0s autopkgtest [00:29:02]: starting date and time: 2025-10-20 00:29:02+0000 0s autopkgtest [00:29:02]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [00:29:02]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1i7duivs/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-13.secgroup --name adt-resolute-arm64-apbs-20251020-002902-juju-7f2275-prod-proposed-migration-environment-20-7da3a588-2d3a-478e-bca6-392d7844e7f1 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-apbs-20251020-002902-juju-7f2275-prod-proposed-migration-environment-20-7da3a588-2d3a-478e-bca6-392d7844e7f1 from image adt/ubuntu-resolute-arm64-server-20251019.img (UUID 66624775-bb7d-402f-bbba-489c1d649d18)... 64s autopkgtest [00:30:06]: testbed dpkg architecture: arm64 65s autopkgtest [00:30:07]: testbed apt version: 3.1.8ubuntu1 65s autopkgtest [00:30:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s autopkgtest [00:30:07]: testbed release detected to be: None 66s autopkgtest [00:30:08]: updating testbed package index (apt update) 66s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 66s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [47.8 kB] 67s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.8 kB] 67s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [396 kB] 67s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 67s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [110 kB] 67s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 67s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [274 kB] 67s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [8020 B] 67s Fetched 984 kB in 1s (1004 kB/s) 68s Reading package lists... 69s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 70s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Calculating upgrade... 71s The following packages will be upgraded: 71s distro-info-data dpkg dpkg-dev libaudit-common libaudit1 libdpkg-perl 71s libp11-kit0 libseccomp2 python-apt-common python3-apt 71s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 3273 kB of archives. 71s After this operation, 503 kB of additional disk space will be used. 71s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 dpkg arm64 1.22.21ubuntu4 [1274 kB] 73s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libaudit-common all 1:4.0.5-1build2 [6596 B] 73s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libaudit1 arm64 1:4.0.5-1build2 [58.6 kB] 73s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 distro-info-data all 0.68 [7378 B] 73s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libp11-kit0 arm64 0.25.9-2 [283 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libseccomp2 arm64 2.6.0-2ubuntu3 [56.1 kB] 73s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python-apt-common all 3.0.0ubuntu2 [21.7 kB] 73s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-apt arm64 3.0.0ubuntu2 [197 kB] 73s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dpkg-dev all 1.22.21ubuntu4 [1088 kB] 74s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libdpkg-perl all 1.22.21ubuntu4 [280 kB] 75s dpkg-preconfigure: unable to re-open stdin: No such file or directory 75s Fetched 3273 kB in 3s (1029 kB/s) 75s (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 ... 83359 files and directories currently installed.) 75s Preparing to unpack .../dpkg_1.22.21ubuntu4_arm64.deb ... 75s Unpacking dpkg (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 75s Setting up dpkg (1.22.21ubuntu4) ... 76s (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 ... 83359 files and directories currently installed.) 76s Preparing to unpack .../libaudit-common_1%3a4.0.5-1build2_all.deb ... 76s Unpacking libaudit-common (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 76s Setting up libaudit-common (1:4.0.5-1build2) ... 76s (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 ... 83359 files and directories currently installed.) 76s Preparing to unpack .../libaudit1_1%3a4.0.5-1build2_arm64.deb ... 76s Unpacking libaudit1:arm64 (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 76s Setting up libaudit1:arm64 (1:4.0.5-1build2) ... 76s (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 ... 83359 files and directories currently installed.) 76s Preparing to unpack .../0-distro-info-data_0.68_all.deb ... 76s Unpacking distro-info-data (0.68) over (0.67~ubuntu1) ... 76s Preparing to unpack .../1-libp11-kit0_0.25.9-2_arm64.deb ... 76s Unpacking libp11-kit0:arm64 (0.25.9-2) over (0.25.5-3ubuntu1) ... 77s Preparing to unpack .../2-libseccomp2_2.6.0-2ubuntu3_arm64.deb ... 77s Unpacking libseccomp2:arm64 (2.6.0-2ubuntu3) over (2.6.0-2ubuntu2) ... 77s Preparing to unpack .../3-python-apt-common_3.0.0ubuntu2_all.deb ... 77s Unpacking python-apt-common (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 77s Preparing to unpack .../4-python3-apt_3.0.0ubuntu2_arm64.deb ... 77s Unpacking python3-apt (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 77s Preparing to unpack .../5-dpkg-dev_1.22.21ubuntu4_all.deb ... 77s Unpacking dpkg-dev (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 77s Preparing to unpack .../6-libdpkg-perl_1.22.21ubuntu4_all.deb ... 77s Unpacking libdpkg-perl (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 77s Setting up distro-info-data (0.68) ... 77s Setting up libseccomp2:arm64 (2.6.0-2ubuntu3) ... 77s Setting up libp11-kit0:arm64 (0.25.9-2) ... 77s Setting up libdpkg-perl (1.22.21ubuntu4) ... 77s Setting up python-apt-common (3.0.0ubuntu2) ... 77s Setting up python3-apt (3.0.0ubuntu2) ... 78s Setting up dpkg-dev (1.22.21ubuntu4) ... 78s Processing triggers for man-db (2.13.1-1) ... 80s Processing triggers for libc-bin (2.42-0ubuntu3) ... 80s autopkgtest [00:30:22]: upgrading testbed (apt dist-upgrade and autopurge) 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Calculating upgrade... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Solving dependencies... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [00:30:24]: rebooting testbed after setup commands that affected boot 110s autopkgtest [00:30:52]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 113s autopkgtest [00:30:55]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 143s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 143s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 143s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 143s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 143s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 143s gpgv: Can't check signature: No public key 143s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 145s autopkgtest [00:31:27]: testing package apbs version 3.4.1-6build2 152s autopkgtest [00:31:34]: build not needed 159s autopkgtest [00:31:41]: test test-apbs: preparing testbed 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s Solving dependencies... 160s The following NEW packages will be installed: 160s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax 160s libamd-comgr2 libamd3 libamdhip64-5 libapbs-dev libapbs3t64 libarpack2t64 160s libblas3 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdrm-amdgpu1 160s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfetk-dev 160s libfetk1.9t64 libgfortran5 libgomp1 libhsa-runtime64-1 libhsakmt1 160s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libjs-jquery libjs-mathjax 160s libjs-sphinxdoc libjs-underscore liblapack3 libllvm17t64 libmaloc-dev 160s libmaloc1 libopenmpi40 libpciaccess0 librdmacm1t64 libspqr4 160s libsuitesparseconfig7 libsuperlu7 libucx0 libumfpack6 libxnvctrl0 160s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 160s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 160s Need to get 81.8 MB of archives. 