMG library 139s which has been modified by Patrice Koehl 139s for improved efficiency and 139s memory usage when solving the Poisson-Boltzmann equation. 139s ---------------------------------------------------------------------- 139s Please cite your use of APBS as: 139s 139s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 139s nanosystems: application to microtubules and the ribosome. Proc. 139s Natl. Acad. Sci. USA 98, 10037-10041 2001. 139s 139s 139s This executable compiled on Jan 3 2025 at 11:01:42 139s 139s Parsing input file apbs-smol-parallel-PE1.in... 139s rank 0 size 1... 139s Parsed input file. 139s Got paths for 1 molecules 139s Reading PQR-format atom data from ion.pqr. 139s 1 atoms 139s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 139s Net charge 1.00e+00 e 139s Preparing to run 6 PBE calculations. 139s ---------------------------------------- 139s CALCULATION #1 (solvated): MULTIGRID 139s Setting up problem... 139s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 139s Debye length: 0 A 139s Current memory usage: 61.280 MB total, 61.280 MB high water 139s Using cubic spline charge discretization. 139s Partition overlap fraction = 0.1 139s Processor array = 2 x 2 x 1 139s Grid dimensions: 65 x 65 x 65 139s Grid spacings: 0.781 x 0.781 x 0.781 139s Grid lengths: 50.000 x 50.000 x 50.000 139s Grid center: (0.000, 0.000, 0.000) 139s Multigrid levels: 5 139s Molecule ID: 1 139s Linearized traditional PBE 139s Multiple Debye-Huckel sphere boundary conditions 139s 0 ion species (0.000 M ionic strength): 139s Solute dielectric: 1.000 139s Solvent dielectric: 78.540 139s Using "molecular" surface definition;harmonic average smoothing 139s Solvent probe radius: 1.400 A 139s Temperature: 298.150 K 139s Electrostatic energies will be calculated 139s Total electrostatic energy = 2.383232191816E+02 kJ/mol 139s Calculating forces... 139s ---------------------------------------- 139s CALCULATION #2 (solvated): MULTIGRID 139s Setting up problem... 139s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 139s Debye length: 0 A 139s Current memory usage: 61.280 MB total, 122.102 MB high water 139s Using cubic spline charge discretization. 139s Partition overlap fraction = 0.1 139s Processor array = 2 x 2 x 1 139s Grid dimensions: 65 x 65 x 65 139s Grid spacings: 0.296 x 0.296 x 0.383 139s Grid lengths: 18.944 x 18.944 x 24.495 139s Grid center: (2.411, -2.411, 0.000) 139s Multigrid levels: 5 139s Molecule ID: 1 139s Linearized traditional PBE 139s Boundary conditions from focusing 139s 0 ion species (0.000 M ionic strength): 139s Solute dielectric: 1.000 139s Solvent dielectric: 78.540 139s Using "molecular" surface definition;harmonic average smoothing 139s Solvent probe radius: 1.400 A 139s Temperature: 298.150 K 139s Electrostatic energies will be calculated 139s Total electrostatic energy = 8.145419898332E+02 kJ/mol 139s Calculating forces... 139s [focusFillBound()]: WARNING: 139s Unusually large potential values 139s detected on the focusing boundary! 139s Convergence not guaranteed for NPBE/NRPBE calculations! 139s 139s ---------------------------------------- 139s CALCULATION #3 (solvated): MULTIGRID 139s Setting up problem... 139s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 139s Debye length: 0 A 139s Current memory usage: 61.280 MB total, 122.102 MB high water 139s Using cubic spline charge discretization. 139s Partition overlap fraction = 0.1 139s Processor array = 2 x 2 x 1 139s Grid dimensions: 65 x 65 x 65 139s Grid spacings: 0.112 x 0.112 x 0.188 139s Grid lengths: 7.178 x 7.178 x 12.000 139s Grid center: (2.411, -2.411, 0.000) 139s Multigrid levels: 5 139s Molecule ID: 1 139s Linearized traditional PBE 139s Boundary conditions from focusing 139s 0 ion species (0.000 M ionic strength): 139s Solute dielectric: 1.000 139s Solvent dielectric: 78.540 139s Using "molecular" surface definition;harmonic average smoothing 139s Solvent probe radius: 1.400 A 139s Temperature: 298.150 K 139s Electrostatic energies will be calculated 139s Total electrostatic energy = 1.485529328612E+03 kJ/mol 139s Calculating forces... 139s ---------------------------------------- 139s CALCULATION #4 (reference): MULTIGRID 139s Setting up problem... 139s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 139s Debye length: 0 A 139s Current memory usage: 61.207 MB total, 122.102 MB high water 139s Using cubic spline charge discretization. 139s Partition overlap fraction = 0.1 139s Processor array = 2 x 2 x 1 139s Grid dimensions: 65 x 65 x 65 139s Grid spacings: 0.781 x 0.781 x 0.781 139s Grid lengths: 50.000 x 50.000 x 50.000 139s Grid center: (0.000, 0.000, 0.000) 139s Multigrid levels: 5 139s Molecule ID: 1 139s Linearized traditional PBE 139s Multiple Debye-Huckel sphere boundary conditions 139s 0 ion species (0.000 M ionic strength): 139s Solute dielectric: 1.000 139s Solvent dielectric: 1.000 139s Using "molecular" surface definition;harmonic average smoothing 139s Solvent probe radius: 1.400 A 139s Temperature: 298.150 K 139s Electrostatic energies will be calculated 139s Total electrostatic energy = 2.977178707009E+02 kJ/mol 139s Calculating forces... 139s ---------------------------------------- 139s CALCULATION #5 (reference): MULTIGRID 139s Setting up problem... 139s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 139s Debye length: 0 A 139s Current memory usage: 61.207 MB total, 122.102 MB high water 139s Using cubic spline charge discretization. 139s Partition overlap fraction = 0.1 139s Processor array = 2 x 2 x 1 139s Grid dimensions: 65 x 65 x 65 139s Grid spacings: 0.296 x 0.296 x 0.383 139s Grid lengths: 18.944 x 18.944 x 24.495 139s Grid center: (2.411, -2.411, 0.000) 139s Multigrid levels: 5 139s Molecule ID: 1 139s Linearized traditional PBE 139s Boundary conditions from focusing 139s 0 ion species (0.000 M ionic strength): 139s Solute dielectric: 1.000 139s Solvent dielectric: 1.000 139s Using "molecular" surface definition;harmonic average smoothing 139s Solvent probe radius: 1.400 A 139s Temperature: 298.150 K 139s Electrostatic energies will be calculated 139s Total electrostatic energy = 8.799304557588E+02 kJ/mol 139s Calculating forces... 139s [focusFillBound()]: WARNING: 139s Unusually large potential values 139s detected on the focusing boundary! 139s Convergence not guaranteed for NPBE/NRPBE calculations! 139s 139s ---------------------------------------- 139s CALCULATION #6 (reference): MULTIGRID 139s Setting up problem... 139s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 139s Debye length: 0 A 139s Current memory usage: 61.207 MB total, 122.102 MB high water 139s Using cubic spline charge discretization. 139s Partition overlap fraction = 0.1 139s Processor array = 2 x 2 x 1 139s Grid dimensions: 65 x 65 x 65 139s Grid spacings: 0.112 x 0.112 x 0.188 139s Grid lengths: 7.178 x 7.178 x 12.000 139s Grid center: (2.411, -2.411, 0.000) 139s Multigrid levels: 5 139s Molecule ID: 1 139s Linearized traditional PBE 139s Boundary conditions from focusing 139s 0 ion species (0.000 M ionic strength): 139s Solute dielectric: 1.000 139s Solvent dielectric: 1.000 139s Using "molecular" surface definition;harmonic average smoothing 139s Solvent probe radius: 1.400 A 139s Temperature: 298.150 K 139s Electrostatic energies will be calculated 139s Total electrostatic energy = 1.542873949131E+03 kJ/mol 139s Calculating forces... 139s ---------------------------------------- 139s PRINT STATEMENTS 139s 139s print energy 1 (solvated) - 2 (reference) end 139s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 139s Global net ELEC energy = -5.734462051928E+01 kJ/mol 139s ---------------------------------------- 139s CLEANING UP AND SHUTTING DOWN... 139s Destroying force arrays. 139s No energy arrays to destroy. 139s Destroying multigrid structures. 139s Destroying finite element structures. 139s Destroying 1 molecules 139s Final memory usage: 0.001 MB total, 122.102 MB high water 139s 139s 139s Thanks for using APBS! 139s 139s Processor 1 results: 139s 2.383232191816e+02 139s 8.145419898332e+02 139s 1.485529328612e+03 139s 2.977178707009e+02 139s 8.799304557588e+02 139s 1.542873949131e+03 139s -5.734462051928e+01 139s 140s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 140s BINARY: /usr/bin/apbs 140s INPUT: apbs-smol-parallel-PE2.in 140s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 140s asc_getToken: Error occurred (bailing out). 140s Vio_scanf: Format problem with input. 140s 140s 140s ---------------------------------------------------------------------- 140s APBS -- Adaptive Poisson-Boltzmann Solver 140s Version APBS 3.4.1 140s 140s Nathan A. Baker (nathan.baker@pnnl.gov) 140s Pacific Northwest National Laboratory 140s 140s Additional contributing authors listed in the code documentation. 140s 140s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 140s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 140s Northwest Division for the U.S. Department of Energy. 140s 140s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 140s Portions Copyright (c) 2002-2020, Nathan A. Baker. 140s Portions Copyright (c) 1999-2002, The Regents of the University of California. 140s Portions Copyright (c) 1995, Michael Holst. 140s All rights reserved. 140s 140s Redistribution and use in source and binary forms, with or without 140s modification, are permitted provided that the following conditions are met: 140s 140s * Redistributions of source code must retain the above copyright notice, this 140s list of conditions and the following disclaimer. 140s 140s * Redistributions in binary form must reproduce the above copyright notice, 140s this list of conditions and the following disclaimer in the documentation 140s and/or other materials provided with the distribution. 140s 140s * Neither the name of the developer nor the names of its contributors may be 140s used to endorse or promote products derived from this software without 140s specific prior written permission. 140s 140s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 140s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 140s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 140s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 140s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 140s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 140s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 140s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 140s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 140s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 140s ---------------------------------------------------------------------- 140s APBS uses FETK (the Finite Element ToolKit) to solve the 140s Poisson-Boltzmann equation numerically. FETK is a portable collection 140s of finite element modeling class libraries developed by the Michael Holst 140s research group and written in an object-oriented form of C. FEtk is 140s designed to solve general coupled systems of nonlinear partial differential 140s equations using adaptive finite element methods, inexact Newton methods, 140s and algebraic multilevel methods. More information about FEtk may be found 140s at . 140s ---------------------------------------------------------------------- 140s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 140s Aqua is a modified form of the Holst group PMG library 140s which has been modified by Patrice Koehl 140s for improved efficiency and 140s memory usage when solving the Poisson-Boltzmann equation. 140s ---------------------------------------------------------------------- 140s Please cite your use of APBS as: 140s 140s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 140s nanosystems: application to microtubules and the ribosome. Proc. 140s Natl. Acad. Sci. USA 98, 10037-10041 2001. 140s 140s 140s This executable compiled on Jan 3 2025 at 11:01:42 140s 140s Parsing input file apbs-smol-parallel-PE2.in... 140s rank 0 size 1... 140s Parsed input file. 140s Got paths for 1 molecules 140s Reading PQR-format atom data from ion.pqr. 140s 1 atoms 140s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 140s Net charge 1.00e+00 e 140s Preparing to run 6 PBE calculations. 140s ---------------------------------------- 140s CALCULATION #1 (solvated): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.280 MB total, 61.280 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.781 x 0.781 x 0.781 140s Grid lengths: 50.000 x 50.000 x 50.000 140s Grid center: (0.000, 0.000, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Multiple Debye-Huckel sphere boundary conditions 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 78.540 140s Using "molecular" surface definition;harmonic average smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 2.383232191909E+02 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s CALCULATION #2 (solvated): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.280 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.296 x 0.296 x 0.383 140s Grid lengths: 18.944 x 18.944 x 24.495 140s Grid center: (-2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 78.540 140s Using "molecular" surface definition;harmonic average smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 8.145369593489E+02 kJ/mol 140s Calculating forces... 140s [focusFillBound()]: WARNING: 140s Unusually large potential values 140s detected on the focusing boundary! 140s Convergence not guaranteed for NPBE/NRPBE calculations! 140s 140s ---------------------------------------- 140s CALCULATION #3 (solvated): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.280 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.112 x 0.112 x 0.188 140s Grid lengths: 7.178 x 7.178 x 12.000 140s Grid center: (-2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 78.540 140s Using "molecular" surface definition;harmonic average smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 1.485524997676E+03 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s CALCULATION #4 (reference): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.207 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.781 x 0.781 x 0.781 140s Grid lengths: 50.000 x 50.000 x 50.000 140s Grid center: (0.000, 0.000, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Multiple Debye-Huckel sphere boundary conditions 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 1.000 140s Using "molecular" surface definition;harmonic average smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 2.977178707146E+02 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s CALCULATION #5 (reference): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.207 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.296 x 0.296 x 0.383 140s Grid lengths: 18.944 x 18.944 x 24.495 140s Grid center: (-2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 1.000 140s Using "molecular" surface definition;harmonic average smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 8.799304557596E+02 kJ/mol 140s Calculating forces... 140s [focusFillBound()]: WARNING: 140s Unusually large potential values 140s detected on the focusing boundary! 140s Convergence not guaranteed for NPBE/NRPBE calculations! 140s 140s ---------------------------------------- 140s CALCULATION #6 (reference): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.207 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.112 x 0.112 x 0.188 140s Grid lengths: 7.178 x 7.178 x 12.000 140s Grid center: (-2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 1.000 140s Using "molecular" surface definition;harmonic average smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 1.542873949141E+03 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s PRINT STATEMENTS 140s 140s print energy 1 (solvated) - 2 (reference) end 140s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 140s Global net ELEC energy = -5.734895146550E+01 kJ/mol 140s ---------------------------------------- 140s CLEANING UP AND SHUTTING DOWN... 140s Destroying force arrays. 140s No energy arrays to destroy. 140s Destroying multigrid structures. 140s Destroying finite element structures. 140s Destroying 1 molecules 140s Final memory usage: 0.001 MB total, 122.102 MB high water 140s 140s 140s Thanks for using APBS! 140s 140s Processor 2 results: 140s 2.383232191909e+02 140s 8.145369593489e+02 140s 1.485524997676e+03 140s 2.977178707146e+02 140s 8.799304557596e+02 140s 1.542873949141e+03 140s -5.734895146550e+01 140s 141s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 141s BINARY: /usr/bin/apbs 141s INPUT: apbs-smol-parallel-PE3.in 141s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 141s Processor 3 results: 141s 2.383232191909e+02 141s 8.145419900310e+02 141s 1.485529328301e+03 141s 2.977178707146e+02 141s 8.799304557596e+02 141s 1.542873949141e+03 141s -5.734462084052e+01 141s 141s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 141s *** PASSED *** 141s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 141s *** PASSED *** 141s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 141s *** PASSED *** 141s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 141s *** PASSED *** 141s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 141s *** PASSED *** 141s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 141s *** PASSED *** 141s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 141s *** PASSED *** 141s Elapsed time: 5.600579 seconds 141s -------------------------------------------------------------------------------- 141s Total elapsed time: 13.34284 seconds 141s Test results have been logged 141s -------------------------------------------------------------------------------- 141s -------------------------------------------------------------------------------- 141s Testing input file apbs-mol-auto.in 141s 141s asc_getToken: Error occurred (bailing out). 141s Vio_scanf: Format problem with input. 141s 141s 141s ---------------------------------------------------------------------- 141s APBS -- Adaptive Poisson-Boltzmann Solver 141s Version APBS 3.4.1 141s 141s Nathan A. Baker (nathan.baker@pnnl.gov) 141s Pacific Northwest National Laboratory 141s 141s Additional contributing authors listed in the code documentation. 141s 141s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 141s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 141s Northwest Division for the U.S. Department of Energy. 141s 141s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 141s Portions Copyright (c) 2002-2020, Nathan A. Baker. 141s Portions Copyright (c) 1999-2002, The Regents of the University of California. 141s Portions Copyright (c) 1995, Michael Holst. 141s All rights reserved. 141s 141s Redistribution and use in source and binary forms, with or without 141s modification, are permitted provided that the following conditions are met: 141s 141s * Redistributions of source code must retain the above copyright notice, this 141s list of conditions and the following disclaimer. 141s 141s * Redistributions in binary form must reproduce the above copyright notice, 141s this list of conditions and the following disclaimer in the documentation 141s and/or other materials provided with the distribution. 141s 141s * Neither the name of the developer nor the names of its contributors may be 141s used to endorse or promote products derived from this software without 141s specific prior written permission. 141s 141s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 141s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 141s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 141s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 141s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 141s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 141s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 141s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 141s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 141s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 141s ---------------------------------------------------------------------- 141s APBS uses FETK (the Finite Element ToolKit) to solve the 141s Poisson-Boltzmann equation numerically. FETK is a portable collection 141s of finite element modeling class libraries developed by the Michael Holst 141s research group and written in an object-oriented form of C. FEtk is 141s designed to solve general coupled systems of nonlinear partial differential 141s equations using adaptive finite element methods, inexact Newton methods, 141s and algebraic multilevel methods. More information about FEtk may be found 141s at . 141s ---------------------------------------------------------------------- 141s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 141s Aqua is a modified form of the Holst group PMG library 141s which has been modified by Patrice Koehl 141s for improved efficiency and 141s memory usage when solving the Poisson-Boltzmann equation. 141s ---------------------------------------------------------------------- 141s Please cite your use of APBS as: 141s 141s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 141s nanosystems: application to microtubules and the ribosome. Proc. 141s Natl. Acad. Sci. USA 98, 10037-10041 2001. 141s 141s 141s This executable compiled on Jan 3 2025 at 11:01:42 141s 141s Parsing input file apbs-smol-parallel-PE3.in... 141s rank 0 size 1... 141s Parsed input file. 141s Got paths for 1 molecules 141s Reading PQR-format atom data from ion.pqr. 141s 1 atoms 141s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 141s Net charge 1.00e+00 e 141s Preparing to run 6 PBE calculations. 141s ---------------------------------------- 141s CALCULATION #1 (solvated): MULTIGRID 141s Setting up problem... 141s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 141s Debye length: 0 A 141s Current memory usage: 61.280 MB total, 61.280 MB high water 141s Using cubic spline charge discretization. 141s Partition overlap fraction = 0.1 141s Processor array = 2 x 2 x 1 141s Grid dimensions: 65 x 65 x 65 141s Grid spacings: 0.781 x 0.781 x 0.781 141s Grid lengths: 50.000 x 50.000 x 50.000 141s Grid center: (0.000, 0.000, 0.000) 141s Multigrid levels: 5 141s Molecule ID: 1 141s Linearized traditional PBE 141s Multiple Debye-Huckel sphere boundary conditions 141s 0 ion species (0.000 M ionic strength): 141s Solute dielectric: 1.000 141s Solvent dielectric: 78.540 141s Using "molecular" surface definition;harmonic average smoothing 141s Solvent probe radius: 1.400 A 141s Temperature: 298.150 K 141s Electrostatic energies will be calculated 141s Total electrostatic energy = 2.383232191909E+02 kJ/mol 141s Calculating forces... 141s ---------------------------------------- 141s CALCULATION #2 (solvated): MULTIGRID 141s Setting up problem... 141s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 141s Debye length: 0 A 141s Current memory usage: 61.280 MB total, 122.102 MB high water 141s Using cubic spline charge discretization. 141s Partition overlap fraction = 0.1 141s Processor array = 2 x 2 x 1 141s Grid dimensions: 65 x 65 x 65 141s Grid spacings: 0.296 x 0.296 x 0.383 141s Grid lengths: 18.944 x 18.944 x 24.495 141s Grid center: (2.411, 2.411, 0.000) 141s Multigrid levels: 5 141s Molecule ID: 1 141s Linearized traditional PBE 141s Boundary conditions from focusing 141s 0 ion species (0.000 M ionic strength): 141s Solute dielectric: 1.000 141s Solvent dielectric: 78.540 141s Using "molecular" surface definition;harmonic average smoothing 141s Solvent probe radius: 1.400 A 141s Temperature: 298.150 K 141s Electrostatic energies will be calculated 141s Total electrostatic energy = 8.145419900310E+02 kJ/mol 141s Calculating forces... 141s [focusFillBound()]: WARNING: 141s Unusually large potential values 141s detected on the focusing boundary! 141s Convergence not guaranteed for NPBE/NRPBE calculations! 141s 141s ---------------------------------------- 141s CALCULATION #3 (solvated): MULTIGRID 141s Setting up problem... 141s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 141s Debye length: 0 A 141s Current memory usage: 61.280 MB total, 122.102 MB high water 141s Using cubic spline charge discretization. 141s Partition overlap fraction = 0.1 141s Processor array = 2 x 2 x 1 141s Grid dimensions: 65 x 65 x 65 141s Grid spacings: 0.112 x 0.112 x 0.188 141s Grid lengths: 7.178 x 7.178 x 12.000 141s Grid center: (2.411, 2.411, 0.000) 141s Multigrid levels: 5 141s Molecule ID: 1 141s Linearized traditional PBE 141s Boundary conditions from focusing 141s 0 ion species (0.000 M ionic strength): 141s Solute dielectric: 1.000 141s Solvent dielectric: 78.540 141s Using "molecular" surface definition;harmonic average smoothing 141s Solvent probe radius: 1.400 A 141s Temperature: 298.150 K 141s Electrostatic energies will be calculated 141s Total electrostatic energy = 1.485529328301E+03 kJ/mol 141s Calculating forces... 141s ---------------------------------------- 141s CALCULATION #4 (reference): MULTIGRID 141s Setting up problem... 141s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 141s Debye length: 0 A 141s Current memory usage: 61.207 MB total, 122.102 MB high water 141s Using cubic spline charge discretization. 141s Partition overlap fraction = 0.1 141s Processor array = 2 x 2 x 1 141s Grid dimensions: 65 x 65 x 65 141s Grid spacings: 0.781 x 0.781 x 0.781 141s Grid lengths: 50.000 x 50.000 x 50.000 141s Grid center: (0.000, 0.000, 0.000) 141s Multigrid levels: 5 141s Molecule ID: 1 141s Linearized traditional PBE 141s Multiple Debye-Huckel sphere boundary conditions 141s 0 ion species (0.000 M ionic strength): 141s Solute dielectric: 1.000 141s Solvent dielectric: 1.000 141s Using "molecular" surface definition;harmonic average smoothing 141s Solvent probe radius: 1.400 A 141s Temperature: 298.150 K 141s Electrostatic energies will be calculated 141s Total electrostatic energy = 2.977178707146E+02 kJ/mol 141s Calculating forces... 141s ---------------------------------------- 141s CALCULATION #5 (reference): MULTIGRID 141s Setting up problem... 141s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 141s Debye length: 0 A 141s Current memory usage: 61.207 MB total, 122.102 MB high water 141s Using cubic spline charge discretization. 141s Partition overlap fraction = 0.1 141s Processor array = 2 x 2 x 1 141s Grid dimensions: 65 x 65 x 65 141s Grid spacings: 0.296 x 0.296 x 0.383 141s Grid lengths: 18.944 x 18.944 x 24.495 141s Grid center: (2.411, 2.411, 0.000) 141s Multigrid levels: 5 141s Molecule ID: 1 141s Linearized traditional PBE 141s Boundary conditions from focusing 141s 0 ion species (0.000 M ionic strength): 141s Solute dielectric: 1.000 141s Solvent dielectric: 1.000 141s Using "molecular" surface definition;harmonic average smoothing 141s Solvent probe radius: 1.400 A 141s Temperature: 298.150 K 141s Electrostatic energies will be calculated 141s Total electrostatic energy = 8.799304557596E+02 kJ/mol 141s Calculating forces... 141s [focusFillBound()]: WARNING: 141s Unusually large potential values 141s detected on the focusing boundary! 141s Convergence not guaranteed for NPBE/NRPBE calculations! 141s 141s ---------------------------------------- 141s CALCULATION #6 (reference): MULTIGRID 141s Setting up problem... 141s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 141s Debye length: 0 A 141s Current memory usage: 61.207 MB total, 122.102 MB high water 141s Using cubic spline charge discretization. 141s Partition overlap fraction = 0.1 141s Processor array = 2 x 2 x 1 141s Grid dimensions: 65 x 65 x 65 141s Grid spacings: 0.112 x 0.112 x 0.188 141s Grid lengths: 7.178 x 7.178 x 12.000 141s Grid center: (2.411, 2.411, 0.000) 141s Multigrid levels: 5 141s Molecule ID: 1 141s Linearized traditional PBE 141s Boundary conditions from focusing 141s 0 ion species (0.000 M ionic strength): 141s Solute dielectric: 1.000 141s Solvent dielectric: 1.000 141s Using "molecular" surface definition;harmonic average smoothing 141s Solvent probe radius: 1.400 A 141s Temperature: 298.150 K 141s Electrostatic energies will be calculated 141s Total electrostatic energy = 1.542873949141E+03 kJ/mol 141s Calculating forces... 141s ---------------------------------------- 141s PRINT STATEMENTS 141s 141s print energy 1 (solvated) - 2 (reference) end 141s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 141s Global net ELEC energy = -5.734462084052E+01 kJ/mol 141s ---------------------------------------- 141s CLEANING UP AND SHUTTING DOWN... 141s Destroying force arrays. 141s No energy arrays to destroy. 141s Destroying multigrid structures. 141s Destroying finite element structures. 141s Destroying 1 molecules 141s Final memory usage: 0.001 MB total, 122.102 MB high water 141s 141s 141s Thanks for using APBS! 141s 242s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 242s EXPECTED COMPUTED: 7 242s EXPECTED EXPECTED: 7 242s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 242s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 242s COMPUTED RESULT 953.292876745 242s COMPUTED RESULT 3258.1578983732998 242s COMPUTED RESULT 5942.108652589999 242s COMPUTED RESULT 1190.8714828309999 242s COMPUTED RESULT 3519.7218230368003 242s COMPUTED RESULT 6171.495796544 242s COMPUTED RESULT -229.38714395599 242s Running tests for actin-dimer-auto section 242s BINARY: /usr/bin/apbs 242s INPUT: apbs-mol-auto.in 242s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 242s asc_getToken: Error occurred (bailing out). 242s Vio_scanf: Format problem with input. 242s 242s 242s ---------------------------------------------------------------------- 242s APBS -- Adaptive Poisson-Boltzmann Solver 242s Version APBS 3.4.1 242s 242s Nathan A. Baker (nathan.baker@pnnl.gov) 242s Pacific Northwest National Laboratory 242s 242s Additional contributing authors listed in the code documentation. 242s 242s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 242s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 242s Northwest Division for the U.S. Department of Energy. 242s 242s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 242s Portions Copyright (c) 2002-2020, Nathan A. Baker. 242s Portions Copyright (c) 1999-2002, The Regents of the University of California. 242s Portions Copyright (c) 1995, Michael Holst. 242s All rights reserved. 242s 242s Redistribution and use in source and binary forms, with or without 242s modification, are permitted provided that the following conditions are met: 242s 242s * Redistributions of source code must retain the above copyright notice, this 242s list of conditions and the following disclaimer. 242s 242s * Redistributions in binary form must reproduce the above copyright notice, 242s this list of conditions and the following disclaimer in the documentation 242s and/or other materials provided with the distribution. 242s 242s * Neither the name of the developer nor the names of its contributors may be 242s used to endorse or promote products derived from this software without 242s specific prior written permission. 242s 242s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 242s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 242s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 242s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 242s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 242s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 242s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 242s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 242s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 242s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 242s ---------------------------------------------------------------------- 242s APBS uses FETK (the Finite Element ToolKit) to solve the 242s Poisson-Boltzmann equation numerically. FETK is a portable collection 242s of finite element modeling class libraries developed by the Michael Holst 242s research group and written in an object-oriented form of C. FEtk is 242s designed to solve general coupled systems of nonlinear partial differential 242s equations using adaptive finite element methods, inexact Newton methods, 242s and algebraic multilevel methods. More information about FEtk may be found 242s at . 242s ---------------------------------------------------------------------- 242s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 242s Aqua is a modified form of the Holst group PMG library 242s which has been modified by Patrice Koehl 242s for improved efficiency and 242s memory usage when solving the Poisson-Boltzmann equation. 242s ---------------------------------------------------------------------- 242s Please cite your use of APBS as: 242s 242s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 242s nanosystems: application to microtubules and the ribosome. Proc. 242s Natl. Acad. Sci. USA 98, 10037-10041 2001. 242s 242s 242s This executable compiled on Jan 3 2025 at 11:01:42 242s 242s Parsing input file apbs-mol-auto.in... 242s rank 0 size 1... 242s Parsed input file. 242s Got paths for 3 molecules 242s Reading PQR-format atom data from mol1.pqr. 242s asc_getToken: Error occurred (bailing out). 242s Vio_scanf: Format problem with input. 242s 5877 atoms 242s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 242s Net charge -1.20e+01 e 242s Reading PQR-format atom data from mol2.pqr. 242s asc_getToken: Error occurred (bailing out). 242s Vio_scanf: Format problem with input. 242s 5877 atoms 242s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 242s Net charge -1.20e+01 e 242s Reading PQR-format atom data from complex.pqr. 242s 11754 atoms 242s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 242s Net charge -2.40e+01 e 242s Preparing to run 6 PBE calculations. 242s ---------------------------------------- 242s CALCULATION #1 (mol1): MULTIGRID 242s Setting up problem... 242s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 242s Debye length: 13.5959 A 242s Current memory usage: 1028.322 MB total, 1028.322 MB high water 242s Using linear spline charge discretization. 242s Grid dimensions: 161 x 161 x 161 242s Grid spacings: 0.975 x 0.756 x 1.012 242s Grid lengths: 156.000 x 121.000 x 162.000 242s Grid center: (2.518, -2.465, 16.742) 242s Multigrid levels: 4 242s Molecule ID: 1 242s Nonlinear traditional PBE 242s Single Debye-Huckel sphere boundary conditions 242s 2 ion species (0.050 M ionic strength): 242s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 242s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 242s Solute dielectric: 2.000 242s Solvent dielectric: 78.400 242s Using "molecular" surface definition; no smoothing 242s Solvent probe radius: 1.400 A 242s Temperature: 298.150 K 242s Electrostatic energies will be calculated 242s Total electrostatic energy = 1.527617850342E+05 kJ/mol 242s Calculating forces... 242s ---------------------------------------- 242s CALCULATION #2 (mol1): MULTIGRID 242s Setting up problem... 242s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 242s Debye length: 13.5959 A 242s Current memory usage: 1028.322 MB total, 2042.113 MB high water 242s Using linear spline charge discretization. 242s Grid dimensions: 161 x 161 x 161 242s Grid spacings: 0.700 x 0.569 x 0.725 242s Grid lengths: 112.000 x 91.000 x 116.000 242s Grid center: (2.518, -2.465, 16.742) 242s Multigrid levels: 4 242s Molecule ID: 1 242s Nonlinear traditional PBE 242s Boundary conditions from focusing 242s 2 ion species (0.050 M ionic strength): 242s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 242s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 242s Solute dielectric: 2.000 242s Solvent dielectric: 78.400 242s Using "molecular" surface definition; no smoothing 242s Solvent probe radius: 1.400 A 242s Temperature: 298.150 K 242s Electrostatic energies will be calculated 242s Total electrostatic energy = 2.919510754196E+05 kJ/mol 242s Calculating forces... 242s ---------------------------------------- 242s CALCULATION #3 (mol2): MULTIGRID 242s Setting up problem... 242s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 242s Debye length: 13.5959 A 242s Current memory usage: 1030.291 MB total, 2042.113 MB high water 242s Using linear spline charge discretization. 242s Grid dimensions: 161 x 161 x 161 242s Grid spacings: 0.975 x 0.756 x 1.012 242s Grid lengths: 156.000 x 121.000 x 162.000 242s Grid center: (2.518, -2.465, 16.742) 242s Multigrid levels: 4 242s Molecule ID: 2 242s Nonlinear traditional PBE 242s Single Debye-Huckel sphere boundary conditions 242s 2 ion species (0.050 M ionic strength): 242s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 242s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 242s Solute dielectric: 2.000 242s Solvent dielectric: 78.400 242s Using "molecular" surface definition; no smoothing 242s Solvent probe radius: 1.400 A 242s Temperature: 298.150 K 242s Electrostatic energies will be calculated 242s Total electrostatic energy = 1.527671844880E+05 kJ/mol 242s Calculating forces... 242s ---------------------------------------- 242s CALCULATION #4 (mol2): MULTIGRID 242s Setting up problem... 242s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 242s Debye length: 13.5959 A 242s Current memory usage: 1030.291 MB total, 2046.048 MB high water 242s Using linear spline charge discretization. 242s Grid dimensions: 161 x 161 x 161 242s Grid spacings: 0.700 x 0.569 x 0.725 242s Grid lengths: 112.000 x 91.000 x 116.000 242s Grid center: (2.518, -2.465, 16.742) 242s Multigrid levels: 4 242s Molecule ID: 2 242s Nonlinear traditional PBE 242s Boundary conditions from focusing 242s 2 ion species (0.050 M ionic strength): 242s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 242s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 242s Solute dielectric: 2.000 242s Solvent dielectric: 78.400 242s Using "molecular" surface definition; no smoothing 242s Solvent probe radius: 1.400 A 242s Temperature: 298.150 K 242s Electrostatic energies will be calculated 242s Total electrostatic energy = 2.915468859278E+05 kJ/mol 242s Calculating forces... 242s ---------------------------------------- 242s CALCULATION #5 (complex): MULTIGRID 242s Setting up problem... 242s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 242s Debye length: 13.5959 A 242s Current memory usage: 1046.446 MB total, 2046.048 MB high water 242s Using linear spline charge discretization. 242s Grid dimensions: 161 x 161 x 161 242s Grid spacings: 0.975 x 0.756 x 1.012 242s Grid lengths: 156.000 x 121.000 x 162.000 242s Grid center: (2.518, -2.465, 16.742) 242s Multigrid levels: 4 242s Molecule ID: 3 242s Nonlinear traditional PBE 242s Single Debye-Huckel sphere boundary conditions 242s 2 ion species (0.050 M ionic strength): 242s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 242s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 242s Solute dielectric: 2.000 242s Solvent dielectric: 78.400 242s Using "molecular" surface definition; no smoothing 242s Solvent probe radius: 1.400 A 242s Temperature: 298.150 K 242s Electrostatic energies will be calculated 242s Total electrostatic energy = 3.056317807611E+05 kJ/mol 242s Calculating forces... 242s ---------------------------------------- 242s CALCULATION #6 (complex): MULTIGRID 242s Setting up problem... 242s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 242s Debye length: 13.5959 A 242s Current memory usage: 1046.446 MB total, 2069.492 MB high water 242s Using linear spline charge discretization. 242s Grid dimensions: 161 x 161 x 161 242s Grid spacings: 0.700 x 0.569 x 0.725 242s Grid lengths: 112.000 x 91.000 x 116.000 242s Grid center: (2.518, -2.465, 16.742) 242s Multigrid levels: 4 242s Molecule ID: 3 242s Nonlinear traditional PBE 242s Boundary conditions from focusing 242s 2 ion species (0.050 M ionic strength): 242s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 242s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 242s Solute dielectric: 2.000 242s Solvent dielectric: 78.400 242s Using "molecular" surface definition; no smoothing 242s Solvent probe radius: 1.400 A 242s Temperature: 298.150 K 242s Electrostatic energies will be calculated 242s Total electrostatic energy = 5.836028296532E+05 kJ/mol 242s Calculating forces... 242s ---------------------------------------- 242s PRINT STATEMENTS 242s 242s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 242s Local net energy (PE 0) = 1.048683058621E+02 kJ/mol 242s Global net ELEC energy = 1.048683058621E+02 kJ/mol 242s ---------------------------------------- 242s CLEANING UP AND SHUTTING DOWN... 242s Destroying force arrays. 242s No energy arrays to destroy. 242s Destroying multigrid structures. 242s Destroying finite element structures. 