160s After this operation, 341 MB of additional disk space will be used. 160s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-lato all 2.015-1 [2781 kB] 161s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 apbs-data all 3.4.1-6build2 [1769 kB] 162s Get:3 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmaloc1 arm64 1.5-2 [88.6 kB] 162s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 162s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsuperlu7 arm64 7.0.1+dfsg1-2 [171 kB] 162s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 162s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libsuitesparseconfig7 arm64 1:7.10.1+dfsg-1 [21.5 kB] 162s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd3 arm64 1:7.10.1+dfsg-1 [34.3 kB] 162s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcamd3 arm64 1:7.10.1+dfsg-1 [30.8 kB] 162s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libccolamd3 arm64 1:7.10.1+dfsg-1 [33.6 kB] 162s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolamd3 arm64 1:7.10.1+dfsg-1 [26.5 kB] 162s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 162s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 163s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcholmod5 arm64 1:7.10.1+dfsg-1 [622 kB] 163s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 libumfpack6 arm64 1:7.10.1+dfsg-1 [258 kB] 163s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfetk1.9t64 arm64 3.4.1-6build2 [592 kB] 163s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapbs3t64 arm64 3.4.1-6build2 [271 kB] 163s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 163s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 163s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 libarpack2t64 arm64 3.9.1-6 [94.9 kB] 163s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10build1 [97.5 kB] 163s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10build1 [8272 B] 163s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 librdmacm1t64 arm64 56.1-1ubuntu1 [71.4 kB] 164s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfabric1 arm64 2.1.0-1.1 [622 kB] 164s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc15 arm64 2.12.2-1 [169 kB] 164s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 libllvm17t64 arm64 1:17.0.6-22build1 [24.8 MB] 165s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build3 [14.0 MB] 165s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-amdgpu1 arm64 2.4.125-1 [21.6 kB] 165s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsakmt1 arm64 6.2.4+ds-1 [64.7 kB] 165s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsa-runtime64-1 arm64 6.1.2-3 [305 kB] 165s Get:31 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamdhip64-5 arm64 5.7.1-6 [9707 kB] 165s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libibumad3 arm64 56.1-1ubuntu1 [31.3 kB] 165s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libibmad5 arm64 56.1-1ubuntu1 [44.1 kB] 165s Get:34 http://ftpmaster.internal/ubuntu resolute/universe arm64 libucx0 arm64 1.19.0+ds-1 [1242 kB] 165s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libpciaccess0 arm64 0.18.1-1ubuntu2 [19.4 kB] 165s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 165s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 ocl-icd-libopencl1 arm64 2.3.3-1 [42.2 kB] 165s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc-plugins arm64 2.12.2-1 [16.6 kB] 165s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmpi40 arm64 5.0.8-8ubuntu1 [3274 kB] 166s Get:40 http://ftpmaster.internal/ubuntu resolute/universe arm64 libspqr4 arm64 1:7.10.1+dfsg-1 [138 kB] 166s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 apbs arm64 3.4.1-6build2 [75.6 kB] 166s Get:42 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 166s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 166s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 166s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 166s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 166s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 apbs-doc all 3.4.1-6build2 [5850 kB] 166s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapbs-dev arm64 3.4.1-6build2 [99.5 kB] 166s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmaloc-dev arm64 1.5-2 [904 kB] 166s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfetk-dev arm64 3.4.1-6build2 [144 kB] 166s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-apbslib arm64 3.4.1-6build2 [207 kB] 166s Fetched 81.8 MB in 6s (13.5 MB/s) 167s Selecting previously unselected package fonts-lato. 167s (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 ... 83363 files and directories currently installed.) 167s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 167s Unpacking fonts-lato (2.015-1) ... 167s Selecting previously unselected package apbs-data. 167s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 167s Unpacking apbs-data (3.4.1-6build2) ... 167s Selecting previously unselected package libmaloc1:arm64. 167s Preparing to unpack .../02-libmaloc1_1.5-2_arm64.deb ... 167s Unpacking libmaloc1:arm64 (1.5-2) ... 167s Selecting previously unselected package libblas3:arm64. 167s Preparing to unpack .../03-libblas3_3.12.1-6build1_arm64.deb ... 167s Unpacking libblas3:arm64 (3.12.1-6build1) ... 167s Selecting previously unselected package libsuperlu7:arm64. 167s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_arm64.deb ... 167s Unpacking libsuperlu7:arm64 (7.0.1+dfsg1-2) ... 167s Selecting previously unselected package libgomp1:arm64. 167s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 167s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 167s Selecting previously unselected package libsuitesparseconfig7:arm64. 167s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_arm64.deb ... 167s Unpacking libsuitesparseconfig7:arm64 (1:7.10.1+dfsg-1) ... 167s Selecting previously unselected package libamd3:arm64. 167s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 167s Unpacking libamd3:arm64 (1:7.10.1+dfsg-1) ... 167s Selecting previously unselected package libcamd3:arm64. 167s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 167s Unpacking libcamd3:arm64 (1:7.10.1+dfsg-1) ... 167s Selecting previously unselected package libccolamd3:arm64. 168s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 168s Unpacking libccolamd3:arm64 (1:7.10.1+dfsg-1) ... 168s Selecting previously unselected package libcolamd3:arm64. 168s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 168s Unpacking libcolamd3:arm64 (1:7.10.1+dfsg-1) ... 168s Selecting previously unselected package libgfortran5:arm64. 168s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 168s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 168s Selecting previously unselected package liblapack3:arm64. 168s Preparing to unpack .../12-liblapack3_3.12.1-6build1_arm64.deb ... 168s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 168s Selecting previously unselected package libcholmod5:arm64. 