242s Destroying 3 molecules 242s Final memory usage: 0.001 MB total, 2069.492 MB high water 242s 242s 242s Thanks for using APBS! 242s 242s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 242s *** PASSED *** 242s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 242s *** PASSED *** 242s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 242s *** PASSED *** 242s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 242s *** PASSED *** 242s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 242s *** PASSED *** 242s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 242s *** PASSED *** 242s Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) 242s *** PASSED *** 242s Elapsed time: 100.92622 seconds 242s -------------------------------------------------------------------------------- 242s -------------------------------------------------------------------------------- 242s Testing input file apbs-smol-auto.in 242s 313s Checking for intermediate energies in input file apbs-mol-auto.out 313s EXPECTED COMPUTED: 7 313s EXPECTED EXPECTED: 7 313s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] 313s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 313s COMPUTED RESULT 152761.7850342 313s COMPUTED RESULT 291951.0754196 313s COMPUTED RESULT 152767.184488 313s COMPUTED RESULT 291546.8859278 313s COMPUTED RESULT 305631.7807611 313s COMPUTED RESULT 583602.8296532 313s COMPUTED RESULT 104.8683058621 313s BINARY: /usr/bin/apbs 313s INPUT: apbs-smol-auto.in 313s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 313s asc_getToken: Error occurred (bailing out). 313s Vio_scanf: Format problem with input. 313s 313s 313s ---------------------------------------------------------------------- 313s APBS -- Adaptive Poisson-Boltzmann Solver 313s Version APBS 3.4.1 313s 313s Nathan A. Baker (nathan.baker@pnnl.gov) 313s Pacific Northwest National Laboratory 313s 313s Additional contributing authors listed in the code documentation. 313s 313s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 313s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 313s Northwest Division for the U.S. Department of Energy. 313s 313s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 313s Portions Copyright (c) 2002-2020, Nathan A. Baker. 313s Portions Copyright (c) 1999-2002, The Regents of the University of California. 313s Portions Copyright (c) 1995, Michael Holst. 313s All rights reserved. 313s 313s Redistribution and use in source and binary forms, with or without 313s modification, are permitted provided that the following conditions are met: 313s 313s * Redistributions of source code must retain the above copyright notice, this 313s list of conditions and the following disclaimer. 313s 313s * Redistributions in binary form must reproduce the above copyright notice, 313s this list of conditions and the following disclaimer in the documentation 313s and/or other materials provided with the distribution. 313s 313s * Neither the name of the developer nor the names of its contributors may be 313s used to endorse or promote products derived from this software without 313s specific prior written permission. 313s 313s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 313s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 313s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 313s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 313s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 313s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 313s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 313s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 313s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 313s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 313s ---------------------------------------------------------------------- 313s APBS uses FETK (the Finite Element ToolKit) to solve the 313s Poisson-Boltzmann equation numerically. FETK is a portable collection 313s of finite element modeling class libraries developed by the Michael Holst 313s research group and written in an object-oriented form of C. FEtk is 313s designed to solve general coupled systems of nonlinear partial differential 313s equations using adaptive finite element methods, inexact Newton methods, 313s and algebraic multilevel methods. More information about FEtk may be found 313s at . 313s ---------------------------------------------------------------------- 313s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 313s Aqua is a modified form of the Holst group PMG library 313s which has been modified by Patrice Koehl 313s for improved efficiency and 313s memory usage when solving the Poisson-Boltzmann equation. 313s ---------------------------------------------------------------------- 313s Please cite your use of APBS as: 313s 313s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 313s nanosystems: application to microtubules and the ribosome. Proc. 313s Natl. Acad. Sci. USA 98, 10037-10041 2001. 313s 313s 313s This executable compiled on Jan 3 2025 at 11:01:42 313s 313s Parsing input file apbs-smol-auto.in... 313s rank 0 size 1... 313s Parsed input file. 313s Got paths for 3 molecules 313s Reading PQR-format atom data from mol1.pqr. 313s asc_getToken: Error occurred (bailing out). 313s Vio_scanf: Format problem with input. 313s 5877 atoms 313s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 313s Net charge -1.20e+01 e 313s Reading PQR-format atom data from mol2.pqr. 313s asc_getToken: Error occurred (bailing out). 313s Vio_scanf: Format problem with input. 313s 5877 atoms 313s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 313s Net charge -1.20e+01 e 313s Reading PQR-format atom data from complex.pqr. 313s 11754 atoms 313s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 313s Net charge -2.40e+01 e 313s Preparing to run 6 PBE calculations. 313s ---------------------------------------- 313s CALCULATION #1 (mol1): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 13.5959 A 313s Current memory usage: 1028.322 MB total, 1028.322 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 161 x 161 x 161 313s Grid spacings: 0.975 x 0.756 x 1.012 313s Grid lengths: 156.000 x 121.000 x 162.000 313s Grid center: (2.518, -2.465, 16.742) 313s Multigrid levels: 4 313s Molecule ID: 1 313s Nonlinear traditional PBE 313s Single Debye-Huckel sphere boundary conditions 313s 2 ion species (0.050 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.400 313s Using "molecular" surface definition;harmonic average smoothing 313s Solvent probe radius: 1.400 A 313s Temperature: 298.150 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 1.528632421825E+05 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #2 (mol1): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 13.5959 A 313s Current memory usage: 1028.322 MB total, 2042.113 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 161 x 161 x 161 313s Grid spacings: 0.700 x 0.569 x 0.725 313s Grid lengths: 112.000 x 91.000 x 116.000 313s Grid center: (2.518, -2.465, 16.742) 313s Multigrid levels: 4 313s Molecule ID: 1 313s Nonlinear traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.050 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.400 313s Using "molecular" surface definition;harmonic average smoothing 313s Solvent probe radius: 1.400 A 313s Temperature: 298.150 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 2.920618662320E+05 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #3 (mol2): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 13.5959 A 313s Current memory usage: 1030.291 MB total, 2042.113 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 161 x 161 x 161 313s Grid spacings: 0.975 x 0.756 x 1.012 313s Grid lengths: 156.000 x 121.000 x 162.000 313s Grid center: (2.518, -2.465, 16.742) 313s Multigrid levels: 4 313s Molecule ID: 2 313s Nonlinear traditional PBE 313s Single Debye-Huckel sphere boundary conditions 313s 2 ion species (0.050 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.400 313s Using "molecular" surface definition;harmonic average smoothing 313s Solvent probe radius: 1.400 A 313s Temperature: 298.150 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 1.529297900572E+05 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #4 (mol2): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 13.5959 A 313s Current memory usage: 1030.291 MB total, 2046.048 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 161 x 161 x 161 313s Grid spacings: 0.700 x 0.569 x 0.725 313s Grid lengths: 112.000 x 91.000 x 116.000 313s Grid center: (2.518, -2.465, 16.742) 313s Multigrid levels: 4 313s Molecule ID: 2 313s Nonlinear traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.050 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.400 313s Using "molecular" surface definition;harmonic average smoothing 313s Solvent probe radius: 1.400 A 313s Temperature: 298.150 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 2.916592202835E+05 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #5 (complex): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 13.5959 A 313s Current memory usage: 1046.446 MB total, 2046.048 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 161 x 161 x 161 313s Grid spacings: 0.975 x 0.756 x 1.012 313s Grid lengths: 156.000 x 121.000 x 162.000 313s Grid center: (2.518, -2.465, 16.742) 313s Multigrid levels: 4 313s Molecule ID: 3 313s Nonlinear traditional PBE 313s Single Debye-Huckel sphere boundary conditions 313s 2 ion species (0.050 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.400 313s Using "molecular" surface definition;harmonic average smoothing 313s Solvent probe radius: 1.400 A 313s Temperature: 298.150 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 3.059244262535E+05 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #6 (complex): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 13.5959 A 313s Current memory usage: 1046.446 MB total, 2069.492 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 161 x 161 x 161 313s Grid spacings: 0.700 x 0.569 x 0.725 313s Grid lengths: 112.000 x 91.000 x 116.000 313s Grid center: (2.518, -2.465, 16.742) 313s Multigrid levels: 4 313s Molecule ID: 3 313s Nonlinear traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.050 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.400 313s Using "molecular" surface definition;harmonic average smoothing 313s Solvent probe radius: 1.400 A 313s Temperature: 298.150 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 5.838306706232E+05 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s PRINT STATEMENTS 313s 313s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 313s Local net energy (PE 0) = 1.095841077688E+02 kJ/mol 313s Global net ELEC energy = 1.095841077688E+02 kJ/mol 313s ---------------------------------------- 313s CLEANING UP AND SHUTTING DOWN... 313s Destroying force arrays. 313s No energy arrays to destroy. 313s Destroying multigrid structures. 313s Destroying finite element structures. 313s Destroying 3 molecules 313s Final memory usage: 0.001 MB total, 2069.492 MB high water 313s 313s 313s Thanks for using APBS! 313s 313s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 313s *** PASSED *** 313s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 313s *** PASSED *** 313s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 313s *** PASSED *** 313s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 313s *** PASSED *** 313s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 313s *** PASSED *** 313s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 313s *** PASSED *** 313s Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) 313s *** PASSED *** 313s Elapsed time: 70.961123 seconds 313s -------------------------------------------------------------------------------- 313s Total elapsed time: 171.887343 seconds 313s Test results have been logged 313s -------------------------------------------------------------------------------- 313s -------------------------------------------------------------------------------- 313s Testing input file alkanes.in 313s 326s Checking for intermediate energies in input file apbs-smol-auto.out 326s EXPECTED COMPUTED: 7 326s EXPECTED EXPECTED: 7 326s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] 326s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 326s COMPUTED RESULT 152863.2421825 326s COMPUTED RESULT 292061.866232 326s COMPUTED RESULT 152929.7900572 326s COMPUTED RESULT 291659.2202835 326s COMPUTED RESULT 305924.4262535 326s COMPUTED RESULT 583830.6706232 326s COMPUTED RESULT 109.5841077688 326s Running tests for alkanes section 326s BINARY: /usr/bin/apbs 326s INPUT: alkanes.in 326s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 326s 326s ---------------------------------------------------------------------- 326s APBS -- Adaptive Poisson-Boltzmann Solver 326s Version APBS 3.4.1 326s 326s Nathan A. Baker (nathan.baker@pnnl.gov) 326s Pacific Northwest National Laboratory 326s 326s Additional contributing authors listed in the code documentation. 326s 326s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 326s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 326s Northwest Division for the U.S. Department of Energy. 326s 326s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 326s Portions Copyright (c) 2002-2020, Nathan A. Baker. 326s Portions Copyright (c) 1999-2002, The Regents of the University of California. 326s Portions Copyright (c) 1995, Michael Holst. 326s All rights reserved. 326s 326s Redistribution and use in source and binary forms, with or without 326s modification, are permitted provided that the following conditions are met: 326s 326s * Redistributions of source code must retain the above copyright notice, this 326s list of conditions and the following disclaimer. 326s 326s * Redistributions in binary form must reproduce the above copyright notice, 326s this list of conditions and the following disclaimer in the documentation 326s and/or other materials provided with the distribution. 326s 326s * Neither the name of the developer nor the names of its contributors may be 326s used to endorse or promote products derived from this software without 326s specific prior written permission. 326s 326s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 326s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 326s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 326s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 326s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 326s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 326s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 326s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 326s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 326s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 326s ---------------------------------------------------------------------- 326s APBS uses FETK (the Finite Element ToolKit) to solve the 326s Poisson-Boltzmann equation numerically. FETK is a portable collection 326s of finite element modeling class libraries developed by the Michael Holst 326s research group and written in an object-oriented form of C. FEtk is 326s designed to solve general coupled systems of nonlinear partial differential 326s equations using adaptive finite element methods, inexact Newton methods, 326s and algebraic multilevel methods. More information about FEtk may be found 326s at . 326s ---------------------------------------------------------------------- 326s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 326s Aqua is a modified form of the Holst group PMG library 326s which has been modified by Patrice Koehl 326s for improved efficiency and 326s memory usage when solving the Poisson-Boltzmann equation. 326s ---------------------------------------------------------------------- 326s Please cite your use of APBS as: 326s 326s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 326s nanosystems: application to microtubules and the ribosome. Proc. 326s Natl. Acad. Sci. USA 98, 10037-10041 2001. 326s 326s 326s This executable compiled on Jan 3 2025 at 11:01:42 326s 326s Parsing input file alkanes.in... 326s rank 0 size 1... 326s Parsed input file. 326s Reading parameter data from parm.dat. 326s Got paths for 11 molecules 326s Reading PDB-format atom data from 2-methylbutane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 17 atoms 326s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 326s Net charge 4.33e+00 e 326s Reading PDB-format atom data from butane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 14 atoms 326s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 326s Net charge 3.51e+00 e 326s Reading PDB-format atom data from cyclohexane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 18 atoms 326s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 326s Net charge 4.93e+00 e 326s Reading PDB-format atom data from cyclopentane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 13 atoms 326s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 326s Net charge 3.88e+00 e 326s Reading PDB-format atom data from ethane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 8 atoms 326s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 326s Net charge 1.87e+00 e 326s Reading PDB-format atom data from hexane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 20 atoms 326s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 326s Net charge 5.16e+00 e 326s Reading PDB-format atom data from isobutane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 14 atoms 326s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 326s Net charge 3.51e+00 e 326s Reading PDB-format atom data from methane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 5 atoms 326s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 326s Net charge 1.05e+00 e 326s Reading PDB-format atom data from neopentane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 17 atoms 326s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 326s Net charge 4.33e+00 e 326s Reading PDB-format atom data from pentane.pdb. 326s asc_getToken: Error occurred (bailing out). 326s Vio_scanf: Format problem with input. 326s 17 atoms 326s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 326s Net charge 4.33e+00 e 326s Reading PDB-format atom data from propane.pdb. 326s 11 atoms 326s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 326s Net charge 2.69e+00 e 326s Preparing to run 11 PBE calculations. 326s ---------------------------------------- 326s CALCULATION #1 (solvated-2-methylbutane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 3.815624614267E+00 326s SASA for atom 1: 0.000000000000E+00 326s SASA for atom 2: 6.122920124655E-01 326s SASA for atom 3: 3.957497153740E+00 326s SASA for atom 4: 4.308445014544E+00 326s SASA for atom 5: 1.843264951960E+01 326s SASA for atom 6: 1.837011296483E+01 326s SASA for atom 7: 1.666599184724E+01 326s SASA for atom 8: 1.480031796315E+01 326s SASA for atom 9: 1.603020354037E+01 326s SASA for atom 10: 1.473778140838E+01 326s SASA for atom 11: 1.611879699297E+01 326s SASA for atom 12: 1.810954398660E+01 326s SASA for atom 13: 1.420100931324E+01 326s SASA for atom 14: 1.437298483886E+01 326s SASA for atom 15: 1.814081226399E+01 326s SASA for atom 16: 2.152820898091E+01 326s 326s Total solvent accessible surface area: 214.202 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 3.243280922127E-02 326s Surface tension*area energy for atom 1: 0.000000000000E+00 326s Surface tension*area energy for atom 2: 5.204482105957E-03 326s Surface tension*area energy for atom 3: 3.363872580679E-02 326s Surface tension*area energy for atom 4: 3.662178262362E-02 326s Surface tension*area energy for atom 5: 1.566775209166E-01 326s Surface tension*area energy for atom 6: 1.561459602010E-01 326s Surface tension*area energy for atom 7: 1.416609307015E-01 326s Surface tension*area energy for atom 8: 1.258027026868E-01 326s Surface tension*area energy for atom 9: 1.362567300932E-01 326s Surface tension*area energy for atom 10: 1.252711419712E-01 326s Surface tension*area energy for atom 11: 1.370097744402E-01 326s Surface tension*area energy for atom 12: 1.539311238861E-01 326s Surface tension*area energy for atom 13: 1.207085791625E-01 326s Surface tension*area energy for atom 14: 1.221703711303E-01 326s Surface tension*area energy for atom 15: 1.541969042439E-01 326s Surface tension*area energy for atom 16: 1.829897763377E-01 326s 326s Total surface tension energy: 1.82072 kJ/mol 326s 326s Total solvent accessible volume: 253.665 A^3 326s 326s Total pressure*volume energy: 60.7274 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.271287875274E+00 326s WCA energy for atom 1: -5.600872869478E+00 326s WCA energy for atom 2: -5.773775123943E+00 326s WCA energy for atom 3: -6.072801488986E+00 326s WCA energy for atom 4: -6.378470721845E+00 326s WCA energy for atom 5: -1.573474558351E+00 326s WCA energy for atom 6: -1.582338715648E+00 326s WCA energy for atom 7: -1.504044838266E+00 326s WCA energy for atom 8: -1.351002262819E+00 326s WCA energy for atom 9: -1.437367175239E+00 326s WCA energy for atom 10: -1.384626257493E+00 326s WCA energy for atom 11: -1.468867560891E+00 326s WCA energy for atom 12: -1.557005662832E+00 326s WCA energy for atom 13: -1.473759654043E+00 326s WCA energy for atom 14: -1.502261431335E+00 326s WCA energy for atom 15: -1.550940901474E+00 326s WCA energy for atom 16: -1.667828659696E+00 326s 326s Total WCA energy: -48.1507 kJ/mol 326s 326s Total non-polar energy = 1.439739455792E+01 kJ/mol 326s ---------------------------------------- 326s CALCULATION #2 (solvated-butane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 4.405515699447E+00 326s SASA for atom 1: 8.213673337951E-01 326s SASA for atom 2: 8.064333822716E-01 326s SASA for atom 3: 4.375647796400E+00 326s SASA for atom 4: 1.855251124959E+01 326s SASA for atom 5: 2.147609518526E+01 326s SASA for atom 6: 1.852645435176E+01 326s SASA for atom 7: 1.660345529247E+01 326s SASA for atom 8: 1.658782115377E+01 326s SASA for atom 9: 1.658260977421E+01 326s SASA for atom 10: 1.658260977421E+01 326s SASA for atom 11: 2.145003828744E+01 326s SASA for atom 12: 1.852124297220E+01 326s SASA for atom 13: 1.856293400871E+01 326s 326s Total solvent accessible surface area: 193.855 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 3.744688344530E-02 326s Surface tension*area energy for atom 1: 6.981622337259E-03 326s Surface tension*area energy for atom 2: 6.854683749309E-03 326s Surface tension*area energy for atom 3: 3.719300626940E-02 326s Surface tension*area energy for atom 4: 1.576963456215E-01 326s Surface tension*area energy for atom 5: 1.825468090747E-01 326s Surface tension*area energy for atom 6: 1.574748619900E-01 326s Surface tension*area energy for atom 7: 1.411293699860E-01 326s Surface tension*area energy for atom 8: 1.409964798071E-01 326s Surface tension*area energy for atom 9: 1.409521830808E-01 326s Surface tension*area energy for atom 10: 1.409521830808E-01 326s Surface tension*area energy for atom 11: 1.823253254433E-01 326s Surface tension*area energy for atom 12: 1.574305652637E-01 326s Surface tension*area energy for atom 13: 1.577849390741E-01 326s 326s Total surface tension energy: 1.64777 kJ/mol 326s 326s Total solvent accessible volume: 217.863 A^3 326s 326s Total pressure*volume energy: 52.1564 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.728858147814E+00 326s WCA energy for atom 1: -6.204037472587E+00 326s WCA energy for atom 2: -6.202937735018E+00 326s WCA energy for atom 3: -6.728762249931E+00 326s WCA energy for atom 4: -1.623549989062E+00 326s WCA energy for atom 5: -1.709092300778E+00 326s WCA energy for atom 6: -1.625196457114E+00 326s WCA energy for atom 7: -1.484289341167E+00 326s WCA energy for atom 8: -1.485410538626E+00 326s WCA energy for atom 9: -1.485593139015E+00 326s WCA energy for atom 10: -1.484878734279E+00 326s WCA energy for atom 11: -1.708585062695E+00 326s WCA energy for atom 12: -1.625094916482E+00 326s WCA energy for atom 13: -1.624416805392E+00 326s 326s Total WCA energy: -41.7207 kJ/mol 326s 326s Total non-polar energy = 1.208346456826E+01 kJ/mol 326s ---------------------------------------- 326s CALCULATION #3 (solvated-cyclohexane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 7.840324549863E-01 326s SASA for atom 1: 8.064333822716E-01 326s SASA for atom 2: 8.288343095569E-01 326s SASA for atom 3: 7.840324549863E-01 326s SASA for atom 4: 7.989664065098E-01 326s SASA for atom 5: 8.363012853187E-01 326s SASA for atom 6: 2.001169752764E+01 326s SASA for atom 7: 1.616048802948E+01 326s SASA for atom 8: 2.001169752764E+01 326s SASA for atom 9: 1.619175630687E+01 326s SASA for atom 10: 1.616048802948E+01 326s SASA for atom 11: 1.993352683418E+01 326s SASA for atom 12: 2.001169752764E+01 326s SASA for atom 13: 1.618133354774E+01 326s SASA for atom 14: 1.617091078861E+01 326s SASA for atom 15: 2.001690890721E+01 326s SASA for atom 16: 1.993873821374E+01 326s SASA for atom 17: 1.617091078861E+01 326s 326s Total solvent accessible surface area: 221.799 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 6.664275867383E-03 326s Surface tension*area energy for atom 1: 6.854683749309E-03 326s Surface tension*area energy for atom 2: 7.045091631234E-03 326s Surface tension*area energy for atom 3: 6.664275867383E-03 326s Surface tension*area energy for atom 4: 6.791214455333E-03 326s Surface tension*area energy for atom 5: 7.108560925209E-03 326s Surface tension*area energy for atom 6: 1.700994289850E-01 326s Surface tension*area energy for atom 7: 1.373641482506E-01 326s Surface tension*area energy for atom 8: 1.700994289850E-01 326s Surface tension*area energy for atom 9: 1.376299286084E-01 326s Surface tension*area energy for atom 10: 1.373641482506E-01 326s Surface tension*area energy for atom 11: 1.694349780905E-01 326s Surface tension*area energy for atom 12: 1.700994289850E-01 326s Surface tension*area energy for atom 13: 1.375413351558E-01 326s Surface tension*area energy for atom 14: 1.374527417032E-01 326s Surface tension*area energy for atom 15: 1.701437257113E-01 326s Surface tension*area energy for atom 16: 1.694792748168E-01 326s Surface tension*area energy for atom 17: 1.374527417032E-01 326s 326s Total surface tension energy: 1.88529 kJ/mol 326s 326s Total solvent accessible volume: 267.435 A^3 326s 326s Total pressure*volume energy: 64.0239 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -5.793234697241E+00 326s WCA energy for atom 1: -5.784370526583E+00 326s WCA energy for atom 2: -5.791799130412E+00 326s WCA energy for atom 3: -5.788504399087E+00 326s WCA energy for atom 4: -5.797319672490E+00 326s WCA energy for atom 5: -5.787358035342E+00 326s WCA energy for atom 6: -1.523887929614E+00 326s WCA energy for atom 7: -1.413678912317E+00 326s WCA energy for atom 8: -1.521751604392E+00 326s WCA energy for atom 9: -1.414741802525E+00 326s WCA energy for atom 10: -1.413367854344E+00 326s WCA energy for atom 11: -1.523407238081E+00 326s WCA energy for atom 12: -1.523000623583E+00 326s WCA energy for atom 13: -1.413922068538E+00 326s WCA energy for atom 14: -1.416316744211E+00 326s WCA energy for atom 15: -1.524577474659E+00 326s WCA energy for atom 16: -1.523300410052E+00 326s WCA energy for atom 17: -1.414522566061E+00 326s 326s Total WCA energy: -52.3691 kJ/mol 326s 326s Total non-polar energy = 1.354016672221E+01 kJ/mol 326s ---------------------------------------- 326s CALCULATION #4 (solvated-cyclopentane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 9.490526193215E+00 326s SASA for atom 1: 9.512927120500E+00 326s SASA for atom 2: 2.299828534626E+00 326s SASA for atom 3: 1.919012770776E+00 326s SASA for atom 4: 2.307295510388E+00 326s SASA for atom 5: 2.325838699632E+01 326s SASA for atom 6: 2.325838699632E+01 326s SASA for atom 7: 2.045987617019E+01 326s SASA for atom 8: 2.067875411190E+01 326s SASA for atom 9: 2.028790064456E+01 326s SASA for atom 10: 1.897463299431E+01 326s SASA for atom 11: 2.048593306801E+01 326s SASA for atom 12: 2.070481100972E+01 326s 326s Total solvent accessible surface area: 193.638 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 8.066947264233E-02 326s Surface tension*area energy for atom 1: 8.085988052425E-02 326s Surface tension*area energy for atom 2: 1.954854254432E-02 326s Surface tension*area energy for atom 3: 1.631160855160E-02 326s Surface tension*area energy for atom 4: 1.961201183830E-02 326s Surface tension*area energy for atom 5: 1.976962894687E-01 326s Surface tension*area energy for atom 6: 1.976962894687E-01 326s Surface tension*area energy for atom 7: 1.739089474466E-01 326s Surface tension*area energy for atom 8: 1.757694099511E-01 326s Surface tension*area energy for atom 9: 1.724471554788E-01 326s Surface tension*area energy for atom 10: 1.612843804516E-01 326s Surface tension*area energy for atom 11: 1.741304310781E-01 326s Surface tension*area energy for atom 12: 1.759908935826E-01 326s 326s Total surface tension energy: 1.64593 kJ/mol 326s 326s Total solvent accessible volume: 217.998 A^3 326s 326s Total pressure*volume energy: 52.1887 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.343496616804E+00 326s WCA energy for atom 1: -6.327869601807E+00 326s WCA energy for atom 2: -6.334858040579E+00 326s WCA energy for atom 3: -6.296075406417E+00 326s WCA energy for atom 4: -6.345600816761E+00 326s WCA energy for atom 5: -1.663697465126E+00 326s WCA energy for atom 6: -1.662444032853E+00 326s WCA energy for atom 7: -1.572325104493E+00 326s WCA energy for atom 8: -1.604626551065E+00 326s WCA energy for atom 9: -1.586431484963E+00 326s WCA energy for atom 10: -1.554291291374E+00 326s WCA energy for atom 11: -1.574315220751E+00 326s WCA energy for atom 12: -1.604941679892E+00 326s 326s Total WCA energy: -44.471 kJ/mol 326s 326s Total non-polar energy = 9.363673200142E+00 kJ/mol 326s ---------------------------------------- 326s CALCULATION #5 (solvated-ethane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 5.995981536705E+00 326s SASA for atom 1: 5.966113633657E+00 326s SASA for atom 2: 2.121552620704E+01 326s SASA for atom 3: 2.124158310486E+01 326s SASA for atom 4: 2.125200586399E+01 326s SASA for atom 5: 2.123116034573E+01 326s SASA for atom 6: 2.125200586399E+01 326s SASA for atom 7: 2.127285138225E+01 326s 326s Total solvent accessible surface area: 139.427 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 5.096584306199E-02 326s Surface tension*area energy for atom 1: 5.071196588609E-02 326s Surface tension*area energy for atom 2: 1.803319727598E-01 326s Surface tension*area energy for atom 3: 1.805534563913E-01 326s Surface tension*area energy for atom 4: 1.806420498439E-01 326s Surface tension*area energy for atom 5: 1.804648629387E-01 326s Surface tension*area energy for atom 6: 1.806420498439E-01 326s Surface tension*area energy for atom 7: 1.808192367491E-01 326s 326s Total surface tension energy: 1.18513 kJ/mol 326s 326s Total solvent accessible volume: 140.346 A^3 326s 326s Total pressure*volume energy: 33.5988 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -7.360066353115E+00 326s WCA energy for atom 1: -7.355483516201E+00 326s WCA energy for atom 2: -1.776106201066E+00 326s WCA energy for atom 3: -1.773973940651E+00 326s WCA energy for atom 4: -1.775401936843E+00 326s WCA energy for atom 5: -1.773464835521E+00 326s WCA energy for atom 6: -1.774382856097E+00 326s WCA energy for atom 7: -1.772366599434E+00 326s 326s Total WCA energy: -25.3612 kJ/mol 326s 326s Total non-polar energy = 9.422717598546E+00 kJ/mol 326s ---------------------------------------- 326s CALCULATION #6 (solvated-hexane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 4.405515699447E+00 326s SASA for atom 1: 8.213673337951E-01 326s SASA for atom 2: 3.285469335181E-01 326s SASA for atom 3: 2.986790304710E-01 326s SASA for atom 4: 1.855251124959E+01 326s SASA for atom 5: 2.147609518526E+01 326s SASA for atom 6: 1.852645435176E+01 326s SASA for atom 7: 1.655655287639E+01 326s SASA for atom 8: 1.655134149682E+01 326s SASA for atom 9: 1.360170066332E+01 326s SASA for atom 10: 1.357043238593E+01 326s SASA for atom 11: 1.381536722546E+01 326s SASA for atom 12: 1.384142412329E+01 326s SASA for atom 13: 7.765654792245E-01 326s SASA for atom 14: 1.684839013200E+01 326s SASA for atom 15: 1.682233323417E+01 326s SASA for atom 16: 4.166572475070E+00 326s SASA for atom 17: 2.179398933870E+01 326s SASA for atom 18: 1.877660057086E+01 326s SASA for atom 19: 1.876096643216E+01 326s 326s Total solvent accessible surface area: 250.291 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 3.744688344530E-02 326s Surface tension*area energy for atom 1: 6.981622337259E-03 326s Surface tension*area energy for atom 2: 2.792648934903E-03 326s Surface tension*area energy for atom 3: 2.538771759003E-03 326s Surface tension*area energy for atom 4: 1.576963456215E-01 326s Surface tension*area energy for atom 5: 1.825468090747E-01 326s Surface tension*area energy for atom 6: 1.574748619900E-01 326s Surface tension*area energy for atom 7: 1.407306994493E-01 326s Surface tension*area energy for atom 8: 1.406864027230E-01 326s Surface tension*area energy for atom 9: 1.156144556382E-01 326s Surface tension*area energy for atom 10: 1.153486752804E-01 326s Surface tension*area energy for atom 11: 1.174306214164E-01 326s Surface tension*area energy for atom 12: 1.176521050479E-01 326s Surface tension*area energy for atom 13: 6.600806573408E-03 326s Surface tension*area energy for atom 14: 1.432113161220E-01 326s Surface tension*area energy for atom 15: 1.429898324905E-01 326s Surface tension*area energy for atom 16: 3.541586603809E-02 326s Surface tension*area energy for atom 17: 1.852489093789E-01 326s Surface tension*area energy for atom 18: 1.596011048523E-01 326s Surface tension*area energy for atom 19: 1.594682146734E-01 326s 326s Total surface tension energy: 2.12748 kJ/mol 326s 326s Total solvent accessible volume: 298.053 A^3 326s 326s Total pressure*volume energy: 71.3539 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.635406071935E+00 326s WCA energy for atom 1: -5.957247427848E+00 326s WCA energy for atom 2: -5.524801144538E+00 326s WCA energy for atom 3: -5.522294168859E+00 326s WCA energy for atom 4: -1.605314409440E+00 326s WCA energy for atom 5: -1.701051761776E+00 326s WCA energy for atom 6: -1.606669162773E+00 326s WCA energy for atom 7: -1.442505934938E+00 326s WCA energy for atom 8: -1.443059002759E+00 326s WCA energy for atom 9: -1.328947132810E+00 326s WCA energy for atom 10: -1.328906972440E+00 326s WCA energy for atom 11: -1.331566344214E+00 326s WCA energy for atom 12: -1.328041776815E+00 326s WCA energy for atom 13: -5.937562025661E+00 326s WCA energy for atom 14: -1.442277774427E+00 326s WCA energy for atom 15: -1.442777091510E+00 326s WCA energy for atom 16: -6.602262542378E+00 326s WCA energy for atom 17: -1.698172146664E+00 326s WCA energy for atom 18: -1.600970858835E+00 326s WCA energy for atom 19: -1.600841970217E+00 326s 326s Total WCA energy: -57.0807 kJ/mol 326s 326s Total non-polar energy = 1.640068943201E+01 kJ/mol 326s ---------------------------------------- 326s CALCULATION #7 (solvated-isobutane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 3.464676753463E+00 326s SASA for atom 1: 1.984493338158E+01 326s SASA for atom 2: 1.778643845361E+01 326s SASA for atom 3: 1.671289426332E+01 326s SASA for atom 4: 0.000000000000E+00 326s SASA for atom 5: 3.531879535319E+00 326s SASA for atom 6: 1.673895116114E+01 326s SASA for atom 7: 1.793756846098E+01 326s SASA for atom 8: 1.973549441072E+01 326s SASA for atom 9: 1.710895911022E+01 326s SASA for atom 10: 4.599657069253E+00 326s SASA for atom 11: 1.937069784121E+01 326s SASA for atom 12: 1.654613011726E+01 326s SASA for atom 13: 1.936548646165E+01 326s 326s Total solvent accessible surface area: 192.744 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 2.944975240444E-02 326s Surface tension*area energy for atom 1: 1.686819337434E-01 326s Surface tension*area energy for atom 2: 1.511847268556E-01 326s Surface tension*area energy for atom 3: 1.420596012382E-01 326s Surface tension*area energy for atom 4: 0.000000000000E+00 326s Surface tension*area energy for atom 5: 3.002097605021E-02 326s Surface tension*area energy for atom 6: 1.422810848697E-01 326s Surface tension*area energy for atom 7: 1.524693319183E-01 326s Surface tension*area energy for atom 8: 1.677517024912E-01 326s Surface tension*area energy for atom 9: 1.454261524369E-01 326s Surface tension*area energy for atom 10: 3.909708508865E-02 326s Surface tension*area energy for atom 11: 1.646509316503E-01 326s Surface tension*area energy for atom 12: 1.406421059967E-01 326s Surface tension*area energy for atom 13: 1.646066349240E-01 326s 326s Total surface tension energy: 1.63832 kJ/mol 326s 326s Total solvent accessible volume: 218.943 A^3 326s 326s Total pressure*volume energy: 52.415 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.381016335247E+00 326s WCA energy for atom 1: -1.612317964554E+00 326s WCA energy for atom 2: -1.588013719598E+00 326s WCA energy for atom 3: -1.532162371190E+00 326s WCA energy for atom 4: -5.987950445279E+00 326s WCA energy for atom 5: -6.393089030861E+00 326s WCA energy for atom 6: -1.533454887042E+00 326s WCA energy for atom 7: -1.587650918485E+00 326s WCA energy for atom 8: -1.614083521570E+00 326s WCA energy for atom 9: -1.442402031577E+00 326s WCA energy for atom 10: -6.408813541353E+00 326s WCA energy for atom 11: -1.605830214390E+00 326s WCA energy for atom 12: -1.529385873788E+00 326s WCA energy for atom 13: -1.605662490385E+00 326s 326s Total WCA energy: -40.8218 kJ/mol 326s 326s Total non-polar energy = 1.323144287435E+01 kJ/mol 326s ---------------------------------------- 326s CALCULATION #8 (solvated-methane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 1.231304303117E+01 326s SASA for atom 1: 2.323233009850E+01 326s SASA for atom 2: 2.345641941977E+01 326s SASA for atom 3: 2.377431357320E+01 326s SASA for atom 4: 2.264344420771E+01 326s 326s Total solvent accessible surface area: 105.42 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 1.046608657649E-01 326s Surface tension*area energy for atom 1: 1.974748058372E-01 326s Surface tension*area energy for atom 2: 1.993795650680E-01 326s Surface tension*area energy for atom 3: 2.020816653722E-01 326s Surface tension*area energy for atom 4: 1.924692757655E-01 326s 326s Total surface tension energy: 0.896066 kJ/mol 326s 326s Total solvent accessible volume: 95.985 A^3 326s 326s Total pressure*volume energy: 22.9788 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -8.133807570805E+00 326s WCA energy for atom 1: -1.962181541765E+00 326s WCA energy for atom 2: -1.964078319162E+00 326s WCA energy for atom 3: -1.963015006647E+00 326s WCA energy for atom 4: -1.957425549100E+00 326s 326s Total WCA energy: -15.9805 kJ/mol 326s 326s Total non-polar energy = 7.894367190329E+00 kJ/mol 326s ---------------------------------------- 326s CALCULATION #9 (solvated-neopentane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 2.441701074100E+00 326s SASA for atom 1: 1.663993494942E+01 326s SASA for atom 2: 1.715586152630E+01 326s SASA for atom 3: 1.645753666466E+01 326s SASA for atom 4: 0.000000000000E+00 326s SASA for atom 5: 2.389432243768E+00 326s SASA for atom 6: 1.638457735076E+01 326s SASA for atom 7: 1.667641460637E+01 326s SASA for atom 8: 1.721839808108E+01 326s SASA for atom 9: 2.419300146815E+00 326s SASA for atom 10: 1.640021148945E+01 326s SASA for atom 11: 1.666599184724E+01 326s SASA for atom 12: 1.719234118325E+01 326s SASA for atom 13: 2.449168049862E+00 326s SASA for atom 14: 1.723403221977E+01 326s SASA for atom 15: 1.639500010989E+01 326s SASA for atom 16: 1.663472356985E+01 326s 326s Total solvent accessible surface area: 210.755 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 2.075445912985E-02 326s Surface tension*area energy for atom 1: 1.414394470700E-01 326s Surface tension*area energy for atom 2: 1.458248229736E-01 326s Surface tension*area energy for atom 3: 1.398890616496E-01 326s Surface tension*area energy for atom 4: 0.000000000000E+00 326s Surface tension*area energy for atom 5: 2.031017407203E-02 326s Surface tension*area energy for atom 6: 1.392689074814E-01 326s Surface tension*area energy for atom 7: 1.417495241541E-01 326s Surface tension*area energy for atom 8: 1.463563836891E-01 326s Surface tension*area energy for atom 9: 2.056405124793E-02 326s Surface tension*area energy for atom 10: 1.394017976603E-01 326s Surface tension*area energy for atom 11: 1.416609307015E-01 326s Surface tension*area energy for atom 12: 1.461349000577E-01 326s Surface tension*area energy for atom 13: 2.081792842383E-02 326s Surface tension*area energy for atom 14: 1.464892738680E-01 326s Surface tension*area energy for atom 15: 1.393575009340E-01 326s Surface tension*area energy for atom 16: 1.413951503437E-01 326s 326s Total surface tension energy: 1.79141 kJ/mol 326s 326s Total solvent accessible volume: 251.127 A^3 326s 326s Total pressure*volume energy: 60.1198 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.011082520236E+00 326s WCA energy for atom 1: -1.497367782613E+00 326s WCA energy for atom 2: -1.498546483218E+00 326s WCA energy for atom 3: -1.492562171495E+00 326s WCA energy for atom 4: -5.447325863939E+00 326s WCA energy for atom 5: -6.004516149175E+00 326s WCA energy for atom 6: -1.492776531092E+00 326s WCA energy for atom 7: -1.496078170066E+00 326s WCA energy for atom 8: -1.501529655270E+00 326s WCA energy for atom 9: -5.996267554365E+00 326s WCA energy for atom 10: -1.492194267752E+00 326s WCA energy for atom 11: -1.496027211216E+00 326s WCA energy for atom 12: -1.500561393960E+00 326s WCA energy for atom 13: -6.000218612907E+00 326s WCA energy for atom 14: -1.500859921426E+00 326s WCA energy for atom 15: -1.492908499790E+00 326s WCA energy for atom 16: -1.494057174414E+00 326s 326s Total WCA energy: -47.4149 kJ/mol 326s 326s Total non-polar energy = 1.449633815052E+01 kJ/mol 326s ---------------------------------------- 326s CALCULATION #10 (solvated-pentane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 4.405515699447E+00 326s SASA for atom 1: 8.213673337951E-01 326s SASA for atom 2: 3.285469335181E-01 326s SASA for atom 3: 7.466975761774E-01 326s SASA for atom 4: 1.855251124959E+01 326s SASA for atom 5: 2.147609518526E+01 326s SASA for atom 6: 1.852645435176E+01 326s SASA for atom 7: 1.655655287639E+01 326s SASA for atom 8: 1.655134149682E+01 326s SASA for atom 9: 1.360170066332E+01 326s SASA for atom 10: 1.357043238593E+01 326s SASA for atom 11: 1.685881289113E+01 326s SASA for atom 12: 1.687444702982E+01 326s SASA for atom 13: 4.196440378117E+00 326s SASA for atom 14: 1.881308022781E+01 326s SASA for atom 15: 1.882350298694E+01 326s SASA for atom 16: 2.182004623652E+01 326s 326s Total solvent accessible surface area: 222.524 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 3.744688344530E-02 326s Surface tension*area energy for atom 1: 6.981622337259E-03 326s Surface tension*area energy for atom 2: 2.792648934903E-03 326s Surface tension*area energy for atom 3: 6.346929397508E-03 326s Surface tension*area energy for atom 4: 1.576963456215E-01 326s Surface tension*area energy for atom 5: 1.825468090747E-01 326s Surface tension*area energy for atom 6: 1.574748619900E-01 326s Surface tension*area energy for atom 7: 1.407306994493E-01 326s Surface tension*area energy for atom 8: 1.406864027230E-01 326s Surface tension*area energy for atom 9: 1.156144556382E-01 326s Surface tension*area energy for atom 10: 1.153486752804E-01 326s Surface tension*area energy for atom 11: 1.432999095746E-01 326s Surface tension*area energy for atom 12: 1.434327997535E-01 326s Surface tension*area energy for atom 13: 3.566974321399E-02 326s Surface tension*area energy for atom 14: 1.599111819364E-01 326s Surface tension*area energy for atom 15: 1.599997753890E-01 326s Surface tension*area energy for atom 16: 1.854703930104E-01 326s 326s Total surface tension energy: 1.89145 kJ/mol 326s 326s Total solvent accessible volume: 258.93 A^3 326s 326s Total pressure*volume energy: 61.9878 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.655804319869E+00 326s WCA energy for atom 1: -6.027315962813E+00 326s WCA energy for atom 2: -5.696430965386E+00 326s WCA energy for atom 3: -6.016749084714E+00 326s WCA energy for atom 4: -1.608595384643E+00 326s WCA energy for atom 5: -1.703300955380E+00 326s WCA energy for atom 6: -1.609931495887E+00 326s WCA energy for atom 7: -1.457107525189E+00 326s WCA energy for atom 8: -1.457741620594E+00 326s WCA energy for atom 9: -1.354235498709E+00 326s WCA energy for atom 10: -1.354106470090E+00 326s WCA energy for atom 11: -1.456736412636E+00 326s WCA energy for atom 12: -1.455995435596E+00 326s WCA energy for atom 13: -6.633650611186E+00 326s WCA energy for atom 14: -1.605996088477E+00 326s WCA energy for atom 15: -1.606549890103E+00 326s WCA energy for atom 16: -1.700042300035E+00 326s 326s Total WCA energy: -49.4003 kJ/mol 326s 326s Total non-polar energy = 1.447900211546E+01 kJ/mol 326s ---------------------------------------- 326s CALCULATION #11 (solvated-propane): APOLAR 326s 326s Solvent Accessible Surface Area (SASA) for each atom: 326s SASA for atom 0: 3.173464698754E+00 326s SASA for atom 1: 1.931858404557E+01 326s SASA for atom 2: 2.014198201675E+01 326s SASA for atom 3: 2.149694070352E+01 326s SASA for atom 4: 1.904078819252E+00 326s SASA for atom 5: 2.067354273233E+01 326s SASA for atom 6: 1.937590922077E+01 326s SASA for atom 7: 3.098794941136E+00 326s SASA for atom 8: 1.942802301642E+01 326s SASA for atom 9: 1.973028303116E+01 326s SASA for atom 10: 2.204934693736E+01 326s 326s Total solvent accessible surface area: 170.391 A^2 326s 326s Surface tension*area energies (gamma * SASA) for each atom: 326s Surface tension*area energy for atom 0: 2.697444993941E-02 326s Surface tension*area energy for atom 1: 1.642079643873E-01 326s Surface tension*area energy for atom 2: 1.712068471424E-01 326s Surface tension*area energy for atom 3: 1.827239959799E-01 326s Surface tension*area energy for atom 4: 1.618466996365E-02 326s Surface tension*area energy for atom 5: 1.757251132248E-01 326s Surface tension*area energy for atom 6: 1.646952283766E-01 326s Surface tension*area energy for atom 7: 2.633975699966E-02 326s Surface tension*area energy for atom 8: 1.651381956396E-01 326s Surface tension*area energy for atom 9: 1.677074057649E-01 326s Surface tension*area energy for atom 10: 1.874194489675E-01 326s 326s Total surface tension energy: 1.44832 kJ/mol 326s 326s Total solvent accessible volume: 183.573 A^3 326s 326s Total pressure*volume energy: 43.9474 kJ/mol 326s 326s WCA dispersion Energies for each atom: 326s WCA energy for atom 0: -6.818670105515E+00 326s WCA energy for atom 1: -1.641297645338E+00 326s WCA energy for atom 2: -1.649584120441E+00 326s WCA energy for atom 3: -1.711408141255E+00 326s WCA energy for atom 4: -6.624720142882E+00 326s WCA energy for atom 5: -1.610117050515E+00 326s WCA energy for atom 6: -1.596858009746E+00 326s WCA energy for atom 7: -6.816460624835E+00 326s WCA energy for atom 8: -1.642782751806E+00 326s WCA energy for atom 9: -1.645779566650E+00 326s WCA energy for atom 10: -1.714436154542E+00 326s 326s Total WCA energy: -33.4721 kJ/mol 326s 326s Total non-polar energy = 1.192358496286E+01 kJ/mol 326s ---------------------------------------- 326s PRINT STATEMENTS 326s 326s print APOL energy 1 (solvated-2-methylbutane) end 326s Global net APOL energy = 1.439739455792E+01 kJ/mol 326s 326s print APOL energy 2 (solvated-butane) end 326s Global net APOL energy = 1.208346456826E+01 kJ/mol 326s 326s print APOL energy 3 (solvated-cyclohexane) end 326s Global net APOL energy = 1.354016672221E+01 kJ/mol 326s 326s print APOL energy 4 (solvated-cyclopentane) end 326s Global net APOL energy = 9.363673200142E+00 kJ/mol 326s 326s print APOL energy 5 (solvated-ethane) end 326s Global net APOL energy = 9.422717598546E+00 kJ/mol 326s 326s print APOL energy 6 (solvated-hexane) end 326s Global net APOL energy = 1.640068943201E+01 kJ/mol 326s 326s print APOL energy 7 (solvated-isobutane) end 326s Global net APOL energy = 1.323144287435E+01 kJ/mol 326s 326s print APOL energy 8 (solvated-methane) end 326s Global net APOL energy = 7.894367190329E+00 kJ/mol 326s 326s print APOL energy 9 (solvated-neopentane) end 326s Global net APOL energy = 1.449633815052E+01 kJ/mol 326s 326s print APOL energy 10 (solvated-pentane) end 326s Global net APOL energy = 1.447900211546E+01 kJ/mol 326s 326s print APOL energy 11 (solvated-propane) end 326s Global net APOL energy = 1.192358496286E+01 kJ/mol 326s ---------------------------------------- 326s CLEANING UP AND SHUTTING DOWN... 326s Destroying force arrays. 326s No energy arrays to destroy. 326s Destroying multigrid structures. 326s Destroying finite element structures. 326s Destroying 11 molecules 326s Final memory usage: 0.001 MB total, 2.267 MB high water 326s 326s 326s Thanks for using APBS! 326s 326s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 326s *** PASSED *** 326s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 326s *** PASSED *** 326s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 326s *** PASSED *** 326s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 326s *** PASSED *** 326s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 326s *** PASSED *** 326s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 326s *** PASSED *** 326s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 326s *** PASSED *** 326s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 326s *** PASSED *** 326s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 326s *** PASSED *** 326s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 326s *** PASSED *** 326s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 326s *** PASSED *** 326s Elapsed time: 13.088512 seconds 326s -------------------------------------------------------------------------------- 326s Total elapsed time: 13.088512 seconds 326s Test results have been logged 326s -------------------------------------------------------------------------------- 326s -------------------------------------------------------------------------------- 326s Testing input file 1d7h-dmso-mol.in 326s 337s Checking for intermediate energies in input file alkanes.out 337s EXPECTED COMPUTED: 11 337s EXPECTED EXPECTED: 11 337s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 337s 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'] 337s COMPUTED RESULT 14.39739455792 337s COMPUTED RESULT 12.08346456826 337s COMPUTED RESULT 13.54016672221 337s COMPUTED RESULT 9.363673200142 337s COMPUTED RESULT 9.422717598546 337s COMPUTED RESULT 16.40068943201 337s COMPUTED RESULT 13.23144287435 337s COMPUTED RESULT 7.894367190329 337s COMPUTED RESULT 14.49633815052 337s COMPUTED RESULT 14.47900211546 337s COMPUTED RESULT 11.92358496286 337s Running tests for FKBP section 337s BINARY: /usr/bin/apbs 337s INPUT: 1d7h-dmso-mol.in 337s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 337s 337s ---------------------------------------------------------------------- 337s APBS -- Adaptive Poisson-Boltzmann Solver 337s Version APBS 3.4.1 337s 337s Nathan A. Baker (nathan.baker@pnnl.gov) 337s Pacific Northwest National Laboratory 337s 337s Additional contributing authors listed in the code documentation. 337s 337s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 337s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 337s Northwest Division for the U.S. Department of Energy. 337s 337s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 337s Portions Copyright (c) 2002-2020, Nathan A. Baker. 337s Portions Copyright (c) 1999-2002, The Regents of the University of California. 337s Portions Copyright (c) 1995, Michael Holst. 337s All rights reserved. 337s 337s Redistribution and use in source and binary forms, with or without 337s modification, are permitted provided that the following conditions are met: 337s 337s * Redistributions of source code must retain the above copyright notice, this 337s list of conditions and the following disclaimer. 337s 337s * Redistributions in binary form must reproduce the above copyright notice, 337s this list of conditions and the following disclaimer in the documentation 337s and/or other materials provided with the distribution. 337s 337s * Neither the name of the developer nor the names of its contributors may be 337s used to endorse or promote products derived from this software without 337s specific prior written permission. 337s 337s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 337s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 337s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 337s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 337s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 337s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 337s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 337s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 337s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 337s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 337s ---------------------------------------------------------------------- 337s APBS uses FETK (the Finite Element ToolKit) to solve the 337s Poisson-Boltzmann equation numerically. FETK is a portable collection 337s of finite element modeling class libraries developed by the Michael Holst 337s research group and written in an object-oriented form of C. FEtk is 337s designed to solve general coupled systems of nonlinear partial differential 337s equations using adaptive finite element methods, inexact Newton methods, 337s and algebraic multilevel methods. More information about FEtk may be found 337s at . 337s ---------------------------------------------------------------------- 337s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 337s Aqua is a modified form of the Holst group PMG library 337s which has been modified by Patrice Koehl 337s for improved efficiency and 337s memory usage when solving the Poisson-Boltzmann equation. 337s ---------------------------------------------------------------------- 337s Please cite your use of APBS as: 337s 337s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 337s nanosystems: application to microtubules and the ribosome. Proc. 337s Natl. Acad. Sci. USA 98, 10037-10041 2001. 337s 337s 337s This executable compiled on Jan 3 2025 at 11:01:42 337s 337s Parsing input file 1d7h-dmso-mol.in... 337s rank 0 size 1... 337s Parsed input file. 337s Got paths for 3 molecules 337s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 1673 atoms 337s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 337s Net charge 9.91e-01 e 337s Reading PQR-format atom data from dmso-min.pqr. 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 10 atoms 337s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 337s Net charge 2.78e-17 e 337s Reading PQR-format atom data from 1d7h-min.pqr. 337s 1663 atoms 337s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 337s Net charge 9.91e-01 e 337s Preparing to run 12 PBE calculations. 337s ---------------------------------------- 337s CALCULATION #1 (complex-solv-coarse): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 30.4176 A 337s Current memory usage: 122.059 MB total, 122.059 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 1.500 x 1.500 x 1.500 337s Grid lengths: 96.000 x 96.000 x 96.000 337s Grid center: (25.875, 18.349, 19.112) 337s Multigrid levels: 5 337s Molecule ID: 1 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 1.060899690259E+04 kJ/mol 337s Calculating forces... 337s [focusFillBound()]: WARNING: 337s Unusually large potential values 337s detected on the focusing boundary! 337s Convergence not guaranteed for NPBE/NRPBE calculations! 337s 337s ---------------------------------------- 337s CALCULATION #2 (complex-solv-fine): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 30.4176 A 337s Current memory usage: 122.059 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.225 x 0.225 x 0.225 337s Grid lengths: 14.400 x 14.400 x 14.400 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 1 337s Linearized traditional PBE 337s Boundary conditions from focusing 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 4.276523673491E+04 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #3 (complex-ref-coarse): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 4.87072 A 337s Current memory usage: 122.059 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 1.500 x 1.500 x 1.500 337s Grid lengths: 96.000 x 96.000 x 96.000 337s Grid center: (25.875, 18.349, 19.112) 337s Multigrid levels: 5 337s Molecule ID: 1 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 2.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 1.399234956777E+04 kJ/mol 337s Calculating forces... 337s [focusFillBound()]: WARNING: 337s Unusually large potential values 337s detected on the focusing boundary! 337s Convergence not guaranteed for NPBE/NRPBE calculations! 337s 337s ---------------------------------------- 337s CALCULATION #4 (complex-ref-fine): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 4.87072 A 337s Current memory usage: 122.059 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.225 x 0.225 x 0.225 337s Grid lengths: 14.400 x 14.400 x 14.400 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 1 337s Linearized traditional PBE 337s Boundary conditions from focusing 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 2.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 4.610066575192E+04 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 30.4176 A 337s Current memory usage: 62.428 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 1.500 x 1.500 x 1.500 337s Grid lengths: 96.000 x 96.000 x 96.000 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 2 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 3.961107503213E+01 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #6 (dmso-solv-fine): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 30.4176 A 337s Current memory usage: 62.428 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.225 x 0.225 x 0.225 337s Grid lengths: 14.400 x 14.400 x 14.400 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 2 337s Linearized traditional PBE 337s Boundary conditions from focusing 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 7.121048606059E+02 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 4.87072 A 337s Current memory usage: 62.428 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 1.500 x 1.500 x 1.500 337s Grid lengths: 96.000 x 96.000 x 96.000 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 2 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 2.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 6.751571424823E+01 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #8 (dmso-ref-fine): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 4.87072 A 337s Current memory usage: 62.428 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.225 x 0.225 x 0.225 337s Grid lengths: 14.400 x 14.400 x 14.400 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 2 337s Linearized traditional PBE 337s Boundary conditions from focusing 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 2.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 7.339101343121E+02 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 30.4176 A 337s Current memory usage: 121.736 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 1.500 x 1.500 x 1.500 337s Grid lengths: 96.000 x 96.000 x 96.000 337s Grid center: (25.875, 18.349, 19.112) 337s Multigrid levels: 5 337s Molecule ID: 3 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 1.058410584089E+04 kJ/mol 337s Calculating forces... 337s [focusFillBound()]: WARNING: 337s Unusually large potential values 337s detected on the focusing boundary! 337s Convergence not guaranteed for NPBE/NRPBE calculations! 337s 337s ---------------------------------------- 337s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 30.4176 A 337s Current memory usage: 121.736 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.225 x 0.225 x 0.225 337s Grid lengths: 14.400 x 14.400 x 14.400 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 3 337s Linearized traditional PBE 337s Boundary conditions from focusing 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 4.205385249581E+04 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 4.87072 A 337s Current memory usage: 121.736 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 1.500 x 1.500 x 1.500 337s Grid lengths: 96.000 x 96.000 x 96.000 337s Grid center: (25.875, 18.349, 19.112) 337s Multigrid levels: 5 337s Molecule ID: 3 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 2.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 1.395961902233E+04 kJ/mol 337s Calculating forces... 337s [focusFillBound()]: WARNING: 337s Unusually large potential values 337s detected on the focusing boundary! 337s Convergence not guaranteed for NPBE/NRPBE calculations! 337s 337s ---------------------------------------- 337s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 4.87072 A 337s Current memory usage: 121.736 MB total, 221.696 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.225 x 0.225 x 0.225 337s Grid lengths: 14.400 x 14.400 x 14.400 337s Grid center: (17.751, 17.770, 20.492) 337s Multigrid levels: 5 337s Molecule ID: 3 337s Linearized traditional PBE 337s Boundary conditions from focusing 337s 2 ion species (0.010 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 2.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 4.538248433997E+04 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s PRINT STATEMENTS 337s 337s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 337s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 337s Global net ELEC energy = -3.335429017008E+03 kJ/mol 337s 337s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 337s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 337s Global net ELEC energy = -2.180527370616E+01 kJ/mol 337s 337s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 337s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 337s Global net ELEC energy = -3.328631844166E+03 kJ/mol 337s 337s 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 337s Local net energy (PE 0) = 1.500810086373E+01 kJ/mol 337s Global net ELEC energy = 1.500810086373E+01 kJ/mol 337s ---------------------------------------- 337s CLEANING UP AND SHUTTING DOWN... 337s Destroying force arrays. 337s No energy arrays to destroy. 337s Destroying multigrid structures. 337s Destroying finite element structures. 337s Destroying 3 molecules 337s Final memory usage: 0.001 MB total, 221.696 MB high water 337s 337s 337s Thanks for using APBS! 337s 337s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 337s *** PASSED *** 337s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 337s *** PASSED *** 337s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 337s *** PASSED *** 337s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 337s *** PASSED *** 337s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 337s *** PASSED *** 337s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 337s *** PASSED *** 337s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 337s *** PASSED *** 337s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 337s *** PASSED *** 337s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 337s *** PASSED *** 337s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 337s *** PASSED *** 337s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 337s *** PASSED *** 337s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 337s *** PASSED *** 337s Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) 337s *** PASSED *** 337s Elapsed time: 10.246562 seconds 337s -------------------------------------------------------------------------------- 337s -------------------------------------------------------------------------------- 337s Testing input file 1d7h-dmso-smol.in 337s 347s Checking for intermediate energies in input file 1d7h-dmso-mol.out 347s EXPECTED COMPUTED: 16 347s EXPECTED EXPECTED: 16 347s 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, 15.00810086373] 347s 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'] 347s COMPUTED RESULT 10608.99690259 347s COMPUTED RESULT 42765.23673491 347s COMPUTED RESULT 13992.34956777 347s COMPUTED RESULT 46100.66575192 347s COMPUTED RESULT 39.61107503213 347s COMPUTED RESULT 712.1048606059 347s COMPUTED RESULT 67.51571424823 347s COMPUTED RESULT 733.9101343121 347s COMPUTED RESULT 10584.10584089 347s COMPUTED RESULT 42053.85249581 347s COMPUTED RESULT 13959.61902233 347s COMPUTED RESULT 45382.48433997 347s COMPUTED RESULT -3335.429017008 347s COMPUTED RESULT -21.80527370616 347s COMPUTED RESULT -3328.631844166 347s COMPUTED RESULT 15.00810086373 347s BINARY: /usr/bin/apbs 347s INPUT: 1d7h-dmso-smol.in 347s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 347s asc_getToken: Error occurred (bailing out). 347s Vio_scanf: Format problem with input. 347s 347s 347s ---------------------------------------------------------------------- 347s APBS -- Adaptive Poisson-Boltzmann Solver 347s Version APBS 3.4.1 347s 347s Nathan A. Baker (nathan.baker@pnnl.gov) 347s Pacific Northwest National Laboratory 347s 347s Additional contributing authors listed in the code documentation. 347s 347s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 347s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 347s Northwest Division for the U.S. Department of Energy. 347s 347s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 347s Portions Copyright (c) 2002-2020, Nathan A. Baker. 347s Portions Copyright (c) 1999-2002, The Regents of the University of California. 347s Portions Copyright (c) 1995, Michael Holst. 347s All rights reserved. 347s 347s Redistribution and use in source and binary forms, with or without 347s modification, are permitted provided that the following conditions are met: 347s 347s * Redistributions of source code must retain the above copyright notice, this 347s list of conditions and the following disclaimer. 347s 347s * Redistributions in binary form must reproduce the above copyright notice, 347s this list of conditions and the following disclaimer in the documentation 347s and/or other materials provided with the distribution. 347s 347s * Neither the name of the developer nor the names of its contributors may be 347s used to endorse or promote products derived from this software without 347s specific prior written permission. 347s 347s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 347s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 347s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 347s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 347s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 347s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 347s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 347s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 347s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 347s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 347s ---------------------------------------------------------------------- 347s APBS uses FETK (the Finite Element ToolKit) to solve the 347s Poisson-Boltzmann equation numerically. FETK is a portable collection 347s of finite element modeling class libraries developed by the Michael Holst 347s research group and written in an object-oriented form of C. FEtk is 347s designed to solve general coupled systems of nonlinear partial differential 347s equations using adaptive finite element methods, inexact Newton methods, 347s and algebraic multilevel methods. More information about FEtk may be found 347s at . 347s ---------------------------------------------------------------------- 347s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 347s Aqua is a modified form of the Holst group PMG library 347s which has been modified by Patrice Koehl 347s for improved efficiency and 347s memory usage when solving the Poisson-Boltzmann equation. 347s ---------------------------------------------------------------------- 347s Please cite your use of APBS as: 347s 347s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 347s nanosystems: application to microtubules and the ribosome. Proc. 347s Natl. Acad. Sci. USA 98, 10037-10041 2001. 347s 347s 347s This executable compiled on Jan 3 2025 at 11:01:42 347s 347s Parsing input file 1d7h-dmso-smol.in... 347s rank 0 size 1... 347s Parsed input file. 347s Got paths for 3 molecules 347s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 347s asc_getToken: Error occurred (bailing out). 347s Vio_scanf: Format problem with input. 347s 1673 atoms 347s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 347s Net charge 9.91e-01 e 347s Reading PQR-format atom data from dmso-min.pqr. 347s asc_getToken: Error occurred (bailing out). 347s Vio_scanf: Format problem with input. 347s 10 atoms 347s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 347s Net charge 2.78e-17 e 347s Reading PQR-format atom data from 1d7h-min.pqr. 347s 1663 atoms 347s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 347s Net charge 9.91e-01 e 347s Preparing to run 12 PBE calculations. 347s ---------------------------------------- 347s CALCULATION #1 (complex-solv-coarse): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 30.4176 A 347s Current memory usage: 122.059 MB total, 122.059 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 1.500 x 1.500 x 1.500 347s Grid lengths: 96.000 x 96.000 x 96.000 347s Grid center: (25.875, 18.349, 19.112) 347s Multigrid levels: 5 347s Molecule ID: 1 347s Linearized traditional PBE 347s Multiple Debye-Huckel sphere boundary conditions 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 78.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 1.074948704824E+04 kJ/mol 347s Calculating forces... 347s [focusFillBound()]: WARNING: 347s Unusually large potential values 347s detected on the focusing boundary! 347s Convergence not guaranteed for NPBE/NRPBE calculations! 347s 347s ---------------------------------------- 347s CALCULATION #2 (complex-solv-fine): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 30.4176 A 347s Current memory usage: 122.059 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 0.225 x 0.225 x 0.225 347s Grid lengths: 14.400 x 14.400 x 14.400 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 1 347s Linearized traditional PBE 347s Boundary conditions from focusing 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 78.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 4.289487256481E+04 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s CALCULATION #3 (complex-ref-coarse): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 4.87072 A 347s Current memory usage: 122.059 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 1.500 x 1.500 x 1.500 347s Grid lengths: 96.000 x 96.000 x 96.000 347s Grid center: (25.875, 18.349, 19.112) 347s Multigrid levels: 5 347s Molecule ID: 1 347s Linearized traditional PBE 347s Multiple Debye-Huckel sphere boundary conditions 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 2.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 1.399234956777E+04 kJ/mol 347s Calculating forces... 347s [focusFillBound()]: WARNING: 347s Unusually large potential values 347s detected on the focusing boundary! 347s Convergence not guaranteed for NPBE/NRPBE calculations! 347s 347s ---------------------------------------- 347s CALCULATION #4 (complex-ref-fine): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length:Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 347s *** PASSED *** 347s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 347s *** PASSED *** 347s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 347s *** PASSED *** 347s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 347s *** PASSED *** 347s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 347s *** PASSED *** 347s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 347s *** PASSED *** 347s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 347s *** PASSED *** 347s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 347s *** PASSED *** 347s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 347s *** PASSED *** 347s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 347s *** PASSED *** 347s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 347s *** PASSED *** 347s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 347s *** PASSED *** 347s Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) 347s *** PASSED *** 347s Elapsed time: 10.26041 seconds 347s -------------------------------------------------------------------------------- 347s -------------------------------------------------------------------------------- 347s Testing input file 1d7i-dss-mol.in 347s 347s 4.87072 A 347s Current memory usage: 122.059 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 0.225 x 0.225 x 0.225 347s Grid lengths: 14.400 x 14.400 x 14.400 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 1 347s Linearized traditional PBE 347s Boundary conditions from focusing 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 2.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 4.610066575192E+04 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 30.4176 A 347s Current memory usage: 62.428 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 1.500 x 1.500 x 1.500 347s Grid lengths: 96.000 x 96.000 x 96.000 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 2 347s Linearized traditional PBE 347s Multiple Debye-Huckel sphere boundary conditions 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 78.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 3.719709905887E+01 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s CALCULATION #6 (dmso-solv-fine): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 30.4176 A 347s Current memory usage: 62.428 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 0.225 x 0.225 x 0.225 347s Grid lengths: 14.400 x 14.400 x 14.400 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 2 347s Linearized traditional PBE 347s Boundary conditions from focusing 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 78.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 7.125747080979E+02 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 4.87072 A 347s Current memory usage: 62.428 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 1.500 x 1.500 x 1.500 347s Grid lengths: 96.000 x 96.000 x 96.000 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 2 347s Linearized traditional PBE 347s Multiple Debye-Huckel sphere boundary conditions 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 2.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 6.751571424823E+01 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s CALCULATION #8 (dmso-ref-fine): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 4.87072 A 347s Current memory usage: 62.428 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 0.225 x 0.225 x 0.225 347s Grid lengths: 14.400 x 14.400 x 14.400 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 2 347s Linearized traditional PBE 347s Boundary conditions from focusing 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 2.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 7.339101343121E+02 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 30.4176 A 347s Current memory usage: 121.736 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 1.500 x 1.500 x 1.500 347s Grid lengths: 96.000 x 96.000 x 96.000 347s Grid center: (25.875, 18.349, 19.112) 347s Multigrid levels: 5 347s Molecule ID: 3 347s Linearized traditional PBE 347s Multiple Debye-Huckel sphere boundary conditions 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 78.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 1.071654753674E+04 kJ/mol 347s Calculating forces... 347s [focusFillBound()]: WARNING: 347s Unusually large potential values 347s detected on the focusing boundary! 347s Convergence not guaranteed for NPBE/NRPBE calculations! 347s 347s ---------------------------------------- 347s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 30.4176 A 347s Current memory usage: 121.736 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 0.225 x 0.225 x 0.225 347s Grid lengths: 14.400 x 14.400 x 14.400 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 3 347s Linearized traditional PBE 347s Boundary conditions from focusing 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 78.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 4.218178203716E+04 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 4.87072 A 347s Current memory usage: 121.736 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 1.500 x 1.500 x 1.500 347s Grid lengths: 96.000 x 96.000 x 96.000 347s Grid center: (25.875, 18.349, 19.112) 347s Multigrid levels: 5 347s Molecule ID: 3 347s Linearized traditional PBE 347s Multiple Debye-Huckel sphere boundary conditions 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 2.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 1.395961902233E+04 kJ/mol 347s Calculating forces... 347s [focusFillBound()]: WARNING: 347s Unusually large potential values 347s detected on the focusing boundary! 347s Convergence not guaranteed for NPBE/NRPBE calculations! 347s 347s ---------------------------------------- 347s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 347s Setting up problem... 347s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 347s Debye length: 4.87072 A 347s Current memory usage: 121.736 MB total, 221.696 MB high water 347s Using linear spline charge discretization. 347s Grid dimensions: 65 x 65 x 65 347s Grid spacings: 0.225 x 0.225 x 0.225 347s Grid lengths: 14.400 x 14.400 x 14.400 347s Grid center: (17.751, 17.770, 20.492) 347s Multigrid levels: 5 347s Molecule ID: 3 347s Linearized traditional PBE 347s Boundary conditions from focusing 347s 2 ion species (0.010 M ionic strength): 347s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 347s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 347s Solute dielectric: 2.000 347s Solvent dielectric: 2.000 347s Using "molecular" surface definition;harmonic average smoothing 347s Solvent probe radius: 0.000 A 347s Temperature: 300.000 K 347s Electrostatic energies will be calculated 347s Total electrostatic energy = 4.538248433997E+04 kJ/mol 347s Calculating forces... 347s ---------------------------------------- 347s PRINT STATEMENTS 347s 347s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 347s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 347s Global net ELEC energy = -3.205793187109E+03 kJ/mol 347s 347s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 347s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 347s Global net ELEC energy = -2.133542621421E+01 kJ/mol 347s 347s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 347s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 347s Global net ELEC energy = -3.200702302816E+03 kJ/mol 347s 347s 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 347s Local net energy (PE 0) = 1.624454192074E+01 kJ/mol 347s Global net ELEC energy = 1.624454192074E+01 kJ/mol 347s ---------------------------------------- 347s CLEANING UP AND SHUTTING DOWN... 347s Destroying force arrays. 347s No energy arrays to destroy. 347s Destroying multigrid structures. 347s Destroying finite element structures. 347s Destroying 3 molecules 347s Final memory usage: 0.001 MB total, 221.696 MB high water 347s 347s 347s Thanks for using APBS! 347s 357s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 357s *** PASSED *** 357s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 357s *** PASSED *** 357s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 357s *** PASSED *** 357s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 357s *** PASSED *** 357s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 357s *** PASSED *** 357s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 357s *** PASSED *** 357s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 357s *** PASSED *** 357s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 357s *** PASSED *** 357s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 357s *** PASSED *** 357s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 357s *** PASSED *** 357s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 357s *** PASSED *** 357s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 357s *** PASSED *** 357s Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) 357s *** PASSED *** 357s Elapsed time: 10.637755 seconds 357s -------------------------------------------------------------------------------- 357s -------------------------------------------------------------------------------- 358s Testing input file 1d7i-dss-smol.in 358s 358s Checking for intermediate energies in input file 1d7h-dmso-smol.out 358s EXPECTED COMPUTED: 16 358s EXPECTED EXPECTED: 16 358s 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, 16.24454192074] 358s 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'] 358s COMPUTED RESULT 10749.48704824 358s COMPUTED RESULT 42894.87256481 358s COMPUTED RESULT 13992.34956777 358s COMPUTED RESULT 46100.66575192 358s COMPUTED RESULT 37.19709905887 358s COMPUTED RESULT 712.5747080979 358s COMPUTED RESULT 67.51571424823 358s COMPUTED RESULT 733.9101343121 358s COMPUTED RESULT 10716.54753674 358s COMPUTED RESULT 42181.78203716 358s COMPUTED RESULT 13959.61902233 358s COMPUTED RESULT 45382.48433997 358s COMPUTED RESULT -3205.793187109 358s COMPUTED RESULT -21.33542621421 358s COMPUTED RESULT -3200.702302816 358s COMPUTED RESULT 16.24454192074 358s BINARY: /usr/bin/apbs 358s INPUT: 1d7i-dss-mol.in 358s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 358s asc_getToken: Error occurred (bailing out). 