168s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_arm64.deb ... 168s Unpacking libcholmod5:arm64 (1:7.10.1+dfsg-1) ... 168s Selecting previously unselected package libumfpack6:arm64. 168s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_arm64.deb ... 168s Unpacking libumfpack6:arm64 (1:7.10.1+dfsg-1) ... 168s Selecting previously unselected package libfetk1.9t64:arm64. 168s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_arm64.deb ... 168s Unpacking libfetk1.9t64:arm64 (3.4.1-6build2) ... 168s Selecting previously unselected package libapbs3t64:arm64. 168s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_arm64.deb ... 168s Unpacking libapbs3t64:arm64 (3.4.1-6build2) ... 168s Selecting previously unselected package fonts-mathjax. 168s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 168s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 168s Selecting previously unselected package libjs-mathjax. 168s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 168s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 169s Selecting previously unselected package libarpack2t64:arm64. 169s Preparing to unpack .../19-libarpack2t64_3.9.1-6_arm64.deb ... 169s Unpacking libarpack2t64:arm64 (3.9.1-6) ... 169s Selecting previously unselected package libevent-core-2.1-7t64:arm64. 169s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 169s Unpacking libevent-core-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 169s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 169s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 169s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 169s Selecting previously unselected package librdmacm1t64:arm64. 169s Preparing to unpack .../22-librdmacm1t64_56.1-1ubuntu1_arm64.deb ... 169s Unpacking librdmacm1t64:arm64 (56.1-1ubuntu1) ... 169s Selecting previously unselected 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172s Selecting previously unselected package libfetk-dev:arm64. 172s Preparing to unpack .../49-libfetk-dev_3.4.1-6build2_arm64.deb ... 172s Unpacking libfetk-dev:arm64 (3.4.1-6build2) ... 172s Selecting previously unselected package python3-apbslib. 172s Preparing to unpack .../50-python3-apbslib_3.4.1-6build2_arm64.deb ... 172s Unpacking python3-apbslib (3.4.1-6build2) ... 172s Setting up libmaloc1:arm64 (1.5-2) ... 172s Setting up libpciaccess0:arm64 (0.18.1-1ubuntu2) ... 172s Setting up fonts-lato (2.015-1) ... 172s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 172s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 172s Setting up libibumad3:arm64 (56.1-1ubuntu1) ... 172s Setting up libibmad5:arm64 (56.1-1ubuntu1) ... 172s Setting up apbs-data (3.4.1-6build2) ... 172s Setting up libgomp1:arm64 (15.2.0-5ubuntu1) ... 172s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 172s Setting up libblas3:arm64 (3.12.1-6build1) ... 172s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 172s Setting up libllvm17t64:arm64 (1:17.0.6-22build1) ... 172s Setting up libhwloc15:arm64 (2.12.2-1) ... 172s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 172s Setting up ocl-icd-libopencl1:arm64 (2.3.3-1) ... 172s Setting up libsuitesparseconfig7:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up librdmacm1t64:arm64 (56.1-1ubuntu1) ... 172s Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 172s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build3) ... 172s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 172s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 172s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 172s Setting up libmaloc-dev (1.5-2) ... 172s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 172s Setting up libdrm-amdgpu1:arm64 (2.4.125-1) ... 172s Setting up libfabric1:arm64 (2.1.0-1.1) ... 172s Setting up liblapack3:arm64 (3.12.1-6build1) ... 172s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 172s Setting up libarpack2t64:arm64 (3.9.1-6) ... 172s Setting up libamd3:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up libcolamd3:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 172s Setting up libhwloc-plugins:arm64 (2.12.2-1) ... 172s Setting up libcamd3:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up libsuperlu7:arm64 (7.0.1+dfsg1-2) ... 172s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 172s Setting up libccolamd3:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up libhsakmt1:arm64 (6.2.4+ds-1) ... 172s Setting up libcholmod5:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up libspqr4:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up apbs-doc (3.4.1-6build2) ... 172s Setting up libumfpack6:arm64 (1:7.10.1+dfsg-1) ... 172s Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ... 172s Setting up libfetk1.9t64:arm64 (3.4.1-6build2) ... 172s Setting up libapbs3t64:arm64 (3.4.1-6build2) ... 172s Setting up libfetk-dev:arm64 (3.4.1-6build2) ... 172s Setting up libamdhip64-5:arm64 (5.7.1-6) ... 172s Setting up libapbs-dev:arm64 (3.4.1-6build2) ... 172s Setting up python3-apbslib (3.4.1-6build2) ... 172s Setting up libucx0:arm64 (1.19.0+ds-1) ... 172s Setting up libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 172s Setting up apbs (3.4.1-6build2) ... 172s Processing triggers for man-db (2.13.1-1) ... 173s Processing triggers for libc-bin (2.42-0ubuntu3) ... 175s autopkgtest [00:31:57]: test test-apbs: [----------------------- 175s TESTING WITH BINARY_NAME:apbs 175s START_DIR:/tmp/autopkgtest.aGVPak/autopkgtest_tmp/build 175s -------------------------------------------------------------------------------- 175s Testing forces from apbs-forces.in 175s 175s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000904 seconds 175s -------------------------------------------------------------------------------- 175s -------------------------------------------------------------------------------- 175s Testing input file apbs-mol-auto.in 175s 178s CHECKING:/usr/local/sbin/apbs 178s CHECKING:/usr/local/bin/apbs 178s CHECKING:/usr/sbin/apbs 178s CHECKING:/usr/bin/apbs 178s NOTE: Using apbs binary:/usr/bin/apbs 178s Testing all sections 178s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 178s ================================================================================ 178s Running tests for born section 178s BINARY: /usr/bin/apbs 178s INPUT: apbs-mol-auto.in 178s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 178s asc_getToken: Error occurred (bailing out). 178s Vio_scanf: Format problem with input. 178s 178s 178s ---------------------------------------------------------------------- 178s APBS -- Adaptive Poisson-Boltzmann Solver 178s Version APBS 3.4.1 178s 178s Nathan A. Baker (nathan.baker@pnnl.gov) 178s Pacific Northwest National Laboratory 178s 178s Additional contributing authors listed in the code documentation. 178s 178s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 178s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 178s Northwest Division for the U.S. Department of Energy. 178s 178s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 178s Portions Copyright (c) 2002-2020, Nathan A. Baker. 178s Portions Copyright (c) 1999-2002, The Regents of the University of California. 178s Portions Copyright (c) 1995, Michael Holst. 178s All rights reserved. 178s 178s Redistribution and use in source and binary forms, with or without 178s modification, are permitted provided that the following conditions are met: 178s 178s * Redistributions of source code must retain the above copyright notice, this 178s list of conditions and the following disclaimer. 178s 178s * Redistributions in binary form must reproduce the above copyright notice, 178s this list of conditions and the following disclaimer in the documentation 178s and/or other materials provided with the distribution. 178s 178s * Neither the name of the developer nor the names of its contributors may be 178s used to endorse or promote products derived from this software without 178s specific prior written permission. 178s 178s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 178s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 178s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 178s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 178s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 178s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 178s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 178s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 178s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 178s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 178s ---------------------------------------------------------------------- 178s APBS uses FETK (the Finite Element ToolKit) to solve the 178s Poisson-Boltzmann equation numerically. FETK is a portable collection 178s of finite element modeling class libraries developed by the Michael Holst 178s research group and written in an object-oriented form of C. FEtk is 178s designed to solve general coupled systems of nonlinear partial differential 178s equations using adaptive finite element methods, inexact Newton methods, 178s and algebraic multilevel methods. More information about FEtk may be found 178s at . 178s ---------------------------------------------------------------------- 178s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 178s Aqua is a modified form of the Holst group PMG library 178s which has been modified by Patrice Koehl 178s for improved efficiency and 178s memory usage when solving the Poisson-Boltzmann equation. 178s ---------------------------------------------------------------------- 178s Please cite your use of APBS as: 178s 178s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 178s nanosystems: application to microtubules and the ribosome. Proc. 178s Natl. Acad. Sci. USA 98, 10037-10041 2001. 178s 178s 178s This executable compiled on Jan 3 2025 at 11:01:42 178s 178s Parsing input file apbs-mol-auto.in... 178s rank 0 size 1... 178s Parsed input file. 178s Got paths for 1 molecules 178s Reading PQR-format atom data from ion.pqr. 178s 1 atoms 178s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 178s Net charge 1.00e+00 e 178s Preparing to run 6 PBE calculations. 178s ---------------------------------------- 178s CALCULATION #1 (solvated): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 61.280 MB total, 61.280 MB high water 178s Using cubic spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.781 x 0.781 x 0.781 178s Grid lengths: 50.000 x 50.000 x 50.000 178s Grid center: (0.000, 0.000, 0.000) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 0 ion species (0.000 M ionic strength): 178s Solute dielectric: 1.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 1.400 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 9.607073836227E+02 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #2 (solvated): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 61.280 MB total, 122.102 MB high water 178s Using cubic spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.383 x 0.383 x 0.383 178s Grid lengths: 24.495 x 24.495 x 24.495 178s Grid center: (0.000, 0.000, 0.000) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 0 ion species (0.000 M ionic strength): 178s Solute dielectric: 1.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 1.400 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 2.200266567971E+03 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #3 (solvated): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 61.280 MB total, 122.102 MB high water 178s Using cubic spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.188 x 0.188 x 0.188 178s Grid lengths: 12.000 x 12.000 x 12.000 178s Grid center: (0.000, 0.000, 0.000) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 0 ion species (0.000 M ionic strength): 178s Solute dielectric: 1.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 1.400 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Potential to be written to potential.dx.gz 178s Total electrostatic energy = 4.732245131587E+03 kJ/mol 178s Calculating forces... 178s Writing potential to potential-PE0.dx.gz 178s ---------------------------------------- 178s CALCULATION #4 (reference): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 61.207 MB total, 122.102 MB high water 178s Using cubic spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.781 x 0.781 x 0.781 178s Grid lengths: 50.000 x 50.000 x 50.000 178s Grid center: (0.000, 0.000, 0.000) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 0 ion species (0.000 M ionic strength): 178s Solute dielectric: 1.000 178s Solvent dielectric: 1.000 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 1.400 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.190871482831E+03 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #5 (reference): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 61.207 MB total, 122.102 MB high water 178s Using cubic spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.383 x 0.383 x 0.383 178s Grid lengths: 24.495 x 24.495 x 24.495 178s Grid center: (0.000, 0.000, 0.000) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 0 ion species (0.000 M ionic strength): 178s Solute dielectric: 1.000 178s Solvent dielectric: 1.000 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 1.400 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 2.430874049735E+03 kJ/mol 178s Calculating forces... 178s [focusFillBound()]: WARNING: 178s Unusually large potential values 178s detected on the focusing boundary! 178s Convergence not guaranteed for NPBE/NRPBE calculations! 178s 178s ---------------------------------------- 178s CALCULATION #6 (reference): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 61.207 MB total, 122.102 MB high water 178s Using cubic spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.188 x 0.188 x 0.188 178s Grid lengths: 12.000 x 12.000 x 12.000 178s Grid center: (0.000, 0.000, 0.000) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 0 ion species (0.000 M ionic strength): 178s Solute dielectric: 1.000 178s Solvent dielectric: 1.000 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 1.400 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 4.962018684215E+03 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s PRINT STATEMENTS 178s 178s print energy 1 (solvated) - 2 (reference) end 178s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 178s Global net ELEC energy = -2.297735526282E+02 kJ/mol 178s ---------------------------------------- 178s CLEANING UP AND SHUTTING DOWN... 178s Destroying force arrays. 