358s Vio_scanf: Format problem with input. 358s 358s 358s ---------------------------------------------------------------------- 358s APBS -- Adaptive Poisson-Boltzmann Solver 358s Version APBS 3.4.1 358s 358s Nathan A. Baker (nathan.baker@pnnl.gov) 358s Pacific Northwest National Laboratory 358s 358s Additional contributing authors listed in the code documentation. 358s 358s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 358s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 358s Northwest Division for the U.S. Department of Energy. 358s 358s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 358s Portions Copyright (c) 2002-2020, Nathan A. Baker. 358s Portions Copyright (c) 1999-2002, The Regents of the University of California. 358s Portions Copyright (c) 1995, Michael Holst. 358s All rights reserved. 358s 358s Redistribution and use in source and binary forms, with or without 358s modification, are permitted provided that the following conditions are met: 358s 358s * Redistributions of source code must retain the above copyright notice, this 358s list of conditions and the following disclaimer. 358s 358s * Redistributions in binary form must reproduce the above copyright notice, 358s this list of conditions and the following disclaimer in the documentation 358s and/or other materials provided with the distribution. 358s 358s * Neither the name of the developer nor the names of its contributors may be 358s used to endorse or promote products derived from this software without 358s specific prior written permission. 358s 358s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 358s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 358s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 358s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 358s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 358s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 358s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 358s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 358s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 358s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 358s ---------------------------------------------------------------------- 358s APBS uses FETK (the Finite Element ToolKit) to solve the 358s Poisson-Boltzmann equation numerically. FETK is a portable collection 358s of finite element modeling class libraries developed by the Michael Holst 358s research group and written in an object-oriented form of C. FEtk is 358s designed to solve general coupled systems of nonlinear partial differential 358s equations using adaptive finite element methods, inexact Newton methods, 358s and algebraic multilevel methods. More information about FEtk may be found 358s at . 358s ---------------------------------------------------------------------- 358s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 358s Aqua is a modified form of the Holst group PMG library 358s which has been modified by Patrice Koehl 358s for improved efficiency and 358s memory usage when solving the Poisson-Boltzmann equation. 358s ---------------------------------------------------------------------- 358s Please cite your use of APBS as: 358s 358s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 358s nanosystems: application to microtubules and the ribosome. Proc. 358s Natl. Acad. Sci. USA 98, 10037-10041 2001. 358s 358s 358s This executable compiled on Jan 3 2025 at 11:01:42 358s 358s Parsing input file 1d7i-dss-mol.in... 358s rank 0 size 1... 358s Parsed input file. 358s Got paths for 3 molecules 358s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 358s asc_getToken: Error occurred (bailing out). 358s Vio_scanf: Format problem with input. 358s 1677 atoms 358s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 358s Net charge 9.91e-01 e 358s Reading PQR-format atom data from dss-min.pqr. 358s asc_getToken: Error occurred (bailing out). 358s Vio_scanf: Format problem with input. 358s 14 atoms 358s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 358s Net charge -8.33e-17 e 358s Reading PQR-format atom data from 1d7i-min.pqr. 358s 1663 atoms 358s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 358s Net charge 9.91e-01 e 358s Preparing to run 12 PBE calculations. 358s ---------------------------------------- 358s CALCULATION #1 (complex-solv-coarse): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 30.4176 A 358s Current memory usage: 122.425 MB total, 122.425 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 1.500 x 1.500 x 1.500 358s Grid lengths: 96.000 x 96.000 x 96.000 358s Grid center: (25.264, 18.988, 19.122) 358s Multigrid levels: 5 358s Molecule ID: 1 358s Linearized traditional PBE 358s Multiple Debye-Huckel sphere boundary conditions 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 78.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 9.160578033846E+03 kJ/mol 358s Calculating forces... 358s [focusFillBound()]: WARNING: 358s Unusually large potential values 358s detected on the focusing boundary! 358s Convergence not guaranteed for NPBE/NRPBE calculations! 358s 358s ---------------------------------------- 358s CALCULATION #2 (complex-solv-fine): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 30.4176 A 358s Current memory usage: 122.425 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 0.225 x 0.225 x 0.225 358s Grid lengths: 14.400 x 14.400 x 14.400 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 1 358s Linearized traditional PBE 358s Boundary conditions from focusing 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 78.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 3.955701871716E+04 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s CALCULATION #3 (complex-ref-coarse): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 4.87072 A 358s Current memory usage: 122.425 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 1.500 x 1.500 x 1.500 358s Grid lengths: 96.000 x 96.000 x 96.000 358s Grid center: (25.264, 18.988, 19.122) 358s Multigrid levels: 5 358s Molecule ID: 1 358s Linearized traditional PBE 358s Multiple Debye-Huckel sphere boundary conditions 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 2.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 1.264965939588E+04 kJ/mol 358s Calculating forces... 358s [focusFillBound()]: WARNING: 358s Unusually large potential values 358s detected on the focusing boundary! 358s Convergence not guaranteed for NPBE/NRPBE calculations! 358s 358s ---------------------------------------- 358s CALCULATION #4 (complex-ref-fine): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 4.87072 A 358s Current memory usage: 122.425 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 0.225 x 0.225 x 0.225 358s Grid lengths: 14.400 x 14.400 x 14.400 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 1 358s Linearized traditional PBE 358s Boundary conditions from focusing 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 2.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 4.301801664829E+04 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s CALCULATION #5 (dss-solv-coarse): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 30.4176 A 358s Current memory usage: 62.528 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 1.500 x 1.500 x 1.500 358s Grid lengths: 96.000 x 96.000 x 96.000 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 2 358s Linearized traditional PBE 358s Multiple Debye-Huckel sphere boundary conditions 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 78.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 9.431133325426E+01 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s CALCULATION #6 (dss-solv-fine): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 30.4176 A 358s Current memory usage: 62.528 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 0.225 x 0.225 x 0.225 358s Grid lengths: 14.400 x 14.400 x 14.400 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 2 358s Linearized traditional PBE 358s Boundary conditions from focusing 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 78.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 1.677348113184E+03 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s CALCULATION #7 (dss-ref-coarse): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 4.87072 A 358s Current memory usage: 62.528 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 1.500 x 1.500 x 1.500 358s Grid lengths: 96.000 x 96.000 x 96.000 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 2 358s Linearized traditional PBE 358s Multiple Debye-Huckel sphere boundary conditions 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 2.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 1.171079106781E+02 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s CALCULATION #8 (dss-ref-fine): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 4.87072 A 358s Current memory usage: 62.528 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 0.225 x 0.225 x 0.225 358s Grid lengths: 14.400 x 14.400 x 14.400 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 2 358s Linearized traditional PBE 358s Boundary conditions from focusing 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 2.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 1.697869784185E+03 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 30.4176 A 358s Current memory usage: 121.977 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 1.500 x 1.500 x 1.500 358s Grid lengths: 96.000 x 96.000 x 96.000 358s Grid center: (25.264, 18.988, 19.122) 358s Multigrid levels: 5 358s Molecule ID: 3 358s Linearized traditional PBE 358s Multiple Debye-Huckel sphere boundary conditions 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 78.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 9.040108332204E+03 kJ/mol 358s Calculating forces... 358s [focusFillBound()]: WARNING: 358s Unusually large potential values 358s detected on the focusing boundary! 358s Convergence not guaranteed for NPBE/NRPBE calculations! 358s 358s ---------------------------------------- 358s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 30.4176 A 358s Current memory usage: 121.977 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 0.225 x 0.225 x 0.225 358s Grid lengths: 14.400 x 14.400 x 14.400 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 3 358s Linearized traditional PBE 358s Boundary conditions from focusing 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 78.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 3.787747796627E+04 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 4.87072 A 358s Current memory usage: 121.977 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 1.500 x 1.500 x 1.500 358s Grid lengths: 96.000 x 96.000 x 96.000 358s Grid center: (25.264, 18.988, 19.122) 358s Multigrid levels: 5 358s Molecule ID: 3 358s Linearized traditional PBE 358s Multiple Debye-Huckel sphere boundary conditions 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 2.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 1.252495566243E+04 kJ/mol 358s Calculating forces... 358s [focusFillBound()]: WARNING: 358s Unusually large potential values 358s detected on the focusing boundary! 358s Convergence not guaranteed for NPBE/NRPBE calculations! 358s 358s ---------------------------------------- 358s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 358s Setting up problem... 358s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 358s Debye length: 4.87072 A 358s Current memory usage: 121.977 MB total, 222.305 MB high water 358s Using linear spline charge discretization. 358s Grid dimensions: 65 x 65 x 65 358s Grid spacings: 0.225 x 0.225 x 0.225 358s Grid lengths: 14.400 x 14.400 x 14.400 358s Grid center: (17.340, 19.211, 20.503) 358s Multigrid levels: 5 358s Molecule ID: 3 358s Linearized traditional PBE 358s Boundary conditions from focusing 358s 2 ion species (0.010 M ionic strength): 358s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 358s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 358s Solute dielectric: 2.000 358s Solvent dielectric: 2.000 358s Using "molecular" surface definition; no smoothing 358s Solvent probe radius: 0.000 A 358s Temperature: 300.000 K 358s Electrostatic energies will be calculated 358s Total electrostatic energy = 4.133237922574E+04 kJ/mol 358s Calculating forces... 358s ---------------------------------------- 358s PRINT STATEMENTS 358s 358s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 358s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 358s Global net ELEC energy = -3.460997931137E+03 kJ/mol 358s 358s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 358s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 358s Global net ELEC energy = -2.052167100108E+01 kJ/mol 358s 358s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 358s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 358s Global net ELEC energy = -3.454901259473E+03 kJ/mol 358s 358s 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 358s Local net energy (PE 0) = 1.442499933664E+01 kJ/mol 358s Global net ELEC energy = 1.442499933664E+01 kJ/mol 358s ---------------------------------------- 358s CLEANING UP AND SHUTTING DOWN... 358s Destroying force arrays. 358s No energy arrays to destroy. 358s Destroying multigrid structures. 358s Destroying finite element structures. 358s Destroying 3 molecules 358s Final memory usage: 0.001 MB total, 222.305 MB high water 358s 358s 358s Thanks for using APBS! 358s 367s Checking for intermediate energies in input file 1d7i-dss-mol.out 367s EXPECTED COMPUTED: 16 367s EXPECTED EXPECTED: 16 367s 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, 14.42499933664] 367s 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'] 367s COMPUTED RESULT 9160.578033846 367s COMPUTED RESULT 39557.01871716 367s COMPUTED RESULT 12649.65939588 367s COMPUTED RESULT 43018.01664829 367s COMPUTED RESULT 94.31133325426 367s COMPUTED RESULT 1677.348113184 367s COMPUTED RESULT 117.1079106781 367s COMPUTED RESULT 1697.869784185 367s COMPUTED RESULT 9040.108332204 367s COMPUTED RESULT 37877.47796627 367s COMPUTED RESULT 12524.95566243 367s COMPUTED RESULT 41332.37922574 367s COMPUTED RESULT -3460.997931137 367s COMPUTED RESULT -20.52167100108 367s COMPUTED RESULT -3454.901259473 367s COMPUTED RESULT 14.42499933664 367s BINARY: /usr/bin/apbs 367s INPUT: 1d7i-dss-smol.in 367s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 367s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 367s *** PASSED *** 367s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 367s *** PASSED *** 367s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 367s *** PASSED *** 367s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 367s *** PASSED *** 367s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 367s *** PASSED *** 367s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 367s *** PASSED *** 367s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 367s *** PASSED *** 367s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 367s *** PASSED *** 367s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 367s *** PASSED *** 367s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 367s *** PASSED *** 367s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 367s *** PASSED *** 367s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 367s *** PASSED *** 367s Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) 367s *** PASSED *** 367s Elapsed time: 9.787353 seconds 367s -------------------------------------------------------------------------------- 367s Total elapsed time: 40.93208 seconds 367s Test results have been logged 367s -------------------------------------------------------------------------------- 367s -------------------------------------------------------------------------------- 367s Testing input file apbs-mol.in 367s 367s asc_getToken: Error occurred (bailing out). 367s Vio_scanf: Format problem with input. 367s 367s 367s ---------------------------------------------------------------------- 367s APBS -- Adaptive Poisson-Boltzmann Solver 367s Version APBS 3.4.1 367s 367s Nathan A. Baker (nathan.baker@pnnl.gov) 367s Pacific Northwest National Laboratory 367s 367s Additional contributing authors listed in the code documentation. 367s 367s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 367s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 367s Northwest Division for the U.S. Department of Energy. 367s 367s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 367s Portions Copyright (c) 2002-2020, Nathan A. Baker. 367s Portions Copyright (c) 1999-2002, The Regents of the University of California. 367s Portions Copyright (c) 1995, Michael Holst. 367s All rights reserved. 367s 367s Redistribution and use in source and binary forms, with or without 367s modification, are permitted provided that the following conditions are met: 367s 367s * Redistributions of source code must retain the above copyright notice, this 367s list of conditions and the following disclaimer. 367s 367s * Redistributions in binary form must reproduce the above copyright notice, 367s this list of conditions and the following disclaimer in the documentation 367s and/or other materials provided with the distribution. 367s 367s * Neither the name of the developer nor the names of its contributors may be 367s used to endorse or promote products derived from this software without 367s specific prior written permission. 367s 367s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 367s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 367s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 367s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 367s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 367s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 367s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 367s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 367s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 367s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 367s ---------------------------------------------------------------------- 367s APBS uses FETK (the Finite Element ToolKit) to solve the 367s Poisson-Boltzmann equation numerically. FETK is a portable collection 367s of finite element modeling class libraries developed by the Michael Holst 367s research group and written in an object-oriented form of C. FEtk is 367s designed to solve general coupled systems of nonlinear partial differential 367s equations using adaptive finite element methods, inexact Newton methods, 367s and algebraic multilevel methods. More information about FEtk may be found 367s at . 367s ---------------------------------------------------------------------- 367s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 367s Aqua is a modified form of the Holst group PMG library 367s which has been modified by Patrice Koehl 367s for improved efficiency and 367s memory usage when solving the Poisson-Boltzmann equation. 367s ---------------------------------------------------------------------- 367s Please cite your use of APBS as: 367s 367s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 367s nanosystems: application to microtubules and the ribosome. Proc. 367s Natl. Acad. Sci. USA 98, 10037-10041 2001. 367s 367s 367s This executable compiled on Jan 3 2025 at 11:01:42 367s 367s Parsing input file 1d7i-dss-smol.in... 367s rank 0 size 1... 367s Parsed input file. 367s Got paths for 3 molecules 367s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 367s asc_getToken: Error occurred (bailing out). 367s Vio_scanf: Format problem with input. 367s 1677 atoms 367s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 367s Net charge 9.91e-01 e 367s Reading PQR-format atom data from dss-min.pqr. 367s asc_getToken: Error occurred (bailing out). 367s Vio_scanf: Format problem with input. 367s 14 atoms 367s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 367s Net charge -8.33e-17 e 367s Reading PQR-format atom data from 1d7i-min.pqr. 367s 1663 atoms 367s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 367s Net charge 9.91e-01 e 367s Preparing to run 12 PBE calculations. 367s ---------------------------------------- 367s CALCULATION #1 (complex-solv-coarse): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 30.4176 A 367s Current memory usage: 122.425 MB total, 122.425 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 1.500 x 1.500 x 1.500 367s Grid lengths: 96.000 x 96.000 x 96.000 367s Grid center: (25.264, 18.988, 19.122) 367s Multigrid levels: 5 367s Molecule ID: 1 367s Linearized traditional PBE 367s Multiple Debye-Huckel sphere boundary conditions 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 78.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 9.634884642408E+03 kJ/mol 367s Calculating forces... 367s [focusFillBound()]: WARNING: 367s Unusually large potential values 367s detected on the focusing boundary! 367s Convergence not guaranteed for NPBE/NRPBE calculations! 367s 367s ---------------------------------------- 367s CALCULATION #2 (complex-solv-fine): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 30.4176 A 367s Current memory usage: 122.425 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 0.225 x 0.225 x 0.225 367s Grid lengths: 14.400 x 14.400 x 14.400 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 1 367s Linearized traditional PBE 367s Boundary conditions from focusing 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 78.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 4.003177540425E+04 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s CALCULATION #3 (complex-ref-coarse): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 4.87072 A 367s Current memory usage: 122.425 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 1.500 x 1.500 x 1.500 367s Grid lengths: 96.000 x 96.000 x 96.000 367s Grid center: (25.264, 18.988, 19.122) 367s Multigrid levels: 5 367s Molecule ID: 1 367s Linearized traditional PBE 367s Multiple Debye-Huckel sphere boundary conditions 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 2.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 1.264965939588E+04 kJ/mol 367s Calculating forces... 367s [focusFillBound()]: WARNING: 367s Unusually large potential values 367s detected on the focusing boundary! 367s Convergence not guaranteed for NPBE/NRPBE calculations! 367s 367s ---------------------------------------- 367s CALCULATION #4 (complex-ref-fine): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 4.87072 A 367s Current memory usage: 122.425 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 0.225 x 0.225 x 0.225 367s Grid lengths: 14.400 x 14.400 x 14.400 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 1 367s Linearized traditional PBE 367s Boundary conditions from focusing 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 2.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 4.301801664829E+04 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s CALCULATION #5 (dss-solv-coarse): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 30.4176 A 367s Current memory usage: 62.528 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 1.500 x 1.500 x 1.500 367s Grid lengths: 96.000 x 96.000 x 96.000 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 2 367s Linearized traditional PBE 367s Multiple Debye-Huckel sphere boundary conditions 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 78.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 7.942232645345E+01 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s CALCULATION #6 (dss-solv-fine): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 30.4176 A 367s Current memory usage: 62.528 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 0.225 x 0.225 x 0.225 367s Grid lengths: 14.400 x 14.400 x 14.400 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 2 367s Linearized traditional PBE 367s Boundary conditions from focusing 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 78.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 1.677798535473E+03 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s CALCULATION #7 (dss-ref-coarse): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 4.87072 A 367s Current memory usage: 62.528 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 1.500 x 1.500 x 1.500 367s Grid lengths: 96.000 x 96.000 x 96.000 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 2 367s Linearized traditional PBE 367s Multiple Debye-Huckel sphere boundary conditions 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 2.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 1.171079106781E+02 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s CALCULATION #8 (dss-ref-fine): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 4.87072 A 367s Current memory usage: 62.528 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 0.225 x 0.225 x 0.225 367s Grid lengths: 14.400 x 14.400 x 14.400 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 2 367s Linearized traditional PBE 367s Boundary conditions from focusing 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 2.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 1.697869784185E+03 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 30.4176 A 367s Current memory usage: 121.977 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 1.500 x 1.500 x 1.500 367s Grid lengths: 96.000 x 96.000 x 96.000 367s Grid center: (25.264, 18.988, 19.122) 367s Multigrid levels: 5 367s Molecule ID: 3 367s Linearized traditional PBE 367s Multiple Debye-Huckel sphere boundary conditions 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 78.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 9.507068451372E+03 kJ/mol 367s Calculating forces... 367s [focusFillBound()]: WARNING: 367s Unusually large potential values 367s detected on the focusing boundary! 367s Convergence not guaranteed for NPBE/NRPBE calculations! 367s 367s ---------------------------------------- 367s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 30.4176 A 367s Current memory usage: 121.977 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 0.225 x 0.225 x 0.225 367s Grid lengths: 14.400 x 14.400 x 14.400 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 3 367s Linearized traditional PBE 367s Boundary conditions from focusing 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 78.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 3.835075772299E+04 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 4.87072 A 367s Current memory usage: 121.977 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 1.500 x 1.500 x 1.500 367s Grid lengths: 96.000 x 96.000 x 96.000 367s Grid center: (25.264, 18.988, 19.122) 367s Multigrid levels: 5 367s Molecule ID: 3 367s Linearized traditional PBE 367s Multiple Debye-Huckel sphere boundary conditions 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 2.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 1.252495566243E+04 kJ/mol 367s Calculating forces... 367s [focusFillBound()]: WARNING: 367s Unusually large potential values 367s detected on the focusing boundary! 367s Convergence not guaranteed for NPBE/NRPBE calculations! 367s 367s ---------------------------------------- 367s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 367s Setting up problem... 367s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 367s Debye length: 4.87072 A 367s Current memory usage: 121.977 MB total, 222.305 MB high water 367s Using linear spline charge discretization. 367s Grid dimensions: 65 x 65 x 65 367s Grid spacings: 0.225 x 0.225 x 0.225 367s Grid lengths: 14.400 x 14.400 x 14.400 367s Grid center: (17.340, 19.211, 20.503) 367s Multigrid levels: 5 367s Molecule ID: 3 367s Linearized traditional PBE 367s Boundary conditions from focusing 367s 2 ion species (0.010 M ionic strength): 367s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 367s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 367s Solute dielectric: 2.000 367s Solvent dielectric: 2.000 367s Using "molecular" surface definition;harmonic average smoothing 367s Solvent probe radius: 0.000 A 367s Temperature: 300.000 K 367s Electrostatic energies will be calculated 367s Total electrostatic energy = 4.133237922574E+04 kJ/mol 367s Calculating forces... 367s ---------------------------------------- 367s PRINT STATEMENTS 367s 367s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 367s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 367s Global net ELEC energy = -2.986241244040E+03 kJ/mol 367s 367s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 367s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 367s Global net ELEC energy = -2.007124871262E+01 kJ/mol 367s 367s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 367s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 367s Global net ELEC energy = -2.981621502756E+03 kJ/mol 367s 367s 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 367s Local net energy (PE 0) = 1.545150742843E+01 kJ/mol 367s Global net ELEC energy = 1.545150742843E+01 kJ/mol 367s ---------------------------------------- 367s CLEANING UP AND SHUTTING DOWN... 367s Destroying force arrays. 367s No energy arrays to destroy. 367s Destroying multigrid structures. 367s Destroying finite element structures. 367s Destroying 3 molecules 367s Final memory usage: 0.001 MB total, 222.305 MB high water 367s 367s 367s Thanks for using APBS! 367s 376s Checking for intermediate energies in input file 1d7i-dss-smol.out 376s EXPECTED COMPUTED: 16 376s EXPECTED EXPECTED: 16 376s 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, 15.45150742843] 376s 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'] 376s COMPUTED RESULT 9634.884642408 376s COMPUTED RESULT 40031.77540425 376s COMPUTED RESULT 12649.65939588 376s COMPUTED RESULT 43018.01664829 376s COMPUTED RESULT 79.42232645345 376s COMPUTED RESULT 1677.798535473 376s COMPUTED RESULT 117.1079106781 376s COMPUTED RESULT 1697.869784185 376s COMPUTED RESULT 9507.068451372 376s COMPUTED RESULT 38350.75772299 376s COMPUTED RESULT 12524.95566243 376s COMPUTED RESULT 41332.37922574 376s COMPUTED RESULT -2986.24124404 376s COMPUTED RESULT -20.07124871262 376s COMPUTED RESULT -2981.621502756 376s COMPUTED RESULT 15.45150742843 376s Running tests for hca-bind section 376s BINARY: /usr/bin/apbs 376s INPUT: apbs-mol.in 376s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 376s asc_getToken: Error occurred (bailing out). 376s Vio_scanf: Format problem with input. 376s 376s 376s ---------------------------------------------------------------------- 376s APBS -- Adaptive Poisson-Boltzmann Solver 376s Version APBS 3.4.1 376s 376s Nathan A. Baker (nathan.baker@pnnl.gov) 376s Pacific Northwest National Laboratory 376s 376s Additional contributing authors listed in the code documentation. 376s 376s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 376s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 376s Northwest Division for the U.S. Department of Energy. 376s 376s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 376s Portions Copyright (c) 2002-2020, Nathan A. Baker. 376s Portions Copyright (c) 1999-2002, The Regents of the University of California. 376s Portions Copyright (c) 1995, Michael Holst. 376s All rights reserved. 376s 376s Redistribution and use in source and binary forms, with or without 376s modification, are permitted provided that the following conditions are met: 376s 376s * Redistributions of source code must retain the above copyright notice, this 376s list of conditions and the following disclaimer. 376s 376s * Redistributions in binary form must reproduce the above copyright notice, 376s this list of conditions and the following disclaimer in the documentation 376s and/or other materials provided with the distribution. 376s 376s * Neither the name of the developer nor the names of its contributors may be 376s used to endorse or promote products derived from this software without 376s specific prior written permission. 376s 376s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 376s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 376s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 376s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 376s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 376s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 376s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 376s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 376s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 376s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 376s ---------------------------------------------------------------------- 376s APBS uses FETK (the Finite Element ToolKit) to solve the 376s Poisson-Boltzmann equation numerically. FETK is a portable collection 376s of finite element modeling class libraries developed by the Michael Holst 376s research group and written in an object-oriented form of C. FEtk is 376s designed to solve general coupled systems of nonlinear partial differential 376s equations using adaptive finite element methods, inexact Newton methods, 376s and algebraic multilevel methods. More information about FEtk may be found 376s at . 376s ---------------------------------------------------------------------- 376s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 376s Aqua is a modified form of the Holst group PMG library 376s which has been modified by Patrice Koehl 376s for improved efficiency and 376s memory usage when solving the Poisson-Boltzmann equation. 376s ---------------------------------------------------------------------- 376s Please cite your use of APBS as: 376s 376s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 376s nanosystems: application to microtubules and the ribosome. Proc. 376s Natl. Acad. Sci. USA 98, 10037-10041 2001. 376s 376s 376s This executable compiled on Jan 3 2025 at 11:01:42 376s 376s Parsing input file apbs-mol.in... 376s rank 0 size 1... 376s Parsed input file. 376s Got paths for 3 molecules 376s Reading PQR-format atom data from acet.pqr. 376s asc_getToken: Error occurred (bailing out). 376s Vio_scanf: Format problem with input. 376s 18 atoms 376s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 376s Net charge -1.00e+00 e 376s Reading PQR-format atom data from hca.pqr. 376s asc_getToken: Error occurred (bailing out). 376s Vio_scanf: Format problem with input. 376s 2482 atoms 376s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 376s Net charge 1.00e+00 e 376s Reading PQR-format atom data from complex.pqr. 376s 2500 atoms 376s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 376s Net charge -1.02e-14 e 376s Preparing to run 9 PBE calculations. 376s ---------------------------------------- 376s CALCULATION #1 (acet): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 62.727 MB total, 62.727 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 1.500 x 1.500 x 1.500 376s Grid lengths: 96.000 x 96.000 x 96.000 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 1 376s Linearized traditional PBE 376s Single Debye-Huckel sphere boundary conditions 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 2.213600726771E+02 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #2 (acet): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 62.727 MB total, 123.701 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 0.581 x 0.581 x 0.581 376s Grid lengths: 37.181 x 37.181 x 37.181 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 1 376s Linearized traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 1.825764811255E+03 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #3 (acet): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 62.727 MB total, 123.701 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 0.225 x 0.225 x 0.225 376s Grid lengths: 14.400 x 14.400 x 14.400 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 1 376s Linearized traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 6.458471211905E+03 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #4 (hca): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 146.516 MB total, 146.516 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 1.500 x 1.500 x 1.500 376s Grid lengths: 96.000 x 96.000 x 96.000 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 2 376s Linearized traditional PBE 376s Single Debye-Huckel sphere boundary conditions 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 2.093606095527E+04 kJ/mol 376s Calculating forces... 376s [focusFillBound()]: WARNING: 376s Unusually large potential values 376s detected on the focusing boundary! 376s Convergence not guaranteed for NPBE/NRPBE calculations! 376s 376s ---------------------------------------- 376s CALCULATION #5 (hca): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 146.516 MB total, 245.092 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 0.581 x 0.581 x 0.581 376s Grid lengths: 37.181 x 37.181 x 37.181 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 2 376s Linearized traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 1.515433544464E+05 kJ/mol 376s Calculating forces... 376s [focusFillBound()]: WARNING: 376s Unusually large potential values 376s detected on the focusing boundary! 376s Convergence not guaranteed for NPBE/NRPBE calculations! 376s 376s ---------------------------------------- 376s CALCULATION #6 (hca): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 146.516 MB total, 245.092 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 0.225 x 0.225 x 0.225 376s Grid lengths: 14.400 x 14.400 x 14.400 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 2 376s Linearized traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 1.786369323561E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #7 (complex): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 146.926 MB total, 245.092 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 1.500 x 1.500 x 1.500 376s Grid lengths: 96.000 x 96.000 x 96.000 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 3 376s Linearized traditional PBE 376s Single Debye-Huckel sphere boundary conditions 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 2.105322784838E+04 kJ/mol 376s Calculating forces... 376s [focusFillBound()]: WARNING: 376s Unusually large potential values 376s detected on the focusing boundary! 376s Convergence not guaranteed for NPBE/NRPBE calculations! 376s 376s ---------------------------------------- 376s CALCULATION #8 (complex): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 146.926 MB total, 245.725 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 0.581 x 0.581 x 0.581 376s Grid lengths: 37.181 x 37.181 x 37.181 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 3 376s Linearized traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 1.533304996252E+05 kJ/mol 376s Calculating forces... 376s [focusFillBound()]: WARNING: 376s Unusually large potential values 376s detected on the focusing boundary! 376s Convergence not guaranteed for NPBE/NRPBE calculations! 376s 376s ---------------------------------------- 376s CALCULATION #9 (complex): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 0 A 376s Current memory usage: 146.926 MB total, 245.725 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 65 x 65 x 65 376s Grid spacings: 0.225 x 0.225 x 0.225 376s Grid lengths: 14.400 x 14.400 x 14.400 376s Grid center: (-6.028, 3.898, 15.179) 376s Multigrid levels: 5 376s Molecule ID: 3 376s Linearized traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.000 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.540 376s Using "molecular" surface definition; no smoothing 376s Solvent probe radius: 0.000 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 1.850429388099E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s PRINT STATEMENTS 376s 376s print energy 3 (complex) - 1 (acet) - 2 (hca) end 376s Local net energy (PE 0) = -5.246475812684E+01 kJ/mol 376s Global net ELEC energy = -5.246475812684E+01 kJ/mol 376s ---------------------------------------- 376s CLEANING UP AND SHUTTING DOWN... 376s Destroying force arrays. 376s No energy arrays to destroy. 376s Destroying multigrid structures. 376s Destroying finite element structures. 