178s No energy arrays to destroy. 178s Destroying multigrid structures. 178s Destroying finite element structures. 178s Destroying 1 molecules 178s Final memory usage: 0.001 MB total, 122.102 MB high water 178s 178s 178s Thanks for using APBS! 178s 178s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 178s *** PASSED *** 178s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 178s *** PASSED *** 178s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 178s *** PASSED *** 178s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 178s *** PASSED *** 178s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 178s *** PASSED *** 178s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 178s *** PASSED *** 178s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 178s *** PASSED *** 178s Elapsed time: 2.597242 seconds 178s -------------------------------------------------------------------------------- 178s -------------------------------------------------------------------------------- 178s Testing input file apbs-smol-auto.in 178s 180s Checking for intermediate energies in input file apbs-mol-auto.out 180s EXPECTED COMPUTED: 7 180s EXPECTED EXPECTED: 7 180s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 180s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 180s COMPUTED RESULT 960.7073836227 180s COMPUTED RESULT 2200.266567971 180s COMPUTED RESULT 4732.245131587 180s COMPUTED RESULT 1190.871482831 180s COMPUTED RESULT 2430.874049735 180s COMPUTED RESULT 4962.018684215 180s COMPUTED RESULT -229.7735526282 180s BINARY: /usr/bin/apbs 180s INPUT: apbs-smol-auto.in 180s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 180s asc_getToken: Error occurred (bailing out). 180s Vio_scanf: Format problem with input. 180s 180s 180s ---------------------------------------------------------------------- 180s APBS -- Adaptive Poisson-Boltzmann Solver 180s Version APBS 3.4.1 180s 180s Nathan A. Baker (nathan.baker@pnnl.gov) 180s Pacific Northwest National Laboratory 180s 180s Additional contributing authors listed in the code documentation. 180s 180s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 180s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 180s Northwest Division for the U.S. Department of Energy. 180s 180s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 180s Portions Copyright (c) 2002-2020, Nathan A. Baker. 180s Portions Copyright (c) 1999-2002, The Regents of the University of California. 180s Portions Copyright (c) 1995, Michael Holst. 180s All rights reserved. 180s 180s Redistribution and use in source and binary forms, with or without 180s modification, are permitted provided that the following conditions are met: 180s 180s * Redistributions of source code must retain the above copyright notice, this 180s list of conditions and the following disclaimer. 180s 180s * Redistributions in binary form must reproduce the above copyright notice, 180s this list of conditions and the following disclaimer in the documentation 180s and/or other materials provided with the distribution. 180s 180s * Neither the name of the developer nor the names of its contributors may be 180s used to endorse or promote products derived from this software without 180s specific prior written permission. 180s 180s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 180s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 180s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 180s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 180s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 180s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 180s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 180s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 180s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 180s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 180s ---------------------------------------------------------------------- 180s APBS uses FETK (the Finite Element ToolKit) to solve the 180s Poisson-Boltzmann equation numerically. FETK is a portable collection 180s of finite element modeling class libraries developed by the Michael Holst 180s research group and written in an object-oriented form of C. FEtk is 180s designed to solve general coupled systems of nonlinear partial differential 180s equations using adaptive finite element methods, inexact Newton methods, 180s and algebraic multilevel methods. More information about FEtk may be found 180s at . 180s ---------------------------------------------------------------------- 180s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 180s Aqua is a modified form of the Holst group PMG library 180s which has been modified by Patrice Koehl 180s for improved efficiency and 180s memory usage when solving the Poisson-Boltzmann equation. 180s ---------------------------------------------------------------------- 180s Please cite your use of APBS as: 180s 180s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 180s nanosystems: application to microtubules and the ribosome. Proc. 180s Natl. Acad. Sci. USA 98, 10037-10041 2001. 180s 180s 180s This executable compiled on Jan 3 2025 at 11:01:42 180s 180s Parsing input file apbs-smol-auto.in... 180s rank 0 size 1... 180s Parsed input file. 180s Got paths for 1 molecules 180s Reading PQR-format atom data from ion.pqr. 180s 1 atoms 180s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 180s Net charge 1.00e+00 e 180s Preparing to run 6 PBE calculations. 180s ---------------------------------------- 180s CALCULATION #1 (solvated): MULTIGRID 180s Setting up problem... 180s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 180s Debye length: 0 A 180s Current memory usage: 61.280 MB total, 61.280 MB high water 180s Using cubic spline charge discretization. 180s Grid dimensions: 65 x 65 x 65 180s Grid spacings: 0.781 x 0.781 x 0.781 180s Grid lengths: 50.000 x 50.000 x 50.000 180s Grid center: (0.000, 0.000, 0.000) 180s Multigrid levels: 5 180s Molecule ID: 1 180s Linearized traditional PBE 180s Multiple Debye-Huckel sphere boundary conditions 180s 0 ion species (0.000 M ionic strength): 180s Solute dielectric: 1.000 180s Solvent dielectric: 78.540 180s Using "molecular" surface definition;harmonic average smoothing 180s Solvent probe radius: 1.400 A 180s Temperature: 298.150 K 180s Electrostatic energies will be calculated 180s Total electrostatic energy = 9.532928767450E+02 kJ/mol 180s Calculating forces... 180s ---------------------------------------- 180s CALCULATION #2 (solvated): MULTIGRID 180s Setting up problem... 180s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 180s Debye length: 0 A 180s Current memory usage: 61.280 MB total, 122.102 MB high water 180s Using cubic spline charge discretization. 180s Grid dimensions: 65 x 65 x 65 180s Grid spacings: 0.383 x 0.383 x 0.383 180s Grid lengths: 24.495 x 24.495 x 24.495 180s Grid center: (0.000, 0.000, 0.000) 180s Multigrid levels: 5 180s Molecule ID: 1 180s Linearized traditional PBE 180s Boundary conditions from focusing 180s 0 ion species (0.000 M ionic strength): 180s Solute dielectric: 1.000 180s Solvent dielectric: 78.540 180s Using "molecular" surface definition;harmonic average smoothing 180s Solvent probe radius: 1.400 A 180s Temperature: 298.150 K 180s Electrostatic energies will be calculated 180s Total electrostatic energy = 2.201243880085E+03 kJ/mol 180s Calculating forces... 