376s Destroying 3 molecules 376s Final memory usage: 0.001 MB total, 245.725 MB high water 376s 376s 376s Thanks for using APBS! 376s 376s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 376s *** PASSED *** 376s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 376s *** PASSED *** 376s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 376s *** PASSED *** 376s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 376s *** PASSED *** 376s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 376s *** PASSED *** 376s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 376s *** PASSED *** 376s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 376s *** PASSED *** 376s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 376s *** PASSED *** 376s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 376s *** PASSED *** 376s Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) 376s *** PASSED *** 376s Elapsed time: 9.012928 seconds 376s -------------------------------------------------------------------------------- 376s -------------------------------------------------------------------------------- 376s Testing input file apbs-smol.in 376s 385s Checking for intermediate energies in input file apbs-mol.out 385s EXPECTED COMPUTED: 10 385s EXPECTED EXPECTED: 10 385s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] 385s 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'] 385s COMPUTED RESULT 221.3600726771 385s COMPUTED RESULT 1825.764811255 385s COMPUTED RESULT 6458.471211905 385s COMPUTED RESULT 20936.06095527 385s COMPUTED RESULT 151543.3544464 385s COMPUTED RESULT 178636.9323561 385s COMPUTED RESULT 21053.22784838 385s COMPUTED RESULT 153330.4996252 385s COMPUTED RESULT 185042.9388099 385s COMPUTED RESULT -52.46475812684 385s BINARY: /usr/bin/apbs 385s INPUT: apbs-smol.in 385s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 385s asc_getToken: Error occurred (bailing out). 385s Vio_scanf: Format problem with input. 385s 385s 385s ---------------------------------------------------------------------- 385s APBS -- Adaptive Poisson-Boltzmann Solver 385s Version APBS 3.4.1 385s 385s Nathan A. Baker (nathan.baker@pnnl.gov) 385s Pacific Northwest National Laboratory 385s 385s Additional contributing authors listed in the code documentation. 385s 385s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 385s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 385s Northwest Division for the U.S. Department of Energy. 385s 385s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 385s Portions Copyright (c) 2002-2020, Nathan A. Baker. 385s Portions Copyright (c) 1999-2002, The Regents of the University of California. 385s Portions Copyright (c) 1995, Michael Holst. 385s All rights reserved. 385s 385s Redistribution and use in source and binary forms, with or without 385s modification, are permitted provided that the following conditions are met: 385s 385s * Redistributions of source code must retain the above copyright notice, this 385s list of conditions and the following disclaimer. 385s 385s * Redistributions in binary form must reproduce the above copyright notice, 385s this list of conditions and the following disclaimer in the documentation 385s and/or other materials provided with the distribution. 385s 385s * Neither the name of the developer nor the names of its contributors may be 385s used to endorse or promote products derived from this software without 385s specific prior written permission. 385s 385s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 385s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 385s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 385s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 385s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 385s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 385s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 385s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 385s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 385s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 385s ---------------------------------------------------------------------- 385s APBS uses FETK (the Finite Element ToolKit) to solve the 385s Poisson-Boltzmann equation numerically. FETK is a portable collection 385s of finite element modeling class libraries developed by the Michael Holst 385s research group and written in an object-oriented form of C. FEtk is 385s designed to solve general coupled systems of nonlinear partial differential 385s equations using adaptive finite element methods, inexact Newton methods, 385s and algebraic multilevel methods. More information about FEtk may be found 385s at . 385s ---------------------------------------------------------------------- 385s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 385s Aqua is a modified form of the Holst group PMG library 385s which has been modified by Patrice Koehl 385s for improved efficiency and 385s memory usage when solving the Poisson-Boltzmann equation. 385s ---------------------------------------------------------------------- 385s Please cite your use of APBS as: 385s 385s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 385s nanosystems: application to microtubules and the ribosome. Proc. 385s Natl. Acad. Sci. USA 98, 10037-10041 2001. 385s 385s 385s This executable compiled on Jan 3 2025 at 11:01:42 385s 385s Parsing input file apbs-smol.in... 385s rank 0 size 1... 385s Parsed input file. 385s Got paths for 3 molecules 385s Reading PQR-format atom data from acet.pqr. 385s asc_getToken: Error occurred (bailing out). 385s Vio_scanf: Format problem with input. 385s 18 atoms 385s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 385s Net charge -1.00e+00 e 385s Reading PQR-format atom data from hca.pqr. 385s asc_getToken: Error occurred (bailing out). 385s Vio_scanf: Format problem with input. 385s 2482 atoms 385s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 385s Net charge 1.00e+00 e 385s Reading PQR-format atom data from complex.pqr. 385s 2500 atoms 385s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 385s Net charge -1.02e-14 e 385s Preparing to run 9 PBE calculations. 385s ---------------------------------------- 385s CALCULATION #1 (acet): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 62.727 MB total, 62.727 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 1.500 x 1.500 x 1.500 385s Grid lengths: 96.000 x 96.000 x 96.000 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 1 385s Linearized traditional PBE 385s Single Debye-Huckel sphere boundary conditions 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 1.884888131017E+02 kJ/mol 385s Calculating forces... 385s ---------------------------------------- 385s CALCULATION #2 (acet): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 62.727 MB total, 123.701 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 0.581 x 0.581 x 0.581 385s Grid lengths: 37.181 x 37.181 x 37.181 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 1 385s Linearized traditional PBE 385s Boundary conditions from focusing 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 1.820045922544E+03 kJ/mol 385s Calculating forces... 385s ---------------------------------------- 385s CALCULATION #3 (acet): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 62.727 MB total, 123.701 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 0.225 x 0.225 x 0.225 385s Grid lengths: 14.400 x 14.400 x 14.400 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 1 385s Linearized traditional PBE 385s Boundary conditions from focusing 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 6.460002606908E+03 kJ/mol 385s Calculating forces... 385s ---------------------------------------- 385s CALCULATION #4 (hca): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 146.516 MB total, 146.516 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 1.500 x 1.500 x 1.500 385s Grid lengths: 96.000 x 96.000 x 96.000 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 2 385s Linearized traditional PBE 385s Single Debye-Huckel sphere boundary conditions 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 2.189161497021E+04 kJ/mol 385s Calculating forces... 385s [focusFillBound()]: WARNING: 385s Unusually large potential values 385s detected on the focusing boundary! 385s Convergence not guaranteed for NPBE/NRPBE calculations! 385s 385s ---------------------------------------- 385s CALCULATION #5 (hca): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 146.516 MB total, 245.092 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 0.581 x 0.581 x 0.581 385s Grid lengths: 37.181 x 37.181 x 37.181 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 2 385s Linearized traditional PBE 385s Boundary conditions from focusing 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 1.520000494925E+05 kJ/mol 385s Calculating forces... 385s [focusFillBound()]: WARNING: 385s Unusually large potential values 385s detected on the focusing boundary! 385s Convergence not guaranteed for NPBE/NRPBE calculations! 385s 385s ---------------------------------------- 385s CALCULATION #6 (hca): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 146.516 MB total, 245.092 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 0.225 x 0.225 x 0.225 385s Grid lengths: 14.400 x 14.400 x 14.400 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 2 385s Linearized traditional PBE 385s Boundary conditions from focusing 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 1.790436191580E+05 kJ/mol 385s Calculating forces... 385s ---------------------------------------- 385s CALCULATION #7 (complex): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 146.926 MB total, 245.092 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 1.500 x 1.500 x 1.500 385s Grid lengths: 96.000 x 96.000 x 96.000 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 3 385s Linearized traditional PBE 385s Single Debye-Huckel sphere boundary conditions 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 2.195842512312E+04 kJ/mol 385s Calculating forces... 385s [focusFillBound()]: WARNING: 385s Unusually large potential values 385s detected on the focusing boundary! 385s Convergence not guaranteed for NPBE/NRPBE calculations! 385s 385s ---------------------------------------- 385s CALCULATION #8 (complex): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 146.926 MB total, 245.725 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 0.581 x 0.581 x 0.581 385s Grid lengths: 37.181 x 37.181 x 37.181 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 3 385s Linearized traditional PBE 385s Boundary conditions from focusing 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 1.537771604355E+05 kJ/mol 385s Calculating forces... 385s [focusFillBound()]: WARNING: 385s Unusually large potential values 385s detected on the focusing boundary! 385s Convergence not guaranteed for NPBE/NRPBE calculations! 385s 385s ---------------------------------------- 385s CALCULATION #9 (complex): MULTIGRID 385s Setting up problem... 385s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 385s Debye length: 0 A 385s Current memory usage: 146.926 MB total, 245.725 MB high water 385s Using linear spline charge discretization. 385s Grid dimensions: 65 x 65 x 65 385s Grid spacings: 0.225 x 0.225 x 0.225 385s Grid lengths: 14.400 x 14.400 x 14.400 385s Grid center: (-6.028, 3.898, 15.179) 385s Multigrid levels: 5 385s Molecule ID: 3 385s Linearized traditional PBE 385s Boundary conditions from focusing 385s 2 ion species (0.000 M ionic strength): 385s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 385s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 385s Solute dielectric: 2.000 385s Solvent dielectric: 78.540 385s Using "molecular" surface definition;harmonic average smoothing 385s Solvent probe radius: 0.000 A 385s Temperature: 298.150 K 385s Electrostatic energies will be calculated 385s Total electrostatic energy = 1.854495619747E+05 kJ/mol 385s Calculating forces... 385s ---------------------------------------- 385s PRINT STATEMENTS 385s 385s print energy 3 (complex) - 1 (acet) - 2 (hca) end 385s Local net energy (PE 0) = -5.405979017059E+01 kJ/mol 385s Global net ELEC energy = -5.405979017059E+01 kJ/mol 385s ---------------------------------------- 385s CLEANING UP AND SHUTTING DOWN... 385s Destroying force arrays. 385s No energy arrays to destroy. 385s Destroying multigrid structures. 385s Destroying finite element structures. 385s Destroying 3 molecules 385s Final memory usage: 0.001 MB total, 245.725 MB high water 385s 385s 385s Thanks for using APBS! 385s 385s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 385s *** PASSED *** 385s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 385s *** PASSED *** 385s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 385s *** PASSED *** 385s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 385s *** PASSED *** 385s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 385s *** PASSED *** 385s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 385s *** PASSED *** 385s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 385s *** PASSED *** 385s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 385s *** PASSED *** 385s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 385s *** PASSED *** 385s Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) 385s *** PASSED *** 385s Elapsed time: 9.06413 seconds 385s -------------------------------------------------------------------------------- 385s Total elapsed time: 18.077058 seconds 385s Test results have been logged 385s -------------------------------------------------------------------------------- 385s -------------------------------------------------------------------------------- 385s Testing input file apbs-mol.in 385s 388s Checking for intermediate energies in input file apbs-smol.out 388s EXPECTED COMPUTED: 10 388s EXPECTED EXPECTED: 10 388s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] 388s 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'] 388s COMPUTED RESULT 188.4888131017 388s COMPUTED RESULT 1820.045922544 388s COMPUTED RESULT 6460.002606908 388s COMPUTED RESULT 21891.61497021 388s COMPUTED RESULT 152000.0494925 388s COMPUTED RESULT 179043.619158 388s COMPUTED RESULT 21958.42512312 388s COMPUTED RESULT 153777.1604355 388s COMPUTED RESULT 185449.5619747 388s COMPUTED RESULT -54.05979017059 388s Running tests for ionize section 388s BINARY: /usr/bin/apbs 388s INPUT: apbs-mol.in 388s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 388s Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 388s *** PASSED *** 388s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 388s *** PASSED *** 388s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 388s *** PASSED *** 388s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 388s *** PASSED *** 388s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 388s *** PASSED *** 388s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 388s *** PASSED *** 388s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 388s *** PASSED *** 388s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 388s *** PASSED *** 388s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 388s *** PASSED *** 388s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 388s *** PASSED *** 388s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 388s *** PASSED *** 388s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 388s *** PASSED *** 388s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 388s *** PASSED *** 388s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 388s *** PASSED *** 388s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 388s *** PASSED *** 388s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 388s *** PASSED *** 388s Elapsed time: 2.238929 seconds 388s -------------------------------------------------------------------------------- 388s -------------------------------------------------------------------------------- 388s Testing input file apbs-smol.in 388s 388s asc_getToken: Error occurred (bailing out). 388s Vio_scanf: Format problem with input. 388s 388s 388s ---------------------------------------------------------------------- 388s APBS -- Adaptive Poisson-Boltzmann Solver 388s Version APBS 3.4.1 388s 388s Nathan A. Baker (nathan.baker@pnnl.gov) 388s Pacific Northwest National Laboratory 388s 388s Additional contributing authors listed in the code documentation. 388s 388s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 388s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 388s Northwest Division for the U.S. Department of Energy. 388s 388s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 388s Portions Copyright (c) 2002-2020, Nathan A. Baker. 388s Portions Copyright (c) 1999-2002, The Regents of the University of California. 388s Portions Copyright (c) 1995, Michael Holst. 388s All rights reserved. 388s 388s Redistribution and use in source and binary forms, with or without 388s modification, are permitted provided that the following conditions are met: 388s 388s * Redistributions of source code must retain the above copyright notice, this 388s list of conditions and the following disclaimer. 388s 388s * Redistributions in binary form must reproduce the above copyright notice, 388s this list of conditions and the following disclaimer in the documentation 388s and/or other materials provided with the distribution. 388s 388s * Neither the name of the developer nor the names of its contributors may be 388s used to endorse or promote products derived from this software without 388s specific prior written permission. 388s 388s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 388s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 388s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 388s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 388s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 388s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 388s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 388s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 388s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 388s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 388s ---------------------------------------------------------------------- 388s APBS uses FETK (the Finite Element ToolKit) to solve the 388s Poisson-Boltzmann equation numerically. FETK is a portable collection 388s of finite element modeling class libraries developed by the Michael Holst 388s research group and written in an object-oriented form of C. FEtk is 388s designed to solve general coupled systems of nonlinear partial differential 388s equations using adaptive finite element methods, inexact Newton methods, 388s and algebraic multilevel methods. More information about FEtk may be found 388s at . 388s ---------------------------------------------------------------------- 388s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 388s Aqua is a modified form of the Holst group PMG library 388s which has been modified by Patrice Koehl 388s for improved efficiency and 388s memory usage when solving the Poisson-Boltzmann equation. 388s ---------------------------------------------------------------------- 388s Please cite your use of APBS as: 388s 388s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 388s nanosystems: application to microtubules and the ribosome. Proc. 388s Natl. Acad. Sci. USA 98, 10037-10041 2001. 388s 388s 388s This executable compiled on Jan 3 2025 at 11:01:42 388s 388s Parsing input file apbs-mol.in... 388s rank 0 size 1... 388s Parsed input file. 388s Got paths for 3 molecules 388s Reading PQR-format atom data from acetic-acid.pqr. 388s asc_getToken: Error occurred (bailing out). 388s Vio_scanf: Format problem with input. 388s 8 atoms 388s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 388s Net charge -1.67e-16 e 388s Reading PQR-format atom data from acetate.pqr. 388s asc_getToken: Error occurred (bailing out). 388s Vio_scanf: Format problem with input. 388s 8 atoms 388s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 388s Net charge -1.00e+00 e 388s Reading PQR-format atom data from proton.pqr. 388s 1 atoms 388s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 388s Net charge 1.00e+00 e 388s Preparing to run 12 PBE calculations. 388s ---------------------------------------- 388s CALCULATION #1 (acetic-solv): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 7.76163 A 388s Current memory usage: 61.598 MB total, 61.598 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.188 x 0.188 x 0.188 388s Grid lengths: 12.000 x 12.000 x 12.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 1 388s Linearized traditional PBE 388s Multiple Debye-Huckel sphere boundary conditions 388s 2 ion species (0.150 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 78.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 5.823898055191E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #2 (acetic-solv): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 7.76163 A 388s Current memory usage: 61.598 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.094 x 0.094 x 0.094 388s Grid lengths: 6.000 x 6.000 x 6.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 1 388s Linearized traditional PBE 388s Boundary conditions from focusing 388s 2 ion species (0.150 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 78.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 9.793274462353E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #3 (acetic-ref): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 0 A 388s Current memory usage: 61.422 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.188 x 0.188 x 0.188 388s Grid lengths: 12.000 x 12.000 x 12.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 1 388s Linearized traditional PBE 388s Multiple Debye-Huckel sphere boundary conditions 388s 2 ion species (0.000 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 2.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 5.846917564309E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #4 (acetic-ref): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 0 A 388s Current memory usage: 61.422 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.094 x 0.094 x 0.094 388s Grid lengths: 6.000 x 6.000 x 6.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 1 388s Linearized traditional PBE 388s Boundary conditions from focusing 388s 2 ion species (0.000 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 2.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 9.815953282539E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #5 (acetate-solv): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 7.76163 A 388s Current memory usage: 61.598 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.188 x 0.188 x 0.188 388s Grid lengths: 12.000 x 12.000 x 12.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 2 388s Linearized traditional PBE 388s Multiple Debye-Huckel sphere boundary conditions 388s 2 ion species (0.150 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 78.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 8.219846763777E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #6 (acetate-solv): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 7.76163 A 388s Current memory usage: 61.598 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.094 x 0.094 x 0.094 388s Grid lengths: 6.000 x 6.000 x 6.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 2 388s Linearized traditional PBE 388s Boundary conditions from focusing 388s 2 ion species (0.150 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 78.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 1.392741988698E+04 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #7 (acetate-ref): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 0 A 388s Current memory usage: 61.422 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.188 x 0.188 x 0.188 388s Grid lengths: 12.000 x 12.000 x 12.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 2 388s Linearized traditional PBE 388s Multiple Debye-Huckel sphere boundary conditions 388s 2 ion species (0.000 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 2.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 8.420373979905E+03 kJ/mol 388s Calculating forces... 388s [focusFillBound()]: WARNING: 388s Unusually large potential values 388s detected on the focusing boundary! 388s Convergence not guaranteed for NPBE/NRPBE calculations! 388s 388s ---------------------------------------- 388s CALCULATION #8 (acetate-ref): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 0 A 388s Current memory usage: 61.422 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.094 x 0.094 x 0.094 388s Grid lengths: 6.000 x 6.000 x 6.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 2 388s Linearized traditional PBE 388s Boundary conditions from focusing 388s 2 ion species (0.000 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 2.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 1.412716615065E+04 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #9 (proton-solv): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 7.76163 A 388s Current memory usage: 61.412 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.188 x 0.188 x 0.188 388s Grid lengths: 12.000 x 12.000 x 12.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 3 388s Linearized traditional PBE 388s Multiple Debye-Huckel sphere boundary conditions 388s 2 ion species (0.150 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 78.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 3.862359524598E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #10 (proton-solv): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 7.76163 A 388s Current memory usage: 61.412 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.094 x 0.094 x 0.094 388s Grid lengths: 6.000 x 6.000 x 6.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 3 388s Linearized traditional PBE 388s Boundary conditions from focusing 388s 2 ion species (0.150 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 78.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 6.288156251610E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s CALCULATION #11 (proton-ref): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 0 A 388s Current memory usage: 61.373 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.188 x 0.188 x 0.188 388s Grid lengths: 12.000 x 12.000 x 12.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 3 388s Linearized traditional PBE 388s Multiple Debye-Huckel sphere boundary conditions 388s 2 ion species (0.000 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 2.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 4.162533113906E+03 kJ/mol 388s Calculating forces... 388s [focusFillBound()]: WARNING: 388s Unusually large potential values 388s detected on the focusing boundary! 388s Convergence not guaranteed for NPBE/NRPBE calculations! 388s 388s ---------------------------------------- 388s CALCULATION #12 (proton-ref): MULTIGRID 388s Setting up problem... 388s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 388s Debye length: 0 A 388s Current memory usage: 61.373 MB total, 122.404 MB high water 388s Using linear spline charge discretization. 388s Grid dimensions: 65 x 65 x 65 388s Grid spacings: 0.094 x 0.094 x 0.094 388s Grid lengths: 6.000 x 6.000 x 6.000 388s Grid center: (0.000, -0.154, 1.287) 388s Multigrid levels: 5 388s Molecule ID: 3 388s Linearized traditional PBE 388s Boundary conditions from focusing 388s 2 ion species (0.000 M ionic strength): 388s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 388s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 388s Solute dielectric: 2.000 388s Solvent dielectric: 2.000 388s Using "molecular" surface definition; no smoothing 388s Solvent probe radius: 0.000 A 388s Temperature: 293.000 K 388s Electrostatic energies will be calculated 388s Total electrostatic energy = 6.585616091973E+03 kJ/mol 388s Calculating forces... 388s ---------------------------------------- 388s PRINT STATEMENTS 388s 388s print energy 1 (acetic-solv) - 2 (acetic-ref) end 388s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 388s Global net ELEC energy = -2.267882018629E+01 kJ/mol 388s 388s print energy 3 (acetate-solv) - 4 (acetate-ref) end 388s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 388s Global net ELEC energy = -1.997462636633E+02 kJ/mol 388s 388s print energy 5 (proton-solv) - 6 (proton-ref) end 388s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 388s Global net ELEC energy = -2.974598403628E+02 kJ/mol 388s 388s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 388s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 388s Global net ELEC energy = -4.745272838398E+02 kJ/mol 388s ---------------------------------------- 388s CLEANING UP AND SHUTTING DOWN... 388s Destroying force arrays. 388s No energy arrays to destroy. 388s Destroying multigrid structures. 388s Destroying finite element structures. 388s Destroying 3 molecules 388s Final memory usage: 0.001 MB total, 122.404 MB high water 388s 388s 388s Thanks for using APBS! 388s 390s Checking for intermediate energies in input file apbs-mol.out 390s EXPECTED COMPUTED: 16 390s EXPECTED EXPECTED: 16 390s 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] 390s 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'] 390s COMPUTED RESULT 5823.898055191 390s COMPUTED RESULT 9793.274462353 390s COMPUTED RESULT 5846.917564309 390s COMPUTED RESULT 9815.953282539 390s COMPUTED RESULT 8219.846763777 390s COMPUTED RESULT 13927.41988698 390s COMPUTED RESULT 8420.373979905 390s COMPUTED RESULT 14127.16615065 390s COMPUTED RESULT 3862.359524598 390s COMPUTED RESULT 6288.15625161 390s COMPUTED RESULT 4162.533113906 390s COMPUTED RESULT 6585.616091973 390s COMPUTED RESULT -22.67882018629 390s COMPUTED RESULT -199.7462636633 390s COMPUTED RESULT -297.4598403628 390s COMPUTED RESULT -474.5272838398 390s BINARY: /usr/bin/apbs 390s INPUT: apbs-smol.in 390s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 390s asc_getToken: Error occurred (bailing out). 390s Vio_scanf: Format problem with input. 390s 390s 390s ---------------------------------------------------------------------- 390s APBS -- Adaptive Poisson-Boltzmann Solver 390s Version APBS 3.4.1 390s 390s Nathan A. Baker (nathan.baker@pnnl.gov) 390s Pacific Northwest National Laboratory 390s 390s Additional contributing authors listed in the code documentation. 390s 390s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 390s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 390s Northwest Division for the U.S. Department of Energy. 390s 390s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 390s Portions Copyright (c) 2002-2020, Nathan A. Baker. 390s Portions Copyright (c) 1999-2002, The Regents of the University of California. 390s Portions Copyright (c) 1995, Michael Holst. 390s All rights reserved. 390s 390s Redistribution and use in source and binary forms, with or without 390s modification, are permitted provided that the following conditions are met: 390s 390s * Redistributions of source code must retain the above copyright notice, this 390s list of conditions and the following disclaimer. 390s 390s * Redistributions in binary form must reproduce the above copyright notice, 390s this list of conditions and the following disclaimer in the documentation 390s and/or other materials provided with the distribution. 390s 390s * Neither the name of the developer nor the names of its contributors may be 390s used to endorse or promote products derived from this software without 390s specific prior written permission. 390s 390s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 390s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 390s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 390s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 390s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 390s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 390s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 390s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 390s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 390s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 390s ---------------------------------------------------------------------- 390s APBS uses FETK (the Finite Element ToolKit) to solve the 390s Poisson-Boltzmann equation numerically. FETK is a portable collection 390s of finite element modeling class libraries developed by the Michael Holst 390s research group and written in an object-oriented form of C. FEtk is 390s designed to solve general coupled systems of nonlinear partial differential 390s equations using adaptive finite element methods, inexact Newton methods, 390s and algebraic multilevel methods. More information about FEtk may be found 390s at . 390s ---------------------------------------------------------------------- 390s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 390s Aqua is a modified form of the Holst group PMG library 390s which has been modified by Patrice Koehl 390s for improved efficiency and 390s memory usage when solving the Poisson-Boltzmann equation. 390s ---------------------------------------------------------------------- 390s Please cite your use of APBS as: 390s 390s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 390s nanosystems: application to microtubules and the ribosome. Proc. 390s Natl. Acad. Sci. USA 98, 10037-10041 2001. 390s 390s 390s This executable compiled on Jan 3 2025 at 11:01:42 390s 390s Parsing input file apbs-smol.in... 390s rank 0 size 1... 390s Parsed input file. 390s Got paths for 3 molecules 390s Reading PQR-format atom data from acetic-acid.pqr. 390s asc_getToken: Error occurred (bailing out). 390s Vio_scanf: Format problem with input. 390s 8 atoms 390s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 390s Net charge -1.67e-16 e 390s Reading PQR-format atom data from acetate.pqr. 390s asc_getToken: Error occurred (bailing out). 390s Vio_scanf: Format problem with input. 390s 8 atoms 390s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 390s Net charge -1.00e+00 e 390s Reading PQR-format atom data from proton.pqr. 390s 1 atoms 390s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 390s Net charge 1.00e+00 e 390s Preparing to run 12 PBE calculations. 390s ---------------------------------------- 390s CALCULATION #1 (acetic-solv): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 7.76163 A 390s Current memory usage: 61.598 MB total, 61.598 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.188 x 0.188 x 0.188 390s Grid lengths: 12.000 x 12.000 x 12.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 1 390s Linearized traditional PBE 390s Multiple Debye-Huckel sphere boundary conditions 390s 2 ion species (0.150 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 78.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 5.824172730822E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #2 (acetic-solv): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 7.76163 A 390s Current memory usage: 61.598 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.094 x 0.094 x 0.094 390s Grid lengths: 6.000 x 6.000 x 6.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 1 390s Linearized traditional PBE 390s Boundary conditions from focusing 390s 2 ion species (0.150 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 78.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 9.793622759239E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #3 (acetic-ref): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 0 A 390s Current memory usage: 61.422 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.188 x 0.188 x 0.188 390s Grid lengths: 12.000 x 12.000 x 12.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 1 390s Linearized traditional PBE 390s Multiple Debye-Huckel sphere boundary conditions 390s 2 ion species (0.000 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 2.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 5.846917564309E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #4 (acetic-ref): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 0 A 390s Current memory usage: 61.422 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.094 x 0.094 x 0.094 390s Grid lengths: 6.000 x 6.000 x 6.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 1 390s Linearized traditional PBE 390s Boundary conditions from focusing 390s 2 ion species (0.000 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 2.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 9.815953282539E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #5 (acetate-solv): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 7.76163 A 390s Current memory usage: 61.598 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.188 x 0.188 x 0.188 390s Grid lengths: 12.000 x 12.000 x 12.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 2 390s Linearized traditional PBE 390s Multiple Debye-Huckel sphere boundary conditions 390s 2 ion species (0.150 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 78.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 8.221328580569E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #6 (acetate-solv): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 7.76163 A 390s Current memory usage: 61.598 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.094 x 0.094 x 0.094 390s Grid lengths: 6.000 x 6.000 x 6.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 2 390s Linearized traditional PBE 390s Boundary conditions from focusing 390s 2 ion species (0.150 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 78.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 1.392867783119E+04 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #7 (acetate-ref): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 0 A 390s Current memory usage: 61.422 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.188 x 0.188 x 0.188 390s Grid lengths: 12.000 x 12.000 x 12.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 2 390s Linearized traditional PBE 390s Multiple Debye-Huckel sphere boundary conditions 390s 2 ion species (0.000 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 2.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 8.420373979905E+03 kJ/mol 390s Calculating forces... 390s [focusFillBound()]: WARNING: 390s Unusually large potential values 390s detected on the focusing boundary! 390s Convergence not guaranteed for NPBE/NRPBE calculations! 390s 390s ---------------------------------------- 390s CALCULATION #8 (acetate-ref): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 0 A 390s Current memory usage: 61.422 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.094 x 0.094 x 0.094 390s Grid lengths: 6.000 x 6.000 x 6.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 2 390s Linearized traditional PBE 390s Boundary conditions from focusing 390s 2 ion species (0.000 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 2.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 1.412716615065E+04 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #9 (proton-solv): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 7.76163 A 390s Current memory usage: 61.412 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.188 x 0.188 x 0.188 390s Grid lengths: 12.000 x 12.000 x 12.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 3 390s Linearized traditional PBE 390s Multiple Debye-Huckel sphere boundary conditions 390s 2 ion species (0.150 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 78.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 3.863066835285E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #10 (proton-solv): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 7.76163 A 390s Current memory usage: 61.412 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.094 x 0.094 x 0.094 390s Grid lengths: 6.000 x 6.000 x 6.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 3 390s Linearized traditional PBE 390s Boundary conditions from focusing 390s 2 ion species (0.150 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 78.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 6.289649216644E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s CALCULATION #11 (proton-ref): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 0 A 390s Current memory usage: 61.373 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.188 x 0.188 x 0.188 390s Grid lengths: 12.000 x 12.000 x 12.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 3 390s Linearized traditional PBE 390s Multiple Debye-Huckel sphere boundary conditions 390s 2 ion species (0.000 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 2.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 4.162533113906E+03 kJ/mol 390s Calculating forces... 390s [focusFillBound()]: WARNING: 390s Unusually large potential values 390s detected on the focusing boundary! 390s Convergence not guaranteed for NPBE/NRPBE calculations! 390s 390s ---------------------------------------- 390s CALCULATION #12 (proton-ref): MULTIGRID 390s Setting up problem... 390s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 390s Debye length: 0 A 390s Current memory usage: 61.373 MB total, 122.404 MB high water 390s Using linear spline charge discretization. 390s Grid dimensions: 65 x 65 x 65 390s Grid spacings: 0.094 x 0.094 x 0.094 390s Grid lengths: 6.000 x 6.000 x 6.000 390s Grid center: (0.000, -0.154, 1.287) 390s Multigrid levels: 5 390s Molecule ID: 3 390s Linearized traditional PBE 390s Boundary conditions from focusing 390s 2 ion species (0.000 M ionic strength): 390s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 390s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 390s Solute dielectric: 2.000 390s Solvent dielectric: 2.000 390s Using "molecular" surface definition;harmonic average smoothing 390s Solvent probe radius: 0.000 A 390s Temperature: 293.000 K 390s Electrostatic energies will be calculated 390s Total electrostatic energy = 6.585616091973E+03 kJ/mol 390s Calculating forces... 390s ---------------------------------------- 390s PRINT STATEMENTS 390s 390s print energy 1 (acetic-solv) - 2 (acetic-ref) end 390s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 390s Global net ELEC energy = -2.233052329981E+01 kJ/mol 390s 390s print energy 3 (acetate-solv) - 4 (acetate-ref) end 390s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 390s Global net ELEC energy = -1.984883194538E+02 kJ/mol 390s 390s print energy 5 (proton-solv) - 6 (proton-ref) end 390s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 390s Global net ELEC energy = -2.959668753288E+02 kJ/mol 390s 390s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 390s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 390s Global net ELEC energy = -4.721246714828E+02 kJ/mol 390s ---------------------------------------- 390s CLEANING UP AND SHUTTING DOWN... 390s Destroying force arrays. 390s No energy arrays to destroy. 390s Destroying multigrid structures. 390s Destroying finite element structures. 390s Destroying 3 molecules 390s Final memory usage: 0.001 MB total, 122.404 MB high water 390s 390s 390s Thanks for using APBS! 390s 390s Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 390s *** PASSED *** 390s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 390s *** PASSED *** 390s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 390s *** PASSED *** 390s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 390s *** PASSED *** 390s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 390s *** PASSED *** 390s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 390s *** PASSED *** 390s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 390s *** PASSED *** 390s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 390s *** PASSED *** 390s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 390s *** PASSED *** 390s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 390s *** PASSED *** 390s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 390s *** PASSED *** 390s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 390s *** PASSED *** 390s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 390s *** PASSED *** 390s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 390s *** PASSED *** 390s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 390s *** PASSED *** 390s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 390s *** PASSED *** 390s Elapsed time: 2.253405 seconds 390s -------------------------------------------------------------------------------- 390s Total elapsed time: 4.492334 seconds 390s Test results have been logged 390s -------------------------------------------------------------------------------- 390s -------------------------------------------------------------------------------- 390s Testing input file ion-pmf.in 390s 398s Checking for intermediate energies in input file apbs-smol.out 398s EXPECTED COMPUTED: 16 398s EXPECTED EXPECTED: 16 398s 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] 398s 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'] 398s COMPUTED RESULT 5824.172730822 398s COMPUTED RESULT 9793.622759239 398s COMPUTED RESULT 5846.917564309 398s COMPUTED RESULT 9815.953282539 398s COMPUTED RESULT 8221.328580569 398s COMPUTED RESULT 13928.67783119 398s COMPUTED RESULT 8420.373979905 398s COMPUTED RESULT 14127.16615065 398s COMPUTED RESULT 3863.066835285 398s COMPUTED RESULT 6289.649216644 398s COMPUTED RESULT 4162.533113906 398s COMPUTED RESULT 6585.616091973 398s COMPUTED RESULT -22.33052329981 398s COMPUTED RESULT -198.4883194538 398s COMPUTED RESULT -295.9668753288 398s COMPUTED RESULT -472.1246714828 398s Running tests for ion-pmf section 398s BINARY: /usr/bin/apbs 398s INPUT: ion-pmf.in 398s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 398s asc_getToken: Error occurred (bailing out). 398s Vio_scanf: Format problem with input. 398s asc_getToken: Error occurred (bailing out). 398s Vio_scanf: Format problem with input. 398s 398s 398s ---------------------------------------------------------------------- 398s APBS -- Adaptive Poisson-Boltzmann Solver 398s Version APBS 3.4.1 398s 398s Nathan A. Baker (nathan.baker@pnnl.gov) 398s Pacific Northwest National Laboratory 398s 398s Additional contributing authors listed in the code documentation. 398s 398s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 398s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 398s Northwest Division for the U.S. Department of Energy. 398s 398s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 398s Portions Copyright (c) 2002-2020, Nathan A. Baker. 398s Portions Copyright (c) 1999-2002, The Regents of the University of California. 398s Portions Copyright (c) 1995, Michael Holst. 398s All rights reserved. 398s 398s Redistribution and use in source and binary forms, with or without 398s modification, are permitted provided that the following conditions are met: 398s 398s * Redistributions of source code must retain the above copyright notice, this 398s list of conditions and the following disclaimer. 398s 398s * Redistributions in binary form must reproduce the above copyright notice, 398s this list of conditions and the following disclaimer in the documentation 398s and/or other materials provided with the distribution. 398s 398s * Neither the name of the developer nor the names of its contributors may be 398s used to endorse or promote products derived from this software without 398s specific prior written permission. 398s 398s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 398s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 398s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 398s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 398s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 398s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 398s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 398s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 398s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 398s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 398s ---------------------------------------------------------------------- 398s APBS uses FETK (the Finite Element ToolKit) to solve the 398s Poisson-Boltzmann equation numerically. FETK is a portable collection 398s of finite element modeling class libraries developed by the Michael Holst 398s research group and written in an object-oriented form of C. FEtk is 398s designed to solve general coupled systems of nonlinear partial differential 398s equations using adaptive finite element methods, inexact Newton methods, 398s and algebraic multilevel methods. More information about FEtk may be found 398s at . 398s ---------------------------------------------------------------------- 398s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 398s Aqua is a modified form of the Holst group PMG library 398s which has been modified by Patrice Koehl 398s for improved efficiency and 398s memory usage when solving the Poisson-Boltzmann equation. 398s ---------------------------------------------------------------------- 398s Please cite your use of APBS as: 398s 398s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 398s nanosystems: application to microtubules and the ribosome. Proc. 398s Natl. Acad. Sci. USA 98, 10037-10041 2001. 398s 398s 398s This executable compiled on Jan 3 2025 at 11:01:42 398s 398s Parsing input file ion-pmf.in... 398s rank 0 size 1... 398s Parsed input file. 398s Reading parameter data from parm.dat. 398s Got paths for 1 molecules 398s Reading PDB-format atom data from ion-pmf.pdb. 398s Vpmg_ibForce: No force for zero ionic strength! 398s Vpmg_ibForce: No force for zero ionic strength! 398s 2 atoms 398s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 398s Net charge 2.00e+00 e 398s Preparing to run 3 PBE calculations. 398s ---------------------------------------- 398s CALCULATION #1 (solv): MULTIGRID 398s Setting up problem... 398s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 398s Debye length: 0 A 398s Current memory usage: 61.106 MB total, 61.106 MB high water 398s Using cubic spline charge discretization. 398s Grid dimensions: 65 x 65 x 65 398s Grid spacings: 0.210 x 0.210 x 0.210 398s Grid lengths: 13.440 x 13.440 x 13.440 398s Grid center: (0.000, 0.000, 0.000) 398s Multigrid levels: 5 398s Molecule ID: 1 398s Linearized traditional PBE 398s Multiple Debye-Huckel sphere boundary conditions 398s 0 ion species (0.000 M ionic strength): 398s Solute dielectric: 1.000 398s Solvent dielectric: 78.540 398s Using spline-based surface definition;window = 0.300 398s Temperature: 298.150 K 398s Electrostatic energies will be calculated 398s All-atom solvent forces will be calculated 398s Total electrostatic energy = 7.839535983197E+03 kJ/mol 398s Calculating forces... 398s Printing per-atom forces for molecule 1 (kJ/mol/A) 398s Legend: 398s tot n -- total force for atom n 398s qf n -- fixed charge force for atom n 398s db n -- dielectric boundary force for atom n 398s ib n -- ionic boundary force for atom n 398s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 398s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 398s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 398s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 398s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 398s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 398s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 398s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 398s Vpmg_ibForce: No force for zero ionic strength! 398s Vpmg_ibForce: No force for zero ionic strength! 398s ---------------------------------------- 398s CALCULATION #2 (ref): MULTIGRID 398s Setting up problem... 398s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 398s Debye length: 0 A 398s Current memory usage: 61.106 MB total, 61.155 MB high water 398s Using cubic spline charge discretization. 398s Grid dimensions: 65 x 65 x 65 398s Grid spacings: 0.210 x 0.210 x 0.210 398s Grid lengths: 13.440 x 13.440 x 13.440 398s Grid center: (0.000, 0.000, 0.000) 398s Multigrid levels: 5 398s Molecule ID: 1 398s Linearized traditional PBE 398s Multiple Debye-Huckel sphere boundary conditions 398s 0 ion species (0.000 M ionic strength): 398s Solute dielectric: 1.000 398s Solvent dielectric: 1.000 398s Using spline-based surface definition;window = 0.300 398s Temperature: 298.150 K 398s Electrostatic energies will be calculated 398s All-atom solvent forces will be calculated 398s Total electrostatic energy = 8.964727588811E+03 kJ/mol 398s Calculating forces... 398s Printing per-atom forces for molecule 1 (kJ/mol/A) 398s Legend: 398s tot n -- total force for atom n 398s qf n -- fixed charge force for atom n 398s db n -- dielectric boundary force for atom n 398s ib n -- ionic boundary force for atom n 398s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 398s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 398s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 398s mgF db 0 0.000e+00 0.000e+00 0.000e+00 398s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 398s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 398s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 398s mgF db 1 0.000e+00 0.000e+00 0.000e+00 398s ---------------------------------------- 398s CALCULATION #3 (asolv): APOLAR 398s Printing per atom forces (kJ/mol/A) 398s Legend: 398s tot n -- Total force for atom n 398s sasa n -- SASA force for atom n 398s sav n -- SAV force for atom n 398s wca n -- WCA force for atom n 398s 398s gamma 0.000720 398s pressure 0.000000 398s bconc 0.033000 398s 398s tot 0 2.715e-02 9.130e-07 9.128e-07 398s sasa 0 -1.100e+01 0.000e+00 0.000e+00 398s sav 0 0.000e+00 0.000e+00 0.000e+00 398s wca 0 -5.827e-01 -2.767e-05 -2.766e-05 398s tot 1 -2.723e-02 9.131e-07 9.134e-07 398s sasa 1 1.112e+01 0.000e+00 0.000e+00 398s sav 1 0.000e+00 0.000e+00 0.000e+00 398s wca 1 5.827e-01 -2.767e-05 -2.768e-05 398s 398s 398s Solvent Accessible Surface Area (SASA) for each atom: 398s SASA for atom 0: 1.153275282828E+02 398s SASA for atom 1: 1.153114143344E+02 398s 398s Total solvent accessible surface area: 230.639 A^2 398s 398s Surface tension*area energies (gamma * SASA) for each atom: 398s Surface tension*area energy for atom 0: 8.303582036361E-02 398s Surface tension*area energy for atom 1: 8.302421832080E-02 398s 398s Total surface tension energy: 0.16606 kJ/mol 398s 398s Total solvent accessible volume: 0 A^3 398s 398s Total pressure*volume energy: 0 kJ/mol 398s 398s WCA dispersion Energies for each atom: 398s WCA energy for atom 0: -6.909718345777E+00 398s WCA energy for atom 1: -6.909411348230E+00 398s 398s Total WCA energy: -13.8191 kJ/mol 398s 398s Total non-polar energy = -1.365306965532E+01 kJ/mol 398s ---------------------------------------- 398s PRINT STATEMENTS 398s 398s print energy 1 (solv) - 2 (ref) end 398s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 398s Global net ELEC energy = -1.125191605614E+03 kJ/mol 398s print force 1 (solv) - 2 (ref) end 398s Printing per-atom forces (kJ/mol/A). 398s Legend: 398s tot n -- Total force for atom n 398s qf n -- Fixed charge force for atom n 398s db n -- Dielectric boundary force for atom n 398s ib n -- Ionic boundary force for atom n 398s tot all -- Total force for system 398s qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 398s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 398s db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 398s tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 398s qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 398s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 398s db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 398s tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 398s tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 398s 398s print APOL energy 1 (asolv) end 398s Global net APOL energy = -1.365306965532E+01 kJ/mol 398s 398s print APOL force 1 (asolv) end 398s Printing per atom forces (kJ/mol/A) 398s Legend: 398s tot n -- Total force for atom n 398s sasa n -- SASA force for atom n 398s sav n -- SAV force for atom n 398s wca n -- WCA force for atom n 398s tot all -- Total force for system 398s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 398s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 398s wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 398s tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 398s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 398s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 398s wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 398s tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 398s tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 398s ---------------------------------------- 398s CLEANING UP AND SHUTTING DOWN... 398s Destroying force arrays. 398s No energy arrays to destroy. 398s Destroying multigrid structures. 398s Destroying finite element structures. 398s Destroying 1 molecules 398s Final memory usage: 60.711 MB total, 62.250 MB high water 398s 398s 398s Thanks for using APBS! 398s 398s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 398s *** PASSED *** 398s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 398s *** PASSED *** 398s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 398s *** PASSED *** 398s Elapsed time: 8.567768000000001 seconds 398s -------------------------------------------------------------------------------- 398s Total elapsed time: 8.567768000000001 seconds 398s Test results have been logged 398s -------------------------------------------------------------------------------- 398s -------------------------------------------------------------------------------- 398s Testing input file apbs-mol-vdw.in 398s 411s Checking for intermediate energies in input file ion-pmf.out 411s EXPECTED COMPUTED: 4 411s EXPECTED EXPECTED: 4 411s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] 411s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 411s COMPUTED RESULT 7839.535983197 411s COMPUTED RESULT 8964.727588811 411s COMPUTED RESULT -1125.191605614 411s COMPUTED RESULT -13.65306965532 411s Running tests for pka-lig section 411s BINARY: /usr/bin/apbs 411s INPUT: apbs-mol-vdw.in 411s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 411s asc_getToken: Error occurred (bailing out). 411s Vio_scanf: Format problem with input. 411s 411s 411s ---------------------------------------------------------------------- 411s APBS -- Adaptive Poisson-Boltzmann Solver 411s Version APBS 3.4.1 411s 411s Nathan A. Baker (nathan.baker@pnnl.gov) 411s Pacific Northwest National Laboratory 411s 411s Additional contributing authors listed in the code documentation. 411s 411s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 411s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 411s Northwest Division for the U.S. Department of Energy. 411s 411s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 411s Portions Copyright (c) 2002-2020, Nathan A. Baker. 411s Portions Copyright (c) 1999-2002, The Regents of the University of California. 411s Portions Copyright (c) 1995, Michael Holst. 411s All rights reserved. 411s 411s Redistribution and use in source and binary forms, with or without 411s modification, are permitted provided that the following conditions are met: 411s 411s * Redistributions of source code must retain the above copyright notice, this 411s list of conditions and the following disclaimer. 411s 411s * Redistributions in binary form must reproduce the above copyright notice, 411s this list of conditions and the following disclaimer in the documentation 411s and/or other materials provided with the distribution. 411s 411s * Neither the name of the developer nor the names of its contributors may be 411s used to endorse or promote products derived from this software without 411s specific prior written permission. 411s 411s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 411s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 411s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 411s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 411s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 411s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 411s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 411s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 411s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 411s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 411s ---------------------------------------------------------------------- 411s APBS uses FETK (the Finite Element ToolKit) to solve the 411s Poisson-Boltzmann equation numerically. FETK is a portable collection 411s of finite element modeling class libraries developed by the Michael Holst 411s research group and written in an object-oriented form of C. FEtk is 411s designed to solve general coupled systems of nonlinear partial differential 411s equations using adaptive finite element methods, inexact Newton methods, 411s and algebraic multilevel methods. More information about FEtk may be found 411s at . 411s ---------------------------------------------------------------------- 411s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 411s Aqua is a modified form of the Holst group PMG library 411s which has been modified by Patrice Koehl 411s for improved efficiency and 411s memory usage when solving the Poisson-Boltzmann equation. 411s ---------------------------------------------------------------------- 411s Please cite your use of APBS as: 411s 411s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 411s nanosystems: application to microtubules and the ribosome. Proc. 411s Natl. Acad. Sci. USA 98, 10037-10041 2001. 411s 411s 411s This executable compiled on Jan 3 2025 at 11:01:42 411s 411s Parsing input file apbs-mol-vdw.in... 411s rank 0 size 1... 411s Parsed input file. 411s Got paths for 3 molecules 411s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 411s asc_getToken: Error occurred (bailing out). 411s Vio_scanf: Format problem with input. 411s 47 atoms 411s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 411s Net charge 1.11e-16 e 411s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 411s asc_getToken: Error occurred (bailing out). 411s Vio_scanf: Format problem with input. 411s 3423 atoms 411s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 411s Net charge 1.00e+00 e 411s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 411s 3470 atoms 411s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 411s Net charge 1.00e+00 e 411s Preparing to run 6 PBE calculations. 411s ---------------------------------------- 411s CALCULATION #1 (lig-coarse): MULTIGRID 411s Setting up problem... 411s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 411s Debye length: 0 A 411s Current memory usage: 204.292 MB total, 204.292 MB high water 411s Using linear spline charge discretization. 411s Grid dimensions: 97 x 97 x 97 411s Grid spacings: 0.729 x 0.729 x 0.729 411s Grid lengths: 70.000 x 70.000 x 70.000 411s Grid center: (28.969, -32.507, 27.022) 411s Multigrid levels: 4 411s Molecule ID: 1 411s Linearized traditional PBE 411s Single Debye-Huckel sphere boundary conditions 411s 2 ion species (0.000 M ionic strength): 411s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 411s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 411s Solute dielectric: 2.000 411s Solvent dielectric: 78.000 411s Using "molecular" surface definition; no smoothing 411s Solvent probe radius: 0.000 A 411s Temperature: 298.150 K 411s Electrostatic energies will be calculated 411s Total electrostatic energy = 2.224988750664E+03 kJ/mol 411s Calculating forces... 411s ---------------------------------------- 411s CALCULATION #2 (lig-fine): MULTIGRID 411s Setting up problem... 411s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 411s Debye length: 0 A 411s Current memory usage: 204.292 MB total, 406.001 MB high water 411s Using linear spline charge discretization. 411s Grid dimensions: 97 x 97 x 97 411s Grid spacings: 0.250 x 0.250 x 0.250 411s Grid lengths: 24.000 x 24.000 x 24.000 411s Grid center: (24.822, -33.153, 21.545) 411s Multigrid levels: 4 411s Molecule ID: 1 411s Linearized traditional PBE 411s Boundary conditions from focusing 411s 2 ion species (0.000 M ionic strength): 411s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 411s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 411s Solute dielectric: 2.000 411s Solvent dielectric: 78.000 411s Using "molecular" surface definition; no smoothing 411s Solvent probe radius: 0.000 A 411s Temperature: 298.150 K 411s Electrostatic energies will be calculated 411s Total electrostatic energy = 1.049695084686E+04 kJ/mol 411s Calculating forces... 411s ---------------------------------------- 411s CALCULATION #3 (pka-coarse): MULTIGRID 411s Setting up problem... 411s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 411s Debye length: 0 A 411s Current memory usage: 291.151 MB total, 406.001 MB high water 411s Using linear spline charge discretization. 411s Grid dimensions: 97 x 97 x 97 411s Grid spacings: 0.729 x 0.729 x 0.729 411s Grid lengths: 70.000 x 70.000 x 70.000 411s Grid center: (28.969, -32.507, 27.022) 411s Multigrid levels: 4 411s Molecule ID: 2 411s Linearized traditional PBE 411s Single Debye-Huckel sphere boundary conditions 411s 2 ion species (0.000 M ionic strength): 411s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 411s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 411s Solute dielectric: 2.000 411s Solvent dielectric: 78.000 411s Using "molecular" surface definition; no smoothing 411s Solvent probe radius: 0.000 A 411s Temperature: 298.150 K 411s Electrostatic energies will be calculated 411s Total electrostatic energy = 1.818450789522E+05 kJ/mol 411s Calculating forces... 411s [focusFillBound()]: WARNING: 411s Unusually large potential values 411s detected on the focusing boundary! 411s Convergence not guaranteed for NPBE/NRPBE calculations! 411s 411s ---------------------------------------- 411s CALCULATION #4 (pka-fine): MULTIGRID 411s Setting up problem... 411s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 411s Debye length: 0 A 411s Current memory usage: 291.151 MB total, 533.426 MB high water 411s Using linear spline charge discretization. 411s Grid dimensions: 97 x 97 x 97 411s Grid spacings: 0.250 x 0.250 x 0.250 411s Grid lengths: 24.000 x 24.000 x 24.000 411s Grid center: (24.822, -33.153, 21.545) 411s Multigrid levels: 4 411s Molecule ID: 2 411s Linearized traditional PBE 411s Boundary conditions from focusing 411s 2 ion species (0.000 M ionic strength): 411s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 411s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 411s Solute dielectric: 2.000 411s Solvent dielectric: 78.000 411s Using "molecular" surface definition; no smoothing 411s Solvent probe radius: 0.000 A 411s Temperature: 298.150 K 411s Electrostatic energies will be calculated 411s Total electrostatic energy = 3.008254338259E+05 kJ/mol 411s Calculating forces... 411s ---------------------------------------- 411s CALCULATION #5 (complex-coarse): MULTIGRID 411s Setting up problem... 411s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 411s Debye length: 0 A 411s Current memory usage: 292.063 MB total, 533.426 MB high water 411s Using linear spline charge discretization. 411s Grid dimensions: 97 x 97 x 97 411s Grid spacings: 0.729 x 0.729 x 0.729 411s Grid lengths: 70.000 x 70.000 x 70.000 411s Grid center: (28.969, -32.507, 27.022) 411s Multigrid levels: 4 411s Molecule ID: 3 411s Linearized traditional PBE 411s Single Debye-Huckel sphere boundary conditions 411s 2 ion species (0.000 M ionic strength): 411s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 411s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 411s Solute dielectric: 2.000 411s Solvent dielectric: 78.000 411s Using "molecular" surface definition; no smoothing 411s Solvent probe radius: 0.000 A 411s Temperature: 298.150 K 411s Electrostatic energies will be calculated 411s Total electrostatic energy = 1.840918409896E+05 kJ/mol 411s Calculating forces... 411s [focusFillBound()]: WARNING: 411s Unusually large potential values 411s detected on the focusing boundary! 411s Convergence not guaranteed for NPBE/NRPBE calculations! 411s 411s ---------------------------------------- 411s CALCULATION #6 (complex-fine): MULTIGRID 411s Setting up problem... 411s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 411s Debye length: 0 A 411s Current memory usage: 292.063 MB total, 534.806 MB high water 411s Using linear spline charge discretization. 411s Grid dimensions: 97 x 97 x 97 411s Grid spacings: 0.250 x 0.250 x 0.250 411s Grid lengths: 24.000 x 24.000 x 24.000 411s Grid center: (24.822, -33.153, 21.545) 411s Multigrid levels: 4 411s Molecule ID: 3 411s Linearized traditional PBE 411s Boundary conditions from focusing 411s 2 ion species (0.000 M ionic strength): 411s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 411s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 411s Solute dielectric: 2.000 411s Solvent dielectric: 78.000 411s Using "molecular" surface definition; no smoothing 411s Solvent probe radius: 0.000 A 411s Temperature: 298.150 K 411s Electrostatic energies will be calculated 411s Total electrostatic energy = 3.113304681884E+05 kJ/mol 411s Calculating forces... 411s ---------------------------------------- 411s PRINT STATEMENTS 411s 411s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 411s Local net energy (PE 0) = 8.083515648803E+00 kJ/mol 411s Global net ELEC energy = 8.083515648803E+00 kJ/mol 411s ---------------------------------------- 411s CLEANING UP AND SHUTTING DOWN... 411s Destroying force arrays. 411s No energy arrays to destroy. 411s Destroying multigrid structures. 411s Destroying finite element structures. 411s Destroying 3 molecules 411s Final memory usage: 0.001 MB total, 534.806 MB high water 411s 411s 411s Thanks for using APBS! 411s 411s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 411s *** PASSED *** 411s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 411s *** PASSED *** 411s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 411s *** PASSED *** 411s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 411s *** PASSED *** 411s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 411s *** PASSED *** 411s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 411s *** PASSED *** 411s Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) 411s *** PASSED *** 411s Elapsed time: 12.636319 seconds 411s -------------------------------------------------------------------------------- 411s -------------------------------------------------------------------------------- 411s Testing input file apbs-smol-vdw.in 411s 421s Checking for intermediate energies in input file apbs-mol-vdw.out 421s EXPECTED COMPUTED: 7 421s EXPECTED EXPECTED: 7 421s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] 421s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 421s COMPUTED RESULT 2224.988750664 421s COMPUTED RESULT 10496.95084686 421s COMPUTED RESULT 181845.0789522 421s COMPUTED RESULT 300825.4338259 421s COMPUTED RESULT 184091.8409896 421s COMPUTED RESULT 311330.4681884 421s COMPUTED RESULT 8.083515648803 421s BINARY: /usr/bin/apbs 421s INPUT: apbs-smol-vdw.in 421s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 421s asc_getToken: Error occurred (bailing out). 421s Vio_scanf: Format problem with input. 421s 421s 421s ---------------------------------------------------------------------- 421s APBS -- Adaptive Poisson-Boltzmann Solver 421s Version APBS 3.4.1 421s 421s Nathan A. Baker (nathan.baker@pnnl.gov) 421s Pacific Northwest National Laboratory 421s 421s Additional contributing authors listed in the code documentation. 421s 421s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 421s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 421s Northwest Division for the U.S. Department of Energy. 421s 421s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 421s Portions Copyright (c) 2002-2020, Nathan A. Baker. 421s Portions Copyright (c) 1999-2002, The Regents of the University of California. 421s Portions Copyright (c) 1995, Michael Holst. 421s All rights reserved. 421s 421s Redistribution and use in source and binary forms, with or without 421s modification, are permitted provided that the following conditions are met: 421s 421s * Redistributions of source code must retain the above copyright notice, this 421s list of conditions and the following disclaimer. 421s 421s * Redistributions in binary form must reproduce the above copyright notice, 421s this list of conditions and the following disclaimer in the documentation 421s and/or other materials provided with the distribution. 421s 421s * Neither the name of the developer nor the names of its contributors may be 421s used to endorse or promote products derived from this software without 421s specific prior written permission. 421s 421s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 421s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 421s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 421s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 421s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 421s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 421s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 421s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 421s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 421s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 421s ---------------------------------------------------------------------- 421s APBS uses FETK (the Finite Element ToolKit) to solve the 421s Poisson-Boltzmann equation numerically. FETK is a portable collection 421s of finite element modeling class libraries developed by the Michael Holst 421s research group and written in an object-oriented form of C. FEtk is 421s designed to solve general coupled systems of nonlinear partial differential 421s equations using adaptive finite element methods, inexact Newton methods, 421s and algebraic multilevel methods. More information about FEtk may be found 421s at . 421s ---------------------------------------------------------------------- 421s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 421s Aqua is a modified form of the Holst group PMG library 421s which has been modified by Patrice Koehl 421s for improved efficiency and 421s memory usage when solving the Poisson-Boltzmann equation. 421s ---------------------------------------------------------------------- 421s Please cite your use of APBS as: 421s 421s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 421s nanosystems: application to microtubules and the ribosome. Proc. 421s Natl. Acad. Sci. USA 98, 10037-10041 2001. 421s 421s 421s This executable compiled on Jan 3 2025 at 11:01:42 421s 421s Parsing input file apbs-smol-vdw.in... 421s rank 0 size 1... 421s Parsed input file. 421s Got paths for 3 molecules 421s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 421s asc_getToken: Error occurred (bailing out). 421s Vio_scanf: Format problem with input. 421s 47 atoms 421s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 421s Net charge 1.11e-16 e 421s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 421s asc_getToken: Error occurred (bailing out). 421s Vio_scanf: Format problem with input. 421s 3423 atoms 421s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 421s Net charge 1.00e+00 e 421s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 421s 3470 atoms 421s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 421s Net charge 1.00e+00 e 421s Preparing to run 6 PBE calculations. 421s ---------------------------------------- 421s CALCULATION #1 (lig-coarse): MULTIGRID 421s Setting up problem... 421s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 421s Debye length: 0 A 421s Current memory usage: 204.292 MB total, 204.292 MB high water 421s Using linear spline charge discretization. 421s Grid dimensions: 97 x 97 x 97 421s Grid spacings: 0.729 x 0.729 x 0.729 421s Grid lengths: 70.000 x 70.000 x 70.000 421s Grid center: (28.969, -32.507, 27.022) 421s Multigrid levels: 4 421s Molecule ID: 1 421s Linearized traditional PBE 421s Single Debye-Huckel sphere boundary conditions 421s 2 ion species (0.000 M ionic strength): 421s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 421s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 421s Solute dielectric: 2.000 421s Solvent dielectric: 78.000 421s Using "molecular" surface definition;harmonic average smoothing 421s Solvent probe radius: 0.000 A 421s Temperature: 298.150 K 421s Electrostatic energies will be calculated 421s Total electrostatic energy = 2.226793167046E+03 kJ/mol 421s Calculating forces... 421s ---------------------------------------- 421s CALCULATION #2 (lig-fine): MULTIGRID 421s Setting up problem... 421s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 421s Debye length: 0 A 421s Current memory usage: 204.292 MB total, 406.001 MB high water 421s Using linear spline charge discretization. 421s Grid dimensions: 97 x 97 x 97 421s Grid spacings: 0.250 x 0.250 x 0.250 421s Grid lengths: 24.000 x 24.000 x 24.000 421s Grid center: (24.822, -33.153, 21.545) 421s Multigrid levels: 4 421s Molecule ID: 1 421s Linearized traditional PBE 421s Boundary conditions from focusing 421s 2 ion species (0.000 M ionic strength): 421s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 421s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 421s Solute dielectric: 2.000 421s Solvent dielectric: 78.000 421s Using "molecular" surface definition;harmonic average smoothing 421s Solvent probe radius: 0.000 A 421s Temperature: 298.150 K 421s Electrostatic energies will be calculated 421s Total electrostatic energy = 1.050504485887E+04 kJ/mol 421s Calculating forces... 421s ---------------------------------------- 421s CALCULATION #3 (pka-coarse): MULTIGRID 421s Setting up problem... 421s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 421s Debye length: 0 A 421s Current memory usage: 291.151 MB total, 406.001 MB high water 421s Using linear spline charge discretization. 421s Grid dimensions: 97 x 97 x 97 421s Grid spacings: 0.729 x 0.729 x 0.729 421s Grid lengths: 70.000 x 70.000 x 70.000 421s Grid center: (28.969, -32.507, 27.022) 421s Multigrid levels: 4 421s Molecule ID: 2 421s Linearized traditional PBE 421s Single Debye-Huckel sphere boundary conditions 421s 2 ion species (0.000 M ionic strength): 421s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 421s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 421s Solute dielectric: 2.000 421s Solvent dielectric: 78.000 421s Using "molecular" surface definition;harmonic average smoothing 421s Solvent probe radius: 0.000 A 421s Temperature: 298.150 K 421s Electrostatic energies will be calculated 421s Total electrostatic energy = 1.827976621645E+05 kJ/mol 421s Calculating forces... 421s [focusFillBound()]: WARNING: 421s Unusually large potential values 421s detected on the focusing boundary! 421s Convergence not guaranteed for NPBE/NRPBE calculations! 421s 421s ---------------------------------------- 421s CALCULATION #4 (pka-fine): MULTIGRID 421s Setting up problem... 421s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 421s Debye length: 0 A 421s Current memory usage: 291.151 MB total, 533.426 MB high water 421s Using linear spline charge discretization. 421s Grid dimensions: 97 x 97 x 97 421s Grid spacings: 0.250 x 0.250 x 0.250 421s Grid lengths: 24.000 x 24.000 x 24.000 421s Grid center: (24.822, -33.153, 21.545) 421s Multigrid levels: 4 421s Molecule ID: 2 421s Linearized traditional PBE 421s Boundary conditions from focusing 421s 2 ion species (0.000 M ionic strength): 421s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 421s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 421s Solute dielectric: 2.000 421s Solvent dielectric: 78.000 421s Using "molecular" surface definition;harmonic average smoothing 421s Solvent probe radius: 0.000 A 421s Temperature: 298.150 K 421s Electrostatic energies will be calculated 421s Total electrostatic energy = 3.017228546773E+05 kJ/mol 421s Calculating forces... 421s ---------------------------------------- 421s CALCULATION #5 (complex-coarse): MULTIGRID 421s Setting up problem... 421s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 421s Debye length: 0 A 421s Current memory usage: 292.063 MB total, 533.426 MB high water 421s Using linear spline charge discretization. 421s Grid dimensions: 97 x 97 x 97 421s Grid spacings: 0.729 x 0.729 x 0.729 421s Grid lengths: 70.000 x 70.000 x 70.000 421s Grid center: (28.969, -32.507, 27.022) 421s Multigrid levels: 4 421s Molecule ID: 3 421s Linearized traditional PBE 421s Single Debye-Huckel sphere boundary conditions 421s 2 ion species (0.000 M ionic strength): 421s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 421s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 421s Solute dielectric: 2.000 421s Solvent dielectric: 78.000 421s Using "molecular" surface definition;harmonic average smoothing 421s Solvent probe radius: 0.000 A 421s Temperature: 298.150 K 421s Electrostatic energies will be calculated 421s Total electrostatic energy = 1.850819075387E+05 kJ/mol 421s Calculating forces... 421s [focusFillBound()]: WARNING: 421s Unusually large potential values 421s detected on the focusing boundary! 421s Convergence not guaranteed for NPBE/NRPBE calculations! 421s 421s ---------------------------------------- 421s CALCULATION #6 (complex-fine): MULTIGRID 421s Setting up problem... 421s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 421s Debye length: 0 A 421s Current memory usage: 292.063 MB total, 534.806 MB high water 421s Using linear spline charge discretization. 