180s ---------------------------------------- 180s CALCULATION #3 (solvated): MULTIGRID 180s Setting up problem... 180s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 180s Debye length: 0 A 180s Current memory usage: 61.280 MB total, 122.102 MB high water 180s Using cubic spline charge discretization. 180s Grid dimensions: 65 x 65 x 65 180s Grid spacings: 0.188 x 0.188 x 0.188 180s Grid lengths: 12.000 x 12.000 x 12.000 180s Grid center: (0.000, 0.000, 0.000) 180s Multigrid levels: 5 180s Molecule ID: 1 180s Linearized traditional PBE 180s Boundary conditions from focusing 180s 0 ion species (0.000 M ionic strength): 180s Solute dielectric: 1.000 180s Solvent dielectric: 78.540 180s Using "molecular" surface definition;harmonic average smoothing 180s Solvent probe radius: 1.400 A 180s Temperature: 298.150 K 180s Electrostatic energies will be calculated 180s Total electrostatic energy = 4.733006258977E+03 kJ/mol 180s Calculating forces... 180s ---------------------------------------- 180s CALCULATION #4 (reference): MULTIGRID 180s Setting up problem... 180s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 180s Debye length: 0 A 180s Current memory usage: 61.207 MB total, 122.102 MB high water 180s Using cubic spline charge discretization. 180s Grid dimensions: 65 x 65 x 65 180s Grid spacings: 0.781 x 0.781 x 0.781 180s Grid lengths: 50.000 x 50.000 x 50.000 180s Grid center: (0.000, 0.000, 0.000) 180s Multigrid levels: 5 180s Molecule ID: 1 180s Linearized traditional PBE 180s Multiple Debye-Huckel sphere boundary conditions 180s 0 ion species (0.000 M ionic strength): 180s Solute dielectric: 1.000 180s Solvent dielectric: 1.000 180s Using "molecular" surface definition;harmonic average smoothing 180s Solvent probe radius: 1.400 A 180s Temperature: 298.150 K 180s Electrostatic energies will be calculated 180s Total electrostatic energy = 1.190871482831E+03 kJ/mol 180s Calculating forces... 180s ---------------------------------------- 180s CALCULATION #5 (reference): MULTIGRID 180s Setting up problem... 180s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 180s Debye length: 0 A 180s Current memory usage: 61.207 MB total, 122.102 MB high water 180s Using cubic spline charge discretization. 180s Grid dimensions: 65 x 65 x 65 180s Grid spacings: 0.383 x 0.383 x 0.383 180s Grid lengths: 24.495 x 24.495 x 24.495 180s Grid center: (0.000, 0.000, 0.000) 180s Multigrid levels: 5 180s Molecule ID: 1 180s Linearized traditional PBE 180s Boundary conditions from focusing 180s 0 ion species (0.000 M ionic strength): 180s Solute dielectric: 1.000 180s Solvent dielectric: 1.000 180s Using "molecular" surface definition;harmonic average smoothing 180s Solvent probe radius: 1.400 A 180s Temperature: 298.150 K 180s Electrostatic energies will be calculated 180s Total electrostatic energy = 2.430874049735E+03 kJ/mol 180s Calculating forces... 180s [focusFillBound()]: WARNING: 180s Unusually large potential values 180s detected on the focusing boundary! 180s Convergence not guaranteed for NPBE/NRPBE calculations! 180s 180s ---------------------------------------- 180s CALCULATION #6 (reference): MULTIGRID 180s Setting up problem... 180s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 180s Debye length: 0 A 180s Current memory usage: 61.207 MB total, 122.102 MB high water 180s Using cubic spline charge discretization. 180s Grid dimensions: 65 x 65 x 65 180s Grid spacings: 0.188 x 0.188 x 0.188 180s Grid lengths: 12.000 x 12.000 x 12.000 180s Grid center: (0.000, 0.000, 0.000) 180s Multigrid levels: 5 180s Molecule ID: 1 180s Linearized traditional PBE 180s Boundary conditions from focusing 180s 0 ion species (0.000 M ionic strength): 180s Solute dielectric: 1.000 180s Solvent dielectric: 1.000 180s Using "molecular" surface definition;harmonic average smoothing 180s Solvent probe radius: 1.400 A 180s Temperature: 298.150 K 180s Electrostatic energies will be calculated 180s Total electrostatic energy = 4.962018684215E+03 kJ/mol 180s Calculating forces... 180s ---------------------------------------- 180s PRINT STATEMENTS 180s 180s print energy 1 (solvated) - 2 (reference) end 180s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 180s Global net ELEC energy = -2.290124252387E+02 kJ/mol 180s ---------------------------------------- 180s CLEANING UP AND SHUTTING DOWN... 180s Destroying force arrays. 180s No energy arrays to destroy. 180s Destroying multigrid structures. 180s Destroying finite element structures. 180s Destroying 1 molecules 180s Final memory usage: 0.001 MB total, 122.102 MB high water 180s 180s 180s Thanks for using APBS! 180s 180s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 180s *** PASSED *** 180s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 180s *** PASSED *** 180s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 180s *** PASSED *** 180s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 180s *** PASSED *** 180s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 180s *** PASSED *** 180s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 180s *** PASSED *** 180s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 180s *** PASSED *** 180s Elapsed time: 2.347998 seconds 180s -------------------------------------------------------------------------------- 180s -------------------------------------------------------------------------------- 180s Testing input file apbs-mol-parallel.in 180s 180s Splitting the input file into 4 separate files using the inputgen utility 180s 184s Checking for intermediate energies in input file apbs-smol-auto.out 184s EXPECTED COMPUTED: 7 184s EXPECTED EXPECTED: 7 184s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 184s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 184s COMPUTED RESULT 953.292876745 184s COMPUTED RESULT 2201.243880085 184s COMPUTED RESULT 4733.006258977 184s COMPUTED RESULT 1190.871482831 184s COMPUTED RESULT 2430.874049735 184s COMPUTED RESULT 4962.018684215 184s COMPUTED RESULT -229.0124252387 184s BINARY: /usr/bin/apbs 184s INPUT: apbs-mol-parallel-PE0.in 184s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 184s asc_getToken: Error occurred (bailing out). 184s Vio_scanf: Format problem with input. 184s 184s 184s ---------------------------------------------------------------------- 184s APBS -- Adaptive Poisson-Boltzmann Solver 184s Version APBS 3.4.1 184s 184s Nathan A. Baker (nathan.baker@pnnl.gov) 184s Pacific Northwest National Laboratory 184s 184s Additional contributing authors listed in the code documentation. 184s 184s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 184s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 184s Northwest Division for the U.S. Department of Energy. 184s 184s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 184s Portions Copyright (c) 2002-2020, Nathan A. Baker. 184s Portions Copyright (c) 1999-2002, The Regents of the University of California. 184s Portions Copyright (c) 1995, Michael Holst. 184s All rights reserved. 184s 184s Redistribution and use in source and binary forms, with or without 184s modification, are permitted provided that the following conditions are met: 184s 184s * Redistributions of source code must retain the above copyright notice, this 184s list of conditions and the following disclaimer. 