421s Grid dimensions: 97 x 97 x 97 421s Grid spacings: 0.250 x 0.250 x 0.250 421s Grid lengths: 24.000 x 24.000 x 24.000 421s Grid center: (24.822, -33.153, 21.545) 421s Multigrid levels: 4 421s Molecule ID: 3 421s Linearized traditional PBE 421s Boundary conditions from focusing 421s 2 ion species (0.000 M ionic strength): 421s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 421s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 421s Solute dielectric: 2.000 421s Solvent dielectric: 78.000 421s Using "molecular" surface definition;harmonic average smoothing 421s Solvent probe radius: 0.000 A 421s Temperature: 298.150 K 421s Electrostatic energies will be calculated 421s Total electrostatic energy = 3.122488625388E+05 kJ/mol 421s Calculating forces... 421s ---------------------------------------- 421s PRINT STATEMENTS 421s 421s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 421s Local net energy (PE 0) = 2.096300255720E+01 kJ/mol 421s Global net ELEC energy = 2.096300255720E+01 kJ/mol 421s ---------------------------------------- 421s CLEANING UP AND SHUTTING DOWN... 421s Destroying force arrays. 421s No energy arrays to destroy. 421s Destroying multigrid structures. 421s Destroying finite element structures. 421s Destroying 3 molecules 421s Final memory usage: 0.001 MB total, 534.806 MB high water 421s 421s 421s Thanks for using APBS! 421s 421s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 421s *** PASSED *** 421s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 421s *** PASSED *** 421s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 421s *** PASSED *** 421s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 421s *** PASSED *** 421s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 421s *** PASSED *** 421s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 421s *** PASSED *** 421s Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) 421s *** PASSED *** 421s Elapsed time: 10.178846 seconds 421s -------------------------------------------------------------------------------- 421s -------------------------------------------------------------------------------- 421s Testing input file apbs-mol-surf.in 421s 433s Checking for intermediate energies in input file apbs-smol-vdw.out 433s EXPECTED COMPUTED: 7 433s EXPECTED EXPECTED: 7 433s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] 433s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 433s COMPUTED RESULT 2226.793167046 433s COMPUTED RESULT 10505.04485887 433s COMPUTED RESULT 182797.6621645 433s COMPUTED RESULT 301722.8546773 433s COMPUTED RESULT 185081.9075387 433s COMPUTED RESULT 312248.8625388 433s COMPUTED RESULT 20.9630025572 433s BINARY: /usr/bin/apbs 433s INPUT: apbs-mol-surf.in 433s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 433s asc_getToken: Error occurred (bailing out). 433s Vio_scanf: Format problem with input. 433s 433s 433s ---------------------------------------------------------------------- 433s APBS -- Adaptive Poisson-Boltzmann Solver 433s Version APBS 3.4.1 433s 433s Nathan A. Baker (nathan.baker@pnnl.gov) 433s Pacific Northwest National Laboratory 433s 433s Additional contributing authors listed in the code documentation. 433s 433s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 433s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 433s Northwest Division for the U.S. Department of Energy. 433s 433s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 433s Portions Copyright (c) 2002-2020, Nathan A. Baker. 433s Portions Copyright (c) 1999-2002, The Regents of the University of California. 433s Portions Copyright (c) 1995, Michael Holst. 433s All rights reserved. 433s 433s Redistribution and use in source and binary forms, with or without 433s modification, are permitted provided that the following conditions are met: 433s 433s * Redistributions of source code must retain the above copyright notice, this 433s list of conditions and the following disclaimer. 433s 433s * Redistributions in binary form must reproduce the above copyright notice, 433s this list of conditions and the following disclaimer in the documentation 433s and/or other materials provided with the distribution. 433s 433s * Neither the name of the developer nor the names of its contributors may be 433s used to endorse or promote products derived from this software without 433s specific prior written permission. 433s 433s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 433s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 433s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 433s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 433s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 433s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 433s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 433s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 433s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 433s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 433s ---------------------------------------------------------------------- 433s APBS uses FETK (the Finite Element ToolKit) to solve the 433s Poisson-Boltzmann equation numerically. FETK is a portable collection 433s of finite element modeling class libraries developed by the Michael Holst 433s research group and written in an object-oriented form of C. FEtk is 433s designed to solve general coupled systems of nonlinear partial differential 433s equations using adaptive finite element methods, inexact Newton methods, 433s and algebraic multilevel methods. More information about FEtk may be found 433s at . 433s ---------------------------------------------------------------------- 433s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 433s Aqua is a modified form of the Holst group PMG library 433s which has been modified by Patrice Koehl 433s for improved efficiency and 433s memory usage when solving the Poisson-Boltzmann equation. 433s ---------------------------------------------------------------------- 433s Please cite your use of APBS as: 433s 433s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 433s nanosystems: application to microtubules and the ribosome. Proc. 433s Natl. Acad. Sci. USA 98, 10037-10041 2001. 433s 433s 433s This executable compiled on Jan 3 2025 at 11:01:42 433s 433s Parsing input file apbs-mol-surf.in... 433s rank 0 size 1... 433s Parsed input file. 433s Got paths for 3 molecules 433s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 433s asc_getToken: Error occurred (bailing out). 433s Vio_scanf: Format problem with input. 433s 47 atoms 433s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 433s Net charge 1.11e-16 e 433s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 433s asc_getToken: Error occurred (bailing out). 433s Vio_scanf: Format problem with input. 433s 3423 atoms 433s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 433s Net charge 1.00e+00 e 433s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 433s 3470 atoms 433s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 433s Net charge 1.00e+00 e 433s Preparing to run 6 PBE calculations. 433s ---------------------------------------- 433s CALCULATION #1 (lig-coarse): MULTIGRID 433s Setting up problem... 433s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 433s Debye length: 0 A 433s Current memory usage: 203.877 MB total, 203.877 MB high water 433s Using linear spline charge discretization. 433s Grid dimensions: 97 x 97 x 97 433s Grid spacings: 0.729 x 0.729 x 0.729 433s Grid lengths: 70.000 x 70.000 x 70.000 433s Grid center: (28.969, -32.507, 27.022) 433s Multigrid levels: 4 433s Molecule ID: 1 433s Linearized traditional PBE 433s Single Debye-Huckel sphere boundary conditions 433s 2 ion species (0.000 M ionic strength): 433s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 433s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 433s Solute dielectric: 2.000 433s Solvent dielectric: 78.000 433s Using "molecular" surface definition; no smoothing 433s Solvent probe radius: 1.400 A 433s Temperature: 298.150 K 433s Electrostatic energies will be calculated 433s Total electrostatic energy = 2.244350164274E+03 kJ/mol 433s Calculating forces... 433s ---------------------------------------- 433s CALCULATION #2 (lig-fine): MULTIGRID 433s Setting up problem... 433s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 433s Debye length: 0 A 433s Current memory usage: 203.877 MB total, 405.586 MB high water 433s Using linear spline charge discretization. 433s Grid dimensions: 97 x 97 x 97 433s Grid spacings: 0.250 x 0.250 x 0.250 433s Grid lengths: 24.000 x 24.000 x 24.000 433s Grid center: (24.822, -33.153, 21.545) 433s Multigrid levels: 4 433s Molecule ID: 1 433s Linearized traditional PBE 433s Boundary conditions from focusing 433s 2 ion species (0.000 M ionic strength): 433s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 433s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 433s Solute dielectric: 2.000 433s Solvent dielectric: 78.000 433s Using "molecular" surface definition; no smoothing 433s Solvent probe radius: 1.400 A 433s Temperature: 298.150 K 433s Electrostatic energies will be calculated 433s Total electrostatic energy = 1.052149475373E+04 kJ/mol 433s Calculating forces... 433s ---------------------------------------- 433s CALCULATION #3 (pka-coarse): MULTIGRID 433s Setting up problem... 433s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 433s Debye length: 0 A 433s Current memory usage: 251.521 MB total, 405.586 MB high water 433s Using linear spline charge discretization. 433s Grid dimensions: 97 x 97 x 97 433s Grid spacings: 0.729 x 0.729 x 0.729 433s Grid lengths: 70.000 x 70.000 x 70.000 433s Grid center: (28.969, -32.507, 27.022) 433s Multigrid levels: 4 433s Molecule ID: 2 433s Linearized traditional PBE 433s Single Debye-Huckel sphere boundary conditions 433s 2 ion species (0.000 M ionic strength): 433s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 433s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 433s Solute dielectric: 2.000 433s Solvent dielectric: 78.000 433s Using "molecular" surface definition; no smoothing 433s Solvent probe radius: 1.400 A 433s Temperature: 298.150 K 433s Electrostatic energies will be calculated 433s Total electrostatic energy = 1.862615690066E+05 kJ/mol 433s Calculating forces... 433s [focusFillBound()]: WARNING: 433s Unusually large potential values 433s detected on the focusing boundary! 433s Convergence not guaranteed for NPBE/NRPBE calculations! 433s 433s ---------------------------------------- 433s CALCULATION #4 (pka-fine): MULTIGRID 433s Setting up problem... 433s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 433s Debye length: 0 A 433s Current memory usage: 251.521 MB total, 493.795 MB high water 433s Using linear spline charge discretization. 433s Grid dimensions: 97 x 97 x 97 433s Grid spacings: 0.250 x 0.250 x 0.250 433s Grid lengths: 24.000 x 24.000 x 24.000 433s Grid center: (24.822, -33.153, 21.545) 433s Multigrid levels: 4 433s Molecule ID: 2 433s Linearized traditional PBE 433s Boundary conditions from focusing 433s 2 ion species (0.000 M ionic strength): 433s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 433s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 433s Solute dielectric: 2.000 433s Solvent dielectric: 78.000 433s Using "molecular" surface definition; no smoothing 433s Solvent probe radius: 1.400 A 433s Temperature: 298.150 K 433s Electrostatic energies will be calculated 433s Total electrostatic energy = 3.051810884053E+05 kJ/mol 433s Calculating forces... 433s ---------------------------------------- 433s CALCULATION #5 (complex-coarse): MULTIGRID 433s Setting up problem... 433s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 433s Debye length: 0 A 433s Current memory usage: 251.858 MB total, 493.795 MB high water 433s Using linear spline charge discretization. 433s Grid dimensions: 97 x 97 x 97 433s Grid spacings: 0.729 x 0.729 x 0.729 433s Grid lengths: 70.000 x 70.000 x 70.000 433s Grid center: (28.969, -32.507, 27.022) 433s Multigrid levels: 4 433s Molecule ID: 3 433s Linearized traditional PBE 433s Single Debye-Huckel sphere boundary conditions 433s 2 ion species (0.000 M ionic strength): 433s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 433s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 433s Solute dielectric: 2.000 433s Solvent dielectric: 78.000 433s Using "molecular" surface definition; no smoothing 433s Solvent probe radius: 1.400 A 433s Temperature: 298.150 K 433s Electrostatic energies will be calculated 433s Total electrostatic energy = 1.886625455219E+05 kJ/mol 433s Calculating forces... 433s [focusFillBound()]: WARNING: 433s Unusually large potential values 433s detected on the focusing boundary! 433s Convergence not guaranteed for NPBE/NRPBE calculations! 433s 433s ---------------------------------------- 433s CALCULATION #6 (complex-fine): MULTIGRID 433s Setting up problem... 433s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 433s Debye length: 0 A 433s Current memory usage: 251.858 MB total, 494.601 MB high water 433s Using linear spline charge discretization. 433s Grid dimensions: 97 x 97 x 97 433s Grid spacings: 0.250 x 0.250 x 0.250 433s Grid lengths: 24.000 x 24.000 x 24.000 433s Grid center: (24.822, -33.153, 21.545) 433s Multigrid levels: 4 433s Molecule ID: 3 433s Linearized traditional PBE 433s Boundary conditions from focusing 433s 2 ion species (0.000 M ionic strength): 433s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 433s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 433s Solute dielectric: 2.000 433s Solvent dielectric: 78.000 433s Using "molecular" surface definition; no smoothing 433s Solvent probe radius: 1.400 A 433s Temperature: 298.150 K 433s Electrostatic energies will be calculated 433s Total electrostatic energy = 3.158218439277E+05 kJ/mol 433s Calculating forces... 433s ---------------------------------------- 433s PRINT STATEMENTS 433s 433s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 433s Local net energy (PE 0) = 1.192607686582E+02 kJ/mol 433s Global net ELEC energy = 1.192607686582E+02 kJ/mol 433s ---------------------------------------- 433s CLEANING UP AND SHUTTING DOWN... 433s Destroying force arrays. 433s No energy arrays to destroy. 433s Destroying multigrid structures. 433s Destroying finite element structures. 433s Destroying 3 molecules 433s Final memory usage: 0.001 MB total, 494.601 MB high water 433s 433s 433s Thanks for using APBS! 433s 433s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 433s *** PASSED *** 433s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 433s *** PASSED *** 433s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 433s *** PASSED *** 433s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 433s *** PASSED *** 433s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 433s *** PASSED *** 433s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 433s *** PASSED *** 433s Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) 433s *** PASSED *** 433s Elapsed time: 11.469041 seconds 433s -------------------------------------------------------------------------------- 433s -------------------------------------------------------------------------------- 433s Testing input file apbs-smol-surf.in 433s 444s Checking for intermediate energies in input file apbs-mol-surf.out 444s EXPECTED COMPUTED: 7 444s EXPECTED EXPECTED: 7 444s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] 444s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 444s COMPUTED RESULT 2244.350164274 444s COMPUTED RESULT 10521.49475373 444s COMPUTED RESULT 186261.5690066 444s COMPUTED RESULT 305181.0884053 444s COMPUTED RESULT 188662.5455219 444s COMPUTED RESULT 315821.8439277 444s COMPUTED RESULT 119.2607686582 444s BINARY: /usr/bin/apbs 444s INPUT: apbs-smol-surf.in 444s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 444s 444s ---------------------------------------------------------------------- 444s APBS -- Adaptive Poisson-Boltzmann Solver 444s Version APBS 3.4.1 444s 444s Nathan A. Baker (nathan.baker@pnnl.gov) 444s Pacific Northwest National Laboratory 444s 444s Additional contributing authors listed in the code documentation. 444s 444s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 444s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 444s Northwest Division for the U.S. Department of Energy. 444s 444s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 444s Portions Copyright (c) 2002-2020, Nathan A. Baker. 444s Portions Copyright (c) 1999-2002, The Regents of the University of California. 444s Portions Copyright (c) 1995, Michael Holst. 444s All rights reserved. 444s 444s Redistribution and use in source and binary forms, with or without 444s modification, are permitted provided that the following conditions are met: 444s 444s * Redistributions of source code must retain the above copyright notice, this 444s list of conditions and the following disclaimer. 444s 444s * Redistributions in binary form must reproduce the above copyright notice, 444s this list of conditions and the following disclaimer in the documentation 444s and/or other materials provided with the distribution. 444s 444s * Neither the name of the developer nor the names of its contributors may be 444s used to endorse or promote products derived from this software without 444s specific prior written permission. 444s 444s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 444s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 444s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 444s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 444s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 444s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 444s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 444s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 444s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 444s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 444s ---------------------------------------------------------------------- 444s APBS uses FETK (the Finite Element ToolKit) to solve the 444s Poisson-Boltzmann equation numerically. FETK is a portable collection 444s of finite element modeling class libraries developed by the Michael Holst 444s research group and written in an object-oriented form of C. FEtk is 444s designed to solve general coupled systems of nonlinear partial differential 444s equations using adaptive finite element methods, inexact Newton methods, 444s and algebraic multilevel methods. More information about FEtk may be found 444s at . 444s ---------------------------------------------------------------------- 444s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 444s Aqua is a modified form of the Holst group PMG library 444s which has been modified by Patrice Koehl 444s for improved efficiency and 444s memory usage when solving the Poisson-Boltzmann equation. 444s ---------------------------------------------------------------------- 444s Please cite your use of APBS as: 444s 444s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 444s nanosystems: application to microtubules and the ribosome. Proc. 444s Natl. Acad. Sci. USA 98, 10037-10041 2001. 444s 444s 444s This executable compiled on Jan 3 2025 at 11:01:42 444s 444s Parsing input file apbs-smol-surf.in... 444s rank 0 size 1... 444s Parsed input file. 444s Got paths for 3 molecules 444s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 47 atoms 444s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 444s Net charge 1.11e-16 e 444s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 3423 atoms 444s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 444s Net charge 1.00e+00 e 444s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 444s 3470 atoms 444s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 444s Net charge 1.00e+00 e 444s Preparing to run 6 PBE calculations. 444s ---------------------------------------- 444s CALCULATION #1 (lig-coarse): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 203.877 MB total, 203.877 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 97 x 97 x 97 444s Grid spacings: 0.729 x 0.729 x 0.729 444s Grid lengths: 70.000 x 70.000 x 70.000 444s Grid center: (28.969, -32.507, 27.022) 444s Multigrid levels: 4 444s Molecule ID: 1 444s Linearized traditional PBE 444s Single Debye-Huckel sphere boundary conditions 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.000 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 1.400 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 2.251466789420E+03 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #2 (lig-fine): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 203.877 MB total, 405.586 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 97 x 97 x 97 444s Grid spacings: 0.250 x 0.250 x 0.250 444s Grid lengths: 24.000 x 24.000 x 24.000 444s Grid center: (24.822, -33.153, 21.545) 444s Multigrid levels: 4 444s Molecule ID: 1 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.000 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 1.400 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.052814502873E+04 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #3 (pka-coarse): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 251.521 MB total, 405.586 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 97 x 97 x 97 444s Grid spacings: 0.729 x 0.729 x 0.729 444s Grid lengths: 70.000 x 70.000 x 70.000 444s Grid center: (28.969, -32.507, 27.022) 444s Multigrid levels: 4 444s Molecule ID: 2 444s Linearized traditional PBE 444s Single Debye-Huckel sphere boundary conditions 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.000 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 1.400 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.864071689626E+05 kJ/mol 444s Calculating forces... 444s [focusFillBound()]: WARNING: 444s Unusually large potential values 444s detected on the focusing boundary! 444s Convergence not guaranteed for NPBE/NRPBE calculations! 444s 444s ---------------------------------------- 444s CALCULATION #4 (pka-fine): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 251.521 MB total, 493.795 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 97 x 97 x 97 444s Grid spacings: 0.250 x 0.250 x 0.250 444s Grid lengths: 24.000 x 24.000 x 24.000 444s Grid center: (24.822, -33.153, 21.545) 444s Multigrid levels: 4 444s Molecule ID: 2 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.000 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 1.400 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 3.053319953673E+05 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #5 (complex-coarse): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 251.858 MB total, 493.795 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 97 x 97 x 97 444s Grid spacings: 0.729 x 0.729 x 0.729 444s Grid lengths: 70.000 x 70.000 x 70.000 444s Grid center: (28.969, -32.507, 27.022) 444s Multigrid levels: 4 444s Molecule ID: 3 444s Linearized traditional PBE 444s Single Debye-Huckel sphere boundary conditions 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.000 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 1.400 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.888027142979E+05 kJ/mol 444s Calculating forces... 444s [focusFillBound()]: WARNING: 444s Unusually large potential values 444s detected on the focusing boundary! 444s Convergence not guaranteed for NPBE/NRPBE calculations! 444s 444s ---------------------------------------- 444s CALCULATION #6 (complex-fine): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 251.858 MB total, 494.601 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 97 x 97 x 97 444s Grid spacings: 0.250 x 0.250 x 0.250 444s Grid lengths: 24.000 x 24.000 x 24.000 444s Grid center: (24.822, -33.153, 21.545) 444s Multigrid levels: 4 444s Molecule ID: 3 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.000 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 1.400 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 3.159690177241E+05 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s PRINT STATEMENTS 444s 444s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 444s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 444s Global net ELEC energy = 1.088773280806E+02 kJ/mol 444s ---------------------------------------- 444s CLEANING UP AND SHUTTING DOWN... 444s Destroying force arrays. 444s No energy arrays to destroy. 444s Destroying multigrid structures. 444s Destroying finite element structures. 444s Destroying 3 molecules 444s Final memory usage: 0.001 MB total, 494.601 MB high water 444s 444s 444s Thanks for using APBS! 444s 444s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 444s *** PASSED *** 444s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 444s *** PASSED *** 444s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 444s *** PASSED *** 444s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 444s *** PASSED *** 444s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 444s *** PASSED *** 444s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 444s *** PASSED *** 444s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 444s *** PASSED *** 444s Elapsed time: 11.108969 seconds 444s -------------------------------------------------------------------------------- 444s Total elapsed time: 45.393175 seconds 444s Test results have been logged 444s -------------------------------------------------------------------------------- 444s -------------------------------------------------------------------------------- 444s Testing input file complex-0_1.in 444s 444s Checking for intermediate energies in input file apbs-smol-surf.out 444s EXPECTED COMPUTED: 7 444s EXPECTED EXPECTED: 7 444s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 444s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 444s COMPUTED RESULT 2251.46678942 444s COMPUTED RESULT 10528.14502873 444s COMPUTED RESULT 186407.1689626 444s COMPUTED RESULT 305331.9953673 444s COMPUTED RESULT 188802.7142979 444s COMPUTED RESULT 315969.0177241 444s COMPUTED RESULT 108.8773280806 444s Running tests for point-pmf section 444s BINARY: /usr/bin/apbs 444s INPUT: complex-0_1.in 444s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 444s 444s ---------------------------------------------------------------------- 444s APBS -- Adaptive Poisson-Boltzmann Solver 444s Version APBS 3.4.1 444s 444s Nathan A. Baker (nathan.baker@pnnl.gov) 444s Pacific Northwest National Laboratory 444s 444s Additional contributing authors listed in the code documentation. 444s 444s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 444s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 444s Northwest Division for the U.S. Department of Energy. 444s 444s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 444s Portions Copyright (c) 2002-2020, Nathan A. Baker. 444s Portions Copyright (c) 1999-2002, The Regents of the University of California. 444s Portions Copyright (c) 1995, Michael Holst. 444s All rights reserved. 444s 444s Redistribution and use in source and binary forms, with or without 444s modification, are permitted provided that the following conditions are met: 444s 444s * Redistributions of source code must retain the above copyright notice, this 444s list of conditions and the following disclaimer. 444s 444s * Redistributions in binary form must reproduce the above copyright notice, 444s this list of conditions and the following disclaimer in the documentation 444s and/or other materials provided with the distribution. 444s 444s * Neither the name of the developer nor the names of its contributors may be 444s used to endorse or promote products derived from this software without 444s specific prior written permission. 444s 444s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 444s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 444s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 444s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 444s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 444s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 444s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 444s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 444s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 444s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 444s ---------------------------------------------------------------------- 444s APBS uses FETK (the Finite Element ToolKit) to solve the 444s Poisson-Boltzmann equation numerically. FETK is a portable collection 444s of finite element modeling class libraries developed by the Michael Holst 444s research group and written in an object-oriented form of C. FEtk is 444s designed to solve general coupled systems of nonlinear partial differential 444s equations using adaptive finite element methods, inexact Newton methods, 444s and algebraic multilevel methods. More information about FEtk may be found 444s at . 444s ---------------------------------------------------------------------- 444s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 444s Aqua is a modified form of the Holst group PMG library 444s which has been modified by Patrice Koehl 444s for improved efficiency and 444s memory usage when solving the Poisson-Boltzmann equation. 444s ---------------------------------------------------------------------- 444s Please cite your use of APBS as: 444s 444s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 444s nanosystems: application to microtubules and the ribosome. Proc. 444s Natl. Acad. Sci. USA 98, 10037-10041 2001. 444s 444s 444s This executable compiled on Jan 3 2025 at 11:01:42 444s 444s Parsing input file complex-0_1.in... 444s rank 0 size 1... 444s Parsed input file. 444s Got paths for 3 molecules 444s Reading PQR-format atom data from mol0.pqr. 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 1 atoms 444s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 444s Net charge 1.00e+00 e 444s Reading PQR-format atom data from mol1.pqr. 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 1 atoms 444s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 444s Net charge 1.00e+00 e 444s Reading PQR-format atom data from complex-0_1.pqr. 444s 2 atoms 444s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 444s Net charge 2.00e+00 e 444s Preparing to run 3 PBE calculations. 444s ---------------------------------------- 444s CALCULATION #1 (point1): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 61.060 MB total, 61.060 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.210 x 0.210 x 0.210 444s Grid lengths: 13.440 x 13.440 x 13.440 444s Grid center: (0.000, 0.000, 0.000) 444s Multigrid levels: 5 444s Molecule ID: 1 444s Linearized traditional PBE 444s Multiple Debye-Huckel sphere boundary conditions 444s 0 ion species (0.000 M ionic strength): 444s Solute dielectric: 78.540 444s Solvent dielectric: 78.540 444s Using spline-based surface definition;window = 0.300 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 9.776035707281E+01 kJ/mol 444s Fixed charge energy = 97.7604 kJ/mol 444s Mobile charge energy = 0 kJ/mol 444s Dielectric energy = 96.5336 kJ/mol 444s Per-atom energies: 444s Atom 0: 9.776035707281E+01 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #2 (point2): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 61.060 MB total, 61.067 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.210 x 0.210 x 0.210 444s Grid lengths: 13.440 x 13.440 x 13.440 444s Grid center: (0.000, 0.000, 0.000) 444s Multigrid levels: 5 444s Molecule ID: 2 444s Linearized traditional PBE 444s Multiple Debye-Huckel sphere boundary conditions 444s 0 ion species (0.000 M ionic strength): 444s Solute dielectric: 78.540 444s Solvent dielectric: 78.540 444s Using spline-based surface definition;window = 0.300 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 8.975920687031E+01 kJ/mol 444s Fixed charge energy = 89.7592 kJ/mol 444s Mobile charge energy = 0 kJ/mol 444s Dielectric energy = 88.6151 kJ/mol 444s Per-atom energies: 444s Atom 0: 8.975920687031E+01 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #3 (complex): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 61.060 MB total, 61.067 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.210 x 0.210 x 0.210 444s Grid lengths: 13.440 x 13.440 x 13.440 444s Grid center: (0.000, 0.000, 0.000) 444s Multigrid levels: 5 444s Molecule ID: 3 444s Linearized traditional PBE 444s Multiple Debye-Huckel sphere boundary conditions 444s 0 ion species (0.000 M ionic strength): 444s Solute dielectric: 78.540 444s Solvent dielectric: 78.540 444s Using spline-based surface definition;window = 0.300 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 2.058277719334E+02 kJ/mol 444s Fixed charge energy = 205.828 kJ/mol 444s Mobile charge energy = 0 kJ/mol 444s Dielectric energy = 201.106 kJ/mol 444s Per-atom energies: 444s Atom 0: 1.069144350786E+02 kJ/mol 444s Atom 1: 9.891333685475E+01 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s PRINT STATEMENTS 444s 444s print energy 3 (complex) - 1 (point1) - 2 (point2) end 444s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 444s Global net ELEC energy = 1.830820799027E+01 kJ/mol 444s ---------------------------------------- 444s CLEANING UP AND SHUTTING DOWN... 444s Destroying force arrays. 444s No energy arrays to destroy. 444s Destroying multigrid structures. 444s Destroying finite element structures. 444s Destroying 3 molecules 444s Final memory usage: 0.001 MB total, 61.067 MB high water 444s 444s 444s Thanks for using APBS! 444s 444s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 444s *** PASSED *** 444s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 444s *** PASSED *** 444s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 444s *** PASSED *** 444s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 444s *** PASSED *** 444s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 444s *** PASSED *** 444s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 444s *** PASSED *** 444s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 444s *** PASSED *** 444s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 444s *** PASSED *** 444s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 444s *** PASSED *** 444s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 444s *** PASSED *** 444s Elapsed time: 0.529191 seconds 444s -------------------------------------------------------------------------------- 444s -------------------------------------------------------------------------------- 444s Testing input file complex-0_2.in 444s 445s Checking for intermediate energies in input file complex-0_1.out 445s EXPECTED COMPUTED: 13 445s EXPECTED EXPECTED: 13 445s 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] 445s 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'] 445s COMPUTED RESULT 97.76035707281 445s COMPUTED RESULT 89.75920687031 445s COMPUTED RESULT 205.8277719334 445s COMPUTED RESULT 0.0 445s COMPUTED RESULT 0.0 445s COMPUTED RESULT 0.0 445s COMPUTED RESULT 97.7604 445s COMPUTED RESULT 89.7592 445s COMPUTED RESULT 205.828 445s COMPUTED RESULT 96.5336 445s COMPUTED RESULT 88.6151 445s COMPUTED RESULT 201.106 445s COMPUTED RESULT 18.30820799027 445s BINARY: /usr/bin/apbs 445s INPUT: complex-0_2.in 445s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 445s asc_getToken: Error occurred (bailing out). 445s Vio_scanf: Format problem with input. 445s 445s 445s ---------------------------------------------------------------------- 445s APBS -- Adaptive Poisson-Boltzmann Solver 445s Version APBS 3.4.1 445s 445s Nathan A. Baker (nathan.baker@pnnl.gov) 445s Pacific Northwest National Laboratory 445s 445s Additional contributing authors listed in the code documentation. 445s 445s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 445s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 445s Northwest Division for the U.S. Department of Energy. 445s 445s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 445s Portions Copyright (c) 2002-2020, Nathan A. Baker. 445s Portions Copyright (c) 1999-2002, The Regents of the University of California. 445s Portions Copyright (c) 1995, Michael Holst. 445s All rights reserved. 445s 445s Redistribution and use in source and binary forms, with or without 445s modification, are permitted provided that the following conditions are met: 445s 445s * Redistributions of source code must retain the above copyright notice, this 445s list of conditions and the following disclaimer. 445s 445s * Redistributions in binary form must reproduce the above copyright notice, 445s this list of conditions and the following disclaimer in the documentation 445s and/or other materials provided with the distribution. 445s 445s * Neither the name of the developer nor the names of its contributors may be 445s used to endorse or promote products derived from this software without 445s specific prior written permission. 445s 445s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 445s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 445s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 445s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 445s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 445s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 445s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 445s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 445s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 445s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 445s ---------------------------------------------------------------------- 445s APBS uses FETK (the Finite Element ToolKit) to solve the 445s Poisson-Boltzmann equation numerically. FETK is a portable collection 445s of finite element modeling class libraries developed by the Michael Holst 445s research group and written in an object-oriented form of C. FEtk is 445s designed to solve general coupled systems of nonlinear partial differential 445s equations using adaptive finite element methods, inexact Newton methods, 445s and algebraic multilevel methods. More information about FEtk may be found 445s at . 445s ---------------------------------------------------------------------- 445s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 445s Aqua is a modified form of the Holst group PMG library 445s which has been modified by Patrice Koehl 445s for improved efficiency and 445s memory usage when solving the Poisson-Boltzmann equation. 445s ---------------------------------------------------------------------- 445s Please cite your use of APBS as: 445s 445s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 445s nanosystems: application to microtubules and the ribosome. Proc. 445s Natl. Acad. Sci. USA 98, 10037-10041 2001. 445s 445s 445s This executable compiled on Jan 3 2025 at 11:01:42 445s 445s Parsing input file complex-0_2.in... 445s rank 0 size 1... 445s Parsed input file. 445s Got paths for 3 molecules 445s Reading PQR-format atom data from mol0.pqr. 445s asc_getToken: Error occurred (bailing out). 445s Vio_scanf: Format problem with input. 445s 1 atoms 445s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 445s Net charge 1.00e+00 e 445s Reading PQR-format atom data from mol2.pqr. 445s asc_getToken: Error occurred (bailing out). 445s Vio_scanf: Format problem with input. 445s 1 atoms 445s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 445s Net charge 1.00e+00 e 445s Reading PQR-format atom data from complex-0_2.pqr. 445s 2 atoms 445s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 445s Net charge 2.00e+00 e 445s Preparing to run 3 PBE calculations. 445s ---------------------------------------- 445s CALCULATION #1 (point1): MULTIGRID 445s Setting up problem... 445s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 445s Debye length: 0 A 445s Current memory usage: 61.060 MB total, 61.060 MB high water 445s Using linear spline charge discretization. 445s Grid dimensions: 65 x 65 x 65 445s Grid spacings: 0.210 x 0.210 x 0.210 445s Grid lengths: 13.440 x 13.440 x 13.440 445s Grid center: (0.000, 0.000, 0.000) 445s Multigrid levels: 5 445s Molecule ID: 1 445s Linearized traditional PBE 445s Multiple Debye-Huckel sphere boundary conditions 445s 0 ion species (0.000 M ionic strength): 445s Solute dielectric: 78.540 445s Solvent dielectric: 78.540 445s Using spline-based surface definition;window = 0.300 445s Temperature: 298.150 K 445s Electrostatic energies will be calculated 445s Total electrostatic energy = 9.776035707281E+01 kJ/mol 445s Fixed charge energy = 97.7604 kJ/mol 445s Mobile charge energy = 0 kJ/mol 445s Dielectric energy = 96.5336 kJ/mol 445s Per-atom energies: 445s Atom 0: 9.776035707281E+01 kJ/mol 445s Calculating forces... 445s ---------------------------------------- 445s CALCULATION #2 (point2): MULTIGRID 445s Setting up problem... 