184s 184s * Redistributions in binary form must reproduce the above copyright notice, 184s this list of conditions and the following disclaimer in the documentation 184s and/or other materials provided with the distribution. 184s 184s * Neither the name of the developer nor the names of its contributors may be 184s used to endorse or promote products derived from this software without 184s specific prior written permission. 184s 184s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 184s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 184s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 184s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 184s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 184s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 184s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 184s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 184s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 184s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 184s ---------------------------------------------------------------------- 184s APBS uses FETK (the Finite Element ToolKit) to solve the 184s Poisson-Boltzmann equation numerically. FETK is a portable collection 184s of finite element modeling class libraries developed by the Michael Holst 184s research group and written in an object-oriented form of C. FEtk is 184s designed to solve general coupled systems of nonlinear partial differential 184s equations using adaptive finite element methods, inexact Newton methods, 184s and algebraic multilevel methods. More information about FEtk may be found 184s at . 184s ---------------------------------------------------------------------- 184s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 184s Aqua is a modified form of the Holst group PMG library 184s which has been modified by Patrice Koehl 184s for improved efficiency and 184s memory usage when solving the Poisson-Boltzmann equation. 184s ---------------------------------------------------------------------- 184s Please cite your use of APBS as: 184s 184s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 184s nanosystems: application to microtubules and the ribosome. Proc. 184s Natl. Acad. Sci. USA 98, 10037-10041 2001. 184s 184s 184s This executable compiled on Jan 3 2025 at 11:01:42 184s 184s Parsing input file apbs-mol-parallel-PE0.in... 184s rank 0 size 1... 184s Parsed input file. 184s Got paths for 1 molecules 184s Reading PQR-format atom data from ion.pqr. 184s 1 atoms 184s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 184s Net charge 1.00e+00 e 184s Preparing to run 6 PBE calculations. 184s ---------------------------------------- 184s CALCULATION #1 (solvated): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.280 MB total, 61.280 MB high water 184s Using cubic spline charge discretization. 184s Partition overlap fraction = 0.1 184s Processor array = 2 x 2 x 1 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.781 x 0.781 x 0.781 184s Grid lengths: 50.000 x 50.000 x 50.000 184s Grid center: (0.000, 0.000, 0.000) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 0 ion species (0.000 M ionic strength): 184s Solute dielectric: 1.000 184s Solvent dielectric: 78.540 184s Using "molecular" surface definition; no smoothing 184s Solvent probe radius: 1.400 A 184s Temperature: 298.150 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 2.401768459022E+02 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #2 (solvated): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.280 MB total, 122.102 MB high water 184s Using cubic spline charge discretization. 184s Partition overlap fraction = 0.1 184s Processor array = 2 x 2 x 1 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.296 x 0.296 x 0.383 184s Grid lengths: 18.944 x 18.944 x 24.495 184s Grid center: (-2.411, -2.411, 0.000) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 0 ion species (0.000 M ionic strength): 184s Solute dielectric: 1.000 184s Solvent dielectric: 78.540 184s Using "molecular" surface definition; no smoothing 184s Solvent probe radius: 1.400 A 184s Temperature: 298.150 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 8.142935592471E+02 kJ/mol 184s Calculating forces... 184s [focusFillBound()]: WARNING: 184s Unusually large potential values 184s detected on the focusing boundary! 184s Convergence not guaranteed for NPBE/NRPBE calculations! 184s 184s ---------------------------------------- 184s CALCULATION #3 (solvated): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.280 MB total, 122.102 MB high water 184s Using cubic spline charge discretization. 184s Partition overlap fraction = 0.1 184s Processor array = 2 x 2 x 1 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.112 x 0.112 x 0.188 184s Grid lengths: 7.178 x 7.178 x 12.000 184s Grid center: (-2.411, -2.411, 0.000) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 0 ion species (0.000 M ionic strength): 184s Solute dielectric: 1.000 184s Solvent dielectric: 78.540 184s Using "molecular" surface definition; no smoothing 184s Solvent probe radius: 1.400 A 184s Temperature: 298.150 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 1.485255308186E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #4 (reference): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.207 MB total, 122.102 MB high water 184s Using cubic spline charge discretization. 184s Partition overlap fraction = 0.1 184s PrProcessor 0 results: 184s 2.401768459022e+02 184s 8.142935592471e+02 184s 1.485255308186e+03 184s 2.977178707009e+02 184s 8.799304557588e+02 184s 1.542873949131e+03 184s -5.761864094552e+01 184s 184s ocessor array = 2 x 2 x 1 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.781 x 0.781 x 0.781 184s Grid lengths: 50.000 x 50.000 x 50.000 184s Grid center: (0.000, 0.000, 0.000) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 0 ion species (0.000 M ionic strength): 184s Solute dielectric: 1.000 184s Solvent dielectric: 1.000 184s Using "molecular" surface definition; no smoothing 184s Solvent probe radius: 1.400 A 184s Temperature: 298.150 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 2.977178707009E+02 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #5 (reference): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.207 MB total, 122.102 MB high water 184s Using cubic spline charge discretization. 184s Partition overlap fraction = 0.1 184s Processor array = 2 x 2 x 1 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.296 x 0.296 x 0.383 184s Grid lengths: 18.944 x 18.944 x 24.495 184s Grid center: (-2.411, -2.411, 0.000) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 0 ion species (0.000 M ionic strength): 184s Solute dielectric: 1.000 184s Solvent dielectric: 1.000 184s Using "molecular" surface definition; no smoothing 184s Solvent probe radius: 1.400 A 184s Temperature: 298.150 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 8.799304557588E+02 kJ/mol 184s Calculating forces... 184s [focusFillBound()]: WARNING: 184s Unusually large potential values 184s detected on the focusing boundary! 184s Convergence not guaranteed for NPBE/NRPBE calculations! 184s 184s ---------------------------------------- 184s CALCULATION #6 (reference): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.207 MB total, 122.102 MB high water 184s Using cubic spline charge discretization. 184s Partition overlap fraction = 0.1 184s Processor array = 2 x 2 x 1 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.112 x 0.112 x 0.188 184s Grid lengths: 7.178 x 7.178 x 12.000 184s Grid center: (-2.411, -2.411, 0.000) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 0 ion species (0.000 M ionic strength): 184s Solute dielectric: 1.000 184s Solvent dielectric: 1.000 184s Using "molecular" surface definition; no smoothing 184s Solvent probe radius: 1.400 A 184s Temperature: 298.150 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 1.542873949131E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s PRINT STATEMENTS 184s 184s print energy 1 (solvated) - 2 (reference) end 184s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 184s Global net ELEC energy = -5.761864094552E+01 kJ/mol 184s ---------------------------------------- 184s CLEANING UP AND SHUTTING DOWN... 184s Destroying force arrays. 184s No energy arrays to destroy. 184s Destroying multigrid structures. 184s Destroying finite element structures. 184s Destroying 1 molecules 184s Final memory usage: 0.001 MB total, 122.102 MB high water 184s 184s 184s Thanks for using APBS! 184s 186s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 186s BINARY: /usr/bin/apbs 186s INPUT: apbs-mol-parallel-PE1.in 186s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 186s Processor 1 results: 186s 2.401768459022e+02 186s 8.142778312125e+02 186s 1.485246667424e+03 186s 2.977178707009e+02 186s 8.799304557588e+02 186s 1.542873949131e+03 186s -5.762728170718e+01 186s 186s asc_getToken: Error occurred (bailing out). 186s Vio_scanf: Format problem with input. 186s 186s 186s ---------------------------------------------------------------------- 186s APBS -- Adaptive Poisson-Boltzmann Solver 186s Version APBS 3.4.1 186s 186s Nathan A. Baker (nathan.baker@pnnl.gov) 186s Pacific Northwest National Laboratory 186s 186s Additional contributing authors listed in the code documentation. 186s 186s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 186s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 186s Northwest Division for the U.S. Department of Energy. 186s 186s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 186s Portions Copyright (c) 2002-2020, Nathan A. Baker. 186s Portions Copyright (c) 1999-2002, The Regents of the University of California. 186s Portions Copyright (c) 1995, Michael Holst. 186s All rights reserved. 186s 186s Redistribution and use in source and binary forms, with or without 186s modification, are permitted provided that the following conditions are met: 186s 186s * Redistributions of source code must retain the above copyright notice, this 186s list of conditions and the following disclaimer. 186s 186s * Redistributions in binary form must reproduce the above copyright notice, 186s this list of conditions and the following disclaimer in the documentation 186s and/or other materials provided with the distribution. 186s 186s * Neither the name of the developer nor the names of its contributors may be 186s used to endorse or promote products derived from this software without 186s specific prior written permission. 186s 186s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 186s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 186s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 186s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 186s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 186s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 186s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 186s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 186s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 186s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 186s ---------------------------------------------------------------------- 186s APBS uses FETK (the Finite Element ToolKit) to solve the 186s Poisson-Boltzmann equation numerically. FETK is a portable collection 186s of finite element modeling class libraries developed by the Michael Holst 186s research group and written in an object-oriented form of C. FEtk is 186s designed to solve general coupled systems of nonlinear partial differential 186s equations using adaptive finite element methods, inexact Newton methods, 186s and algebraic multilevel methods. More information about FEtk may be found 186s at . 186s ---------------------------------------------------------------------- 186s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 186s Aqua is a modified form of the Holst group PMG library 186s which has been modified by Patrice Koehl 186s for improved efficiency and 186s memory usage when solving the Poisson-Boltzmann equation. 186s ---------------------------------------------------------------------- 186s Please cite your use of APBS as: 186s 186s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 186s nanosystems: application to microtubules and the ribosome. Proc. 186s Natl. Acad. Sci. USA 98, 10037-10041 2001. 186s 186s 186s This executable compiled on Jan 3 2025 at 11:01:42 186s 186s Parsing input file apbs-mol-parallel-PE1.in... 186s rank 0 size 1... 186s Parsed input file. 186s Got paths for 1 molecules 186s Reading PQR-format atom data from ion.pqr. 186s 1 atoms 186s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 186s Net charge 1.00e+00 e 186s Preparing to run 6 PBE calculations. 186s ---------------------------------------- 186s CALCULATION #1 (solvated): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 186s Debye length: 0 A 186s Current memory usage: 61.280 MB total, 61.280 MB high water 186s Using cubic spline charge discretization. 186s Partition overlap fraction = 0.1 186s Processor array = 2 x 2 x 1 186s Grid dimensions: 65 x 65 x 65 186s Grid spacings: 0.781 x 0.781 x 0.781 186s Grid lengths: 50.000 x 50.000 x 50.000 186s Grid center: (0.000, 0.000, 0.000) 186s Multigrid levels: 5 186s Molecule ID: 1 186s Linearized traditional PBE 186s Multiple Debye-Huckel sphere boundary conditions 186s 0 ion species (0.000 M ionic strength): 186s Solute dielectric: 1.000 186s Solvent dielectric: 78.540 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 2.401768459022E+02 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #2 (solvated): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 186s Debye length: 0 A 186s Current memory usage: 61.280 MB total, 122.102 MB high water 186s Using cubic spline charge discretization. 186s Partition overlap fraction = 0.1 186s Processor array = 2 x 2 x 1 186s Grid dimensions: 65 x 65 x 65 186s Grid spacings: 0.296 x 0.296 x 0.383 186s Grid lengths: 18.944 x 18.944 x 24.495 186s Grid center: (2.411, -2.411, 0.000) 186s Multigrid levels: 5 186s Molecule ID: 1 186s Linearized traditional PBE 186s Boundary conditions from focusing 186s 0 ion species (0.000 M ionic strength): 186s Solute dielectric: 1.000 186s Solvent dielectric: 78.540 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 8.142778312125E+02 kJ/mol 186s Calculating forces... 186s [focusFillBound()]: WARNING: 186s Unusually large potential values 186s detected on the focusing boundary! 186s Convergence not guaranteed for NPBE/NRPBE calculations! 186s 186s ---