445s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 445s Debye length: 0 A 445s Current memory usage: 61.060 MB total, 61.067 MB high water 445s Using linear spline charge discretization. 445s Grid dimensions: 65 x 65 x 65 445s Grid spacings: 0.210 x 0.210 x 0.210 445s Grid lengths: 13.440 x 13.440 x 13.440 445s Grid center: (0.000, 0.000, 0.000) 445s Multigrid levels: 5 445s Molecule ID: 2 445s Linearized traditional PBE 445s Multiple Debye-Huckel sphere boundary conditions 445s 0 ion species (0.000 M ionic strength): 445s Solute dielectric: 78.540 445s Solvent dielectric: 78.540 445s Using spline-based surface definition;window = 0.300 445s Temperature: 298.150 K 445s Electrostatic energies will be calculated 445s Total electrostatic energy = 1.017611498797E+02 kJ/mol 445s Fixed charge energy = 101.761 kJ/mol 445s Mobile charge energy = 0 kJ/mol 445s Dielectric energy = 100.656 kJ/mol 445s Per-atom energies: 445s Atom 0: 1.017611498797E+02 kJ/mol 445s Calculating forces... 445s ---------------------------------------- 445s CALCULATION #3 (complex): MULTIGRID 445s Setting up problem... 445s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 445s Debye length: 0 A 445s Current memory usage: 61.060 MB total, 61.068 MB high water 445s Using linear spline charge discretization. 445s Grid dimensions: 65 x 65 x 65 445s Grid spacings: 0.210 x 0.210 x 0.210 445s Grid lengths: 13.440 x 13.440 x 13.440 445s Grid center: (0.000, 0.000, 0.000) 445s Multigrid levels: 5 445s Molecule ID: 3 445s Linearized traditional PBE 445s Multiple Debye-Huckel sphere boundary conditions 445s 0 ion species (0.000 M ionic strength): 445s Solute dielectric: 78.540 445s Solvent dielectric: 78.540 445s Using spline-based surface definition;window = 0.300 445s Temperature: 298.150 K 445s Electrostatic energies will be calculated 445s Total electrostatic energy = 2.084282010393E+02 kJ/mol 445s Fixed charge energy = 208.428 kJ/mol 445s Mobile charge energy = 0 kJ/mol 445s Dielectric energy = 203.83 kJ/mol 445s Per-atom energies: 445s Atom 0: 1.022136878480E+02 kJ/mol 445s Atom 1: 1.062145131913E+02 kJ/mol 445s Calculating forces... 445s ---------------------------------------- 445s PRINT STATEMENTS 445s 445s print energy 3 (complex) - 1 (point1) - 2 (point2) end 445s Local net energy (PE 0) = 8.906694086751E+00 kJ/mol 445s Global net ELEC energy = 8.906694086751E+00 kJ/mol 445s ---------------------------------------- 445s CLEANING UP AND SHUTTING DOWN... 445s Destroying force arrays. 445s No energy arrays to destroy. 445s Destroying multigrid structures. 445s Destroying finite element structures. 445s Destroying 3 molecules 445s Final memory usage: 0.001 MB total, 61.068 MB high water 445s 445s 445s Thanks for using APBS! 445s 445s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 445s *** PASSED *** 445s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 445s *** PASSED *** 445s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 445s *** PASSED *** 445s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 445s *** PASSED *** 445s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 445s *** PASSED *** 445s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) 445s *** PASSED *** 445s Elapsed time: 0.523186 seconds 445s -------------------------------------------------------------------------------- 445s -------------------------------------------------------------------------------- 445s Testing input file complex-0_3.in 445s 445s Checking for intermediate energies in input file complex-0_2.out 445s EXPECTED COMPUTED: 13 445s EXPECTED EXPECTED: 13 445s 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, 8.906694086751] 445s 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'] 445s COMPUTED RESULT 97.76035707281 445s COMPUTED RESULT 101.7611498797 445s COMPUTED RESULT 208.4282010393 445s COMPUTED RESULT 0.0 445s COMPUTED RESULT 0.0 445s COMPUTED RESULT 0.0 445s COMPUTED RESULT 97.7604 445s COMPUTED RESULT 101.761 445s COMPUTED RESULT 208.428 445s COMPUTED RESULT 96.5336 445s COMPUTED RESULT 100.656 445s COMPUTED RESULT 203.83 445s COMPUTED RESULT 8.906694086751 445s BINARY: /usr/bin/apbs 445s INPUT: complex-0_3.in 445s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 445s asc_getToken: Error occurred (bailing out). 445s Vio_scanf: Format problem with input. 445s 445s 445s ---------------------------------------------------------------------- 445s APBS -- Adaptive Poisson-Boltzmann Solver 445s Version APBS 3.4.1 445s 445s Nathan A. Baker (nathan.baker@pnnl.gov) 445s Pacific Northwest National Laboratory 445s 445s Additional contributing authors listed in the code documentation. 445s 445s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 445s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 445s Northwest Division for the U.S. Department of Energy. 445s 445s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 445s Portions Copyright (c) 2002-2020, Nathan A. Baker. 445s Portions Copyright (c) 1999-2002, The Regents of the University of California. 445s Portions Copyright (c) 1995, Michael Holst. 445s All rights reserved. 445s 445s Redistribution and use in source and binary forms, with or without 445s modification, are permitted provided that the following conditions are met: 445s 445s * Redistributions of source code must retain the above copyright notice, this 445s list of conditions and the following disclaimer. 445s 445s * Redistributions in binary form must reproduce the above copyright notice, 445s this list of conditions and the following disclaimer in the documentation 445s and/or other materials provided with the distribution. 445s 445s * Neither the name of the developer nor the names of its contributors may be 445s used to endorse or promote products derived from this software without 445s specific prior written permission. 445s 445s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 445s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 445s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 445s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 445s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 445s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 445s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 445s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 445s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 445s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 445s ---------------------------------------------------------------------- 445s APBS uses FETK (the Finite Element ToolKit) to solve the 445s Poisson-Boltzmann equation numerically. FETK is a portable collection 445s of finite element modeling class libraries developed by the Michael Holst 445s research group and written in an object-oriented form of C. FEtk is 445s designed to solve general coupled systems of nonlinear partial differential 445s equations using adaptive finite element methods, inexact Newton methods, 445s and algebraic multilevel methods. More information about FEtk may be found 445s at . 445s ---------------------------------------------------------------------- 445s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 445s Aqua is a modified form of the Holst group PMG library 445s which has been modified by Patrice Koehl 445s for improved efficiency and 445s memory usage when solving the Poisson-Boltzmann equation. 445s ---------------------------------------------------------------------- 445s Please cite your use of APBS as: 445s 445s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 445s nanosystems: application to microtubules and the ribosome. Proc. 445s Natl. Acad. Sci. USA 98, 10037-10041 2001. 445s 445s 445s This executable compiled on Jan 3 2025 at 11:01:42 445s 445s Parsing input file complex-0_3.in... 445s rank 0 size 1... 445s Parsed input file. 445s Got paths for 3 molecules 445s Reading PQR-format atom data from mol0.pqr. 445s asc_getToken: Error occurred (bailing out). 445s Vio_scanf: Format problem with input. 445s 1 atoms 445s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 445s Net charge 1.00e+00 e 445s Reading PQR-format atom data from mol3.pqr. 445s asc_getToken: Error occurred (bailing out). 445s Vio_scanf: Format problem with input. 445s 1 atoms 445s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 445s Net charge 1.00e+00 e 445s Reading PQR-format atom data from complex-0_3.pqr. 445s 2 atoms 445s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 445s Net charge 2.00e+00 e 445s Preparing to run 3 PBE calculations. 445s ---------------------------------------- 445s CALCULATION #1 (point1): MULTIGRID 445s Setting up problem... 445s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 445s Debye length: 0 A 445s Current memory usage: 61.060 MB total, 61.060 MB high water 445s Using linear spline charge discretization. 445s Grid dimensions: 65 x 65 x 65 445s Grid spacings: 0.210 x 0.210 x 0.210 445s Grid lengths: 13.440 x 13.440 x 13.440 445s Grid center: (0.000, 0.000, 0.000) 445s Multigrid levels: 5 445s Molecule ID: 1 445s Linearized traditional PBE 445s Multiple Debye-Huckel sphere boundary conditions 445s 0 ion species (0.000 M ionic strength): 445s Solute dielectric: 78.540 445s Solvent dielectric: 78.540 445s Using spline-based surface definition;window = 0.300 445s Temperature: 298.150 K 445s Electrostatic energies will be calculated 445s Total electrostatic energy = 9.776035707281E+01 kJ/mol 445s Fixed charge energy = 97.7604 kJ/mol 445s Mobile charge energy = 0 kJ/mol 445s Dielectric energy = 96.5336 kJ/mol 445s Per-atom energies: 445s Atom 0: 9.776035707281E+01 kJ/mol 445s Calculating forces... 445s ---------------------------------------- 445s CALCULATION #2 (point2): MULTIGRID 445s Setting up problem... 445s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 445s Debye length: 0 A 445s Current memory usage: 61.060 MB total, 61.067 MB high water 445s Using linear spline charge discretization. 445s Grid dimensions: 65 x 65 x 65 445s Grid spacings: 0.210 x 0.210 x 0.210 445s Grid lengths: 13.440 x 13.440 x 13.440 445s Grid center: (0.000, 0.000, 0.000) 445s Multigrid levels: 5 445s Molecule ID: 2 445s Linearized traditional PBE 445s Multiple Debye-Huckel sphere boundary conditions 445s 0 ion species (0.000 M ionic strength): 445s Solute dielectric: 78.540 445s Solvent dielectric: 78.540 445s Using spline-based surface definition;window = 0.300 445s Temperature: 298.150 K 445s Electrostatic energies will be calculated 445s Total electrostatic energy = 1.337661883222E+02 kJ/mol 445s Fixed charge energy = 133.766 kJ/mol 445s Mobile charge energy = 0 kJ/mol 445s Dielectric energy = 132.672 kJ/mol 445s Per-atom energies: 445s Atom 0: 1.337661883222E+02 kJ/mol 445s Calculating forces... 445s ---------------------------------------- 445s CALCULATION #3 (complex): MULTIGRID 445s Setting up problem... 445s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 445s Debye length: 0 A 445s Current memory usage: 61.060 MB total, 61.068 MB high water 445s Using linear spline charge discretization. 445s Grid dimensions: 65 x 65 x 65 445s Grid spacings: 0.210 x 0.210 x 0.210 445s Grid lengths: 13.440 x 13.440 x 13.440 445s Grid center: (0.000, 0.000, 0.000) 445s Multigrid levels: 5 445s Molecule ID: 3 445s Linearized traditional PBE 445s Multiple Debye-Huckel sphere boundary conditions 445s 0 ion species (0.000 M ionic strength): 445s Solute dielectric: 78.540 445s Solvent dielectric: 78.540 445s Using spline-based surface definition;window = 0.300 445s Temperature: 298.150 K 445s Electrostatic energies will be calculated 445s Total electrostatic energy = 2.374361452120E+02 kJ/mol 445s Fixed charge energy = 237.436 kJ/mol 445s Mobile charge energy = 0 kJ/mol 445s Dielectric energy = 232.924 kJ/mol 445s Per-atom energies: 445s Atom 0: 1.007151570480E+02 kJ/mol 445s Atom 1: 1.367209881640E+02 kJ/mol 445s Calculating forces... 445s ---------------------------------------- 445s PRINT STATEMENTS 445s 445s print energy 3 (complex) - 1 (point1) - 2 (point2) end 445s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 445s Global net ELEC energy = 5.909599816984E+00 kJ/mol 445s ---------------------------------------- 445s CLEANING UP AND SHUTTING DOWN... 445s Destroying force arrays. 445s No energy arrays to destroy. 445s Destroying multigrid structures. 445s Destroying finite element structures. 445s Destroying 3 molecules 445s Final memory usage: 0.001 MB total, 61.068 MB high water 445s 445s 445s Thanks for using APBS! 445s 445s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 445s *** PASSED *** 445s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 445s *** PASSED *** 445s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 445s *** PASSED *** 445s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 445s *** PASSED *** 445s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 445s *** PASSED *** 445s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 445s *** PASSED *** 445s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 445s *** PASSED *** 445s Elapsed time: 0.498869 seconds 445s -------------------------------------------------------------------------------- 445s -------------------------------------------------------------------------------- 445s Testing input file complex-0_4.in 445s 446s Checking for intermediate energies in input file complex-0_3.out 446s EXPECTED COMPUTED: 13 446s EXPECTED EXPECTED: 13 446s 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] 446s 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'] 446s COMPUTED RESULT 97.76035707281 446s COMPUTED RESULT 133.7661883222 446s COMPUTED RESULT 237.436145212 446s COMPUTED RESULT 0.0 446s COMPUTED RESULT 0.0 446s COMPUTED RESULT 0.0 446s COMPUTED RESULT 97.7604 446s COMPUTED RESULT 133.766 446s COMPUTED RESULT 237.436 446s COMPUTED RESULT 96.5336 446s COMPUTED RESULT 132.672 446s COMPUTED RESULT 232.924 446s COMPUTED RESULT 5.909599816984 446s BINARY: /usr/bin/apbs 446s INPUT: complex-0_4.in 446s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 446s asc_getToken: Error occurred (bailing out). 446s Vio_scanf: Format problem with input. 446s 446s 446s ---------------------------------------------------------------------- 446s APBS -- Adaptive Poisson-Boltzmann Solver 446s Version APBS 3.4.1 446s 446s Nathan A. Baker (nathan.baker@pnnl.gov) 446s Pacific Northwest National Laboratory 446s 446s Additional contributing authors listed in the code documentation. 446s 446s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 446s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 446s Northwest Division for the U.S. Department of Energy. 446s 446s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 446s Portions Copyright (c) 2002-2020, Nathan A. Baker. 446s Portions Copyright (c) 1999-2002, The Regents of the University of California. 446s Portions Copyright (c) 1995, Michael Holst. 446s All rights reserved. 446s 446s Redistribution and use in source and binary forms, with or without 446s modification, are permitted provided that the following conditions are met: 446s 446s * Redistributions of source code must retain the above copyright notice, this 446s list of conditions and the following disclaimer. 446s 446s * Redistributions in binary form must reproduce the above copyright notice, 446s this list of conditions and the following disclaimer in the documentation 446s and/or other materials provided with the distribution. 446s 446s * Neither the name of the developer nor the names of its contributors may be 446s used to endorse or promote products derived from this software without 446s specific prior written permission. 446s 446s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 446s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 446s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 446s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 446s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 446s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 446s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 446s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 446s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 446s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 446s ---------------------------------------------------------------------- 446s APBS uses FETK (the Finite Element ToolKit) to solve the 446s Poisson-Boltzmann equation numerically. FETK is a portable collection 446s of finite element modeling class libraries developed by the Michael Holst 446s research group and written in an object-oriented form of C. FEtk is 446s designed to solve general coupled systems of nonlinear partial differential 446s equations using adaptive finite element methods, inexact Newton methods, 446s and algebraic multilevel methods. More information about FEtk may be found 446s at . 446s ---------------------------------------------------------------------- 446s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 446s Aqua is a modified form of the Holst group PMG library 446s which has been modified by Patrice Koehl 446s for improved efficiency and 446s memory usage when solving the Poisson-Boltzmann equation. 446s ---------------------------------------------------------------------- 446s Please cite your use of APBS as: 446s 446s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 446s nanosystems: application to microtubules and the ribosome. Proc. 446s Natl. Acad. Sci. USA 98, 10037-10041 2001. 446s 446s 446s This executable compiled on Jan 3 2025 at 11:01:42 446s 446s Parsing input file complex-0_4.in... 446s rank 0 size 1... 446s Parsed input file. 446s Got paths for 3 molecules 446s Reading PQR-format atom data from mol0.pqr. 446s asc_getToken: Error occurred (bailing out). 446s Vio_scanf: Format problem with input. 446s 1 atoms 446s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 446s Net charge 1.00e+00 e 446s Reading PQR-format atom data from mol4.pqr. 446s asc_getToken: Error occurred (bailing out). 446s Vio_scanf: Format problem with input. 446s 1 atoms 446s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 446s Net charge 1.00e+00 e 446s Reading PQR-format atom data from complex-0_4.pqr. 446s 2 atoms 446s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 446s Net charge 2.00e+00 e 446s Preparing to run 3 PBE calculations. 446s ---------------------------------------- 446s CALCULATION #1 (point1): MULTIGRID 446s Setting up problem... 446s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 446s Debye length: 0 A 446s Current memory usage: 61.060 MB total, 61.060 MB high water 446s Using linear spline charge discretization. 446s Grid dimensions: 65 x 65 x 65 446s Grid spacings: 0.210 x 0.210 x 0.210 446s Grid lengths: 13.440 x 13.440 x 13.440 446s Grid center: (0.000, 0.000, 0.000) 446s Multigrid levels: 5 446s Molecule ID: 1 446s Linearized traditional PBE 446s Multiple Debye-Huckel sphere boundary conditions 446s 0 ion species (0.000 M ionic strength): 446s Solute dielectric: 78.540 446s Solvent dielectric: 78.540 446s Using spline-based surface definition;window = 0.300 446s Temperature: 298.150 K 446s Electrostatic energies will be calculated 446s Total electrostatic energy = 9.776035707281E+01 kJ/mol 446s Fixed charge energy = 97.7604 kJ/mol 446s Mobile charge energy = 0 kJ/mol 446s Dielectric energy = 96.5336 kJ/mol 446s Per-atom energies: 446s Atom 0: 9.776035707281E+01 kJ/mol 446s Calculating forces... 446s ---------------------------------------- 446s CALCULATION #2 (point2): MULTIGRID 446s Setting up problem... 446s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 446s Debye length: 0 A 446s Current memory usage: 61.060 MB total, 61.067 MB high water 446s Using linear spline charge discretization. 446s Grid dimensions: 65 x 65 x 65 446s Grid spacings: 0.210 x 0.210 x 0.210 446s Grid lengths: 13.440 x 13.440 x 13.440 446s Grid center: (0.000, 0.000, 0.000) 446s Multigrid levels: 5 446s Molecule ID: 2 446s Linearized traditional PBE 446s Multiple Debye-Huckel sphere boundary conditions 446s 0 ion species (0.000 M ionic strength): 446s Solute dielectric: 78.540 446s Solvent dielectric: 78.540 446s Using spline-based surface definition;window = 0.300 446s Temperature: 298.150 K 446s Electrostatic energies will be calculated 446s Total electrostatic energy = 1.017611498797E+02 kJ/mol 446s Fixed charge energy = 101.761 kJ/mol 446s Mobile charge energy = 0 kJ/mol 446s Dielectric energy = 100.654 kJ/mol 446s Per-atom energies: 446s Atom 0: 1.017611498797E+02 kJ/mol 446s Calculating forces... 446s ---------------------------------------- 446s CALCULATION #3 (complex): MULTIGRID 446s Setting up problem... 446s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 446s Debye length: 0 A 446s Current memory usage: 61.061 MB total, 61.068 MB high water 446s Using linear spline charge discretization. 446s Grid dimensions: 65 x 65 x 65 446s Grid spacings: 0.210 x 0.210 x 0.210 446s Grid lengths: 13.440 x 13.440 x 13.440 446s Grid center: (0.000, 0.000, 0.000) 446s Multigrid levels: 5 446s Molecule ID: 3 446s Linearized traditional PBE 446s Multiple Debye-Huckel sphere boundary conditions 446s 0 ion species (0.000 M ionic strength): 446s Solute dielectric: 78.540 446s Solvent dielectric: 78.540 446s Using spline-based surface definition;window = 0.300 446s Temperature: 298.150 K 446s Electrostatic energies will be calculated 446s Total electrostatic energy = 2.039516519000E+02 kJ/mol 446s Fixed charge energy = 203.952 kJ/mol 446s Mobile charge energy = 0 kJ/mol 446s Dielectric energy = 199.493 kJ/mol 446s Per-atom energies: 446s Atom 0: 9.997541697022E+01 kJ/mol 446s Atom 1: 1.039762349297E+02 kJ/mol 446s Calculating forces... 446s ---------------------------------------- 446s PRINT STATEMENTS 446s 446s print energy 3 (complex) - 1 (point1) - 2 (point2) end 446s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 446s Global net ELEC energy = 4.430144947418E+00 kJ/mol 446s ---------------------------------------- 446s CLEANING UP AND SHUTTING DOWN... 446s Destroying force arrays. 446s No energy arrays to destroy. 446s Destroying multigrid structures. 446s Destroying finite element structures. 446s Destroying 3 molecules 446s Final memory usage: 0.001 MB total, 61.068 MB high water 446s 446s 446s Thanks for using APBS! 446s 446s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 446s *** PASSED *** 446s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 446s *** PASSED *** 446s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 446s *** PASSED *** 446s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 446s *** PASSED *** 446s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 446s *** PASSED *** 446s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 446s *** PASSED *** 446s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 446s *** PASSED *** 446s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 446s *** PASSED *** 446s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 446s *** PASSED *** 446s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 446s *** PASSED *** 446s Elapsed time: 0.620389 seconds 446s -------------------------------------------------------------------------------- 446s Total elapsed time: 2.171635 seconds 446s Test results have been logged 446s -------------------------------------------------------------------------------- 446s -------------------------------------------------------------------------------- 446s Testing input file apbs-mol.in 446s 447s Checking for intermediate energies in input file complex-0_4.out 447s EXPECTED COMPUTED: 13 447s EXPECTED EXPECTED: 13 447s 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] 447s 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'] 447s COMPUTED RESULT 97.76035707281 447s COMPUTED RESULT 101.7611498797 447s COMPUTED RESULT 203.9516519 447s COMPUTED RESULT 0.0 447s COMPUTED RESULT 0.0 447s COMPUTED RESULT 0.0 447s COMPUTED RESULT 97.7604 447s COMPUTED RESULT 101.761 447s COMPUTED RESULT 203.952 447s COMPUTED RESULT 96.5336 447s COMPUTED RESULT 100.654 447s COMPUTED RESULT 199.493 447s COMPUTED RESULT 4.430144947418 447s Running tests for solv section 447s BINARY: /usr/bin/apbs 447s INPUT: apbs-mol.in 447s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 447s asc_getToken: Error occurred (bailing out). 447s Vio_scanf: Format problem with input. 447s 447s 447s ---------------------------------------------------------------------- 447s APBS -- Adaptive Poisson-Boltzmann Solver 447s Version APBS 3.4.1 447s 447s Nathan A. Baker (nathan.baker@pnnl.gov) 447s Pacific Northwest National Laboratory 447s 447s Additional contributing authors listed in the code documentation. 447s 447s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 447s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 447s Northwest Division for the U.S. Department of Energy. 447s 447s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 447s Portions Copyright (c) 2002-2020, Nathan A. Baker. 447s Portions Copyright (c) 1999-2002, The Regents of the University of California. 447s Portions Copyright (c) 1995, Michael Holst. 447s All rights reserved. 447s 447s Redistribution and use in source and binary forms, with or without 447s modification, are permitted provided that the following conditions are met: 447s 447s * Redistributions of source code must retain the above copyright notice, this 447s list of conditions and the following disclaimer. 447s 447s * Redistributions in binary form must reproduce the above copyright notice, 447s this list of conditions and the following disclaimer in the documentation 447s and/or other materials provided with the distribution. 447s 447s * Neither the name of the developer nor the names of its contributors may be 447s used to endorse or promote products derived from this software without 447s specific prior written permission. 447s 447s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 447s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 447s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 447s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 447s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 447s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 447s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 447s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 447s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 447s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 447s ---------------------------------------------------------------------- 447s APBS uses FETK (the Finite Element ToolKit) to solve the 447s Poisson-Boltzmann equation numerically. FETK is a portable collection 447s of finite element modeling class libraries developed by the Michael Holst 447s research group and written in an object-oriented form of C. FEtk is 447s designed to solve general coupled systems of nonlinear partial differential 447s equations using adaptive finite element methods, inexact Newton methods, 447s and algebraic multilevel methods. More information about FEtk may be found 447s at . 447s ---------------------------------------------------------------------- 447s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 447s Aqua is a modified form of the Holst group PMG library 447s which has been modified by Patrice Koehl 447s for improved efficiency and 447s memory usage when solving the Poisson-Boltzmann equation. 447s ---------------------------------------------------------------------- 447s Please cite your use of APBS as: 447s 447s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 447s nanosystems: application to microtubules and the ribosome. Proc. 447s Natl. Acad. Sci. USA 98, 10037-10041 2001. 447s 447s 447s This executable compiled on Jan 3 2025 at 11:01:42 447s 447s Parsing input file apbs-mol.in... 447s rank 0 size 1... 447s Parsed input file. 447s Got paths for 2 molecules 447s Reading PQR-format atom data from methanol.pqr. 447s asc_getToken: Error occurred (bailing out). 447s Vio_scanf: Format problem with input. 447s 3 atoms 447s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 447s Net charge 5.55e-17 e 447s Reading PQR-format atom data from methoxide.pqr. 447s 2 atoms 447s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 447s Net charge -1.00e+00 e 447s Preparing to run 4 PBE calculations. 447s ---------------------------------------- 447s CALCULATION #1 (methanol-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.253 MB total, 61.253 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.309, 0.000, -0.242) 447s Multigrid levels: 5 447s Molecule ID: 1 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 78.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 1.847663548071E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #2 (methanol-ref): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.253 MB total, 61.328 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.309, 0.000, -0.242) 447s Multigrid levels: 5 447s Molecule ID: 1 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 1.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 1.883912182952E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #3 (methoxide-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.250 MB total, 61.328 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.000, 0.000, -0.128) 447s Multigrid levels: 5 447s Molecule ID: 2 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 78.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 2.732623683321E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #4 (methoxide-ref): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.250 MB total, 61.328 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.000, 0.000, -0.128) 447s Multigrid levels: 5 447s Molecule ID: 2 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 1.000 447s Using "molecular" surface definitionTesting computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 447s *** PASSED *** 447s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 447s *** PASSED *** 447s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 447s *** PASSED *** 447s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 447s *** PASSED *** 447s Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) 447s *** PASSED *** 447s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 447s *** PASSED *** 447s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 447s *** PASSED *** 447s Elapsed time: 0.824559 seconds 447s -------------------------------------------------------------------------------- 447s -------------------------------------------------------------------------------- 447s Testing input file apbs-smol.in 447s 447s ; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 3.123035854133E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s PRINT STATEMENTS 447s 447s print energy 1 (methanol-solv) - 2 (methanol-ref) end 447s Local net energy (PE 0) = -3.624863488075E+01 kJ/mol 447s Global net ELEC energy = -3.624863488075E+01 kJ/mol 447s 447s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 447s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 447s Global net ELEC energy = -3.904121708125E+02 kJ/mol 447s 447s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 447s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 447s Global net ELEC energy = -3.541635359318E+02 kJ/mol 447s ---------------------------------------- 447s CLEANING UP AND SHUTTING DOWN... 447s Destroying force arrays. 447s No energy arrays to destroy. 447s Destroying multigrid structures. 447s Destroying finite element structures. 447s Destroying 2 molecules 447s Final memory usage: 0.001 MB total, 61.328 MB high water 447s 447s 447s Thanks for using APBS! 447s 447s Checking for intermediate energies in input file apbs-mol.out 447s EXPECTED COMPUTED: 7 447s EXPECTED EXPECTED: 7 447s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] 447s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 447s COMPUTED RESULT 1847.663548071 447s COMPUTED RESULT 1883.912182952 447s COMPUTED RESULT 2732.623683321 447s COMPUTED RESULT 3123.035854133 447s COMPUTED RESULT -36.24863488075 447s COMPUTED RESULT -390.4121708125 447s COMPUTED RESULT -354.1635359318 447s BINARY: /usr/bin/apbs 447s INPUT: apbs-smol.in 447s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 447s asc_getToken: Error occurred (bailing out). 447s Vio_scanf: Format problem with input. 447s 447s 447s ---------------------------------------------------------------------- 447s APBS -- Adaptive Poisson-Boltzmann Solver 447s Version APBS 3.4.1 447s 447s Nathan A. Baker (nathan.baker@pnnl.gov) 447s Pacific Northwest National Laboratory 447s 447s Additional contributing authors listed in the code documentation. 447s 447s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 447s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 447s Northwest Division for the U.S. Department of Energy. 447s 447s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 447s Portions Copyright (c) 2002-2020, Nathan A. Baker. 447s Portions Copyright (c) 1999-2002, The Regents of the University of California. 447s Portions Copyright (c) 1995, Michael Holst. 447s All rights reserved. 447s 447s Redistribution and use in source and binary forms, with or without 447s modification, are permitted provided that the following conditions are met: 447s 447s * Redistributions of source code must retain the above copyright notice, this 447s list of conditions and the following disclaimer. 447s 447s * Redistributions in binary form must reproduce the above copyright notice, 447s this list of conditions and the following disclaimer in the documentation 447s and/or other materials provided with the distribution. 447s 447s * Neither the name of the developer nor the names of its contributors may be 447s used to endorse or promote products derived from this software without 447s specific prior written permission. 447s 447s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 447s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 447s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 447s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 447s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 447s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 447s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 447s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 447s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 447s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 447s ---------------------------------------------------------------------- 447s APBS uses FETK (the Finite Element ToolKit) to solve the 447s Poisson-Boltzmann equation numerically. FETK is a portable collection 447s of finite element modeling class libraries developed by the Michael Holst 447s research group and written in an object-oriented form of C. FEtk is 447s designed to solve general coupled systems of nonlinear partial differential 447s equations using adaptive finite element methods, inexact Newton methods, 447s and algebraic multilevel methods. More information about FEtk may be found 447s at . 447s ---------------------------------------------------------------------- 447s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 447s Aqua is a modified form of the Holst group PMG library 447s which has been modified by Patrice Koehl 447s for improved efficiency and 447s memory usage when solving the Poisson-Boltzmann equation. 447s ---------------------------------------------------------------------- 447s Please cite your use of APBS as: 447s 447s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 447s nanosystems: application to microtubules and the ribosome. Proc. 447s Natl. Acad. Sci. USA 98, 10037-10041 2001. 447s 447s 447s This executable compiled on Jan 3 2025 at 11:01:42 447s 447s Parsing input file apbs-smol.in... 447s rank 0 size 1... 447s Parsed input file. 447s Got paths for 2 molecules 447s Reading PQR-format atom data from methanol.pqr. 447s asc_getToken: Error occurred (bailing out). 447s Vio_scanf: Format problem with input. 447s 3 atoms 447s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 447s Net charge 5.55e-17 e 447s Reading PQR-format atom data from methoxide.pqr. 447s 2 atoms 447s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 447s Net charge -1.00e+00 e 447s Preparing to run 4 PBE calculations. 447s ---------------------------------------- 447s CALCULATION #1 (methanol-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.253 MB total, 61.253 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.309, 0.000, -0.242) 447s Multigrid levels: 5 447s Molecule ID: 1 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 78.000 447s Using "molecular" surface definition;harmonic average smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 1.847860440020E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #2 (methanol-ref): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.253 MB total, 61.328 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.309, 0.000, -0.242) 447s Multigrid levels: 5 447s Molecule ID: 1 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 1.000 447s Using "molecular" surface definition;harmonic average smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 1.885436377745E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #3 (methoxide-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.250 MB total, 61.328 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.000, 0.000, -0.128) 447s Multigrid levels: 5 447s Molecule ID: 2 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 78.000 447s Using "molecular" surface definition;harmonic average smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 2.734040568569E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #4 (methoxide-ref): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 0 A 447s Current memory usage: 61.250 MB total, 61.328 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.250 x 0.250 x 0.250 447s Grid lengths: 16.000 x 16.000 x 16.000 447s Grid center: (0.000, 0.000, -0.128) 447s Multigrid levels: 5 447s Molecule ID: 2 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.000 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 447s Solute dielectric: 2.000 447s Solvent dielectric: 1.00Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 447s *** PASSED *** 447s 0 447s Using "molecular" surface definition;harmonic average smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 300.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 3.125279428954E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s PRINT STATEMENTS 447s 447s print energy 1 (methanol-solv) - 2 (methanol-ref) end 447s Local net energy (PE 0) = -3.757593772492E+01 kJ/mol 447s Global net ELEC energy = -3.757593772492E+01 kJ/mol 447s 447s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 447s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 447s Global net ELEC energy = -3.912388603848E+02 kJ/mol 447s 447s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 447s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 447s Global net ELEC energy = -3.536629226599E+02 kJ/mol 447s ---------------------------------------- 447s CLEANING UP AND SHUTTING DOWN... 447s Destroying force arrays. 447s No energy arrays to destroy. 447s Destroying multigrid structures. 447s Destroying finite element structures. 447s Destroying 2 molecules 447s Final memory usage: 0.001 MB total, 61.328 MB high water 447s 447s 447s Thanks for using APBS! 447s 447s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 447s *** PASSED *** 447s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 447s *** PASSED *** 447s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 447s *** PASSED *** 447s Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) 447s *** PASSED *** 447s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 447s *** PASSED *** 447s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 447s *** PASSED *** 447s Elapsed time: 0.587957 seconds 447s -------------------------------------------------------------------------------- 447s Total elapsed time: 1.412516 seconds 447s Test results have been logged 447s -------------------------------------------------------------------------------- 447s Checking for intermediate energies in input file apbs-smol.out 447s EXPECTED COMPUTED: 7 447s EXPECTED EXPECTED: 7 447s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] 447s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 447s COMPUTED RESULT 1847.86044002 447s COMPUTED RESULT 1885.436377745 447s COMPUTED RESULT 2734.040568569 447s COMPUTED RESULT 3125.279428954 447s COMPUTED RESULT -37.57593772492 447s COMPUTED RESULT -391.2388603848 447s COMPUTED RESULT -353.6629226599 448s autopkgtest [00:52:43]: test test-apbs: -----------------------] 449s test-apbs PASS 449s autopkgtest [00:52:44]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 449s autopkgtest [00:52:44]: @@@@@@@@@@@@@@@@@@@@ summary 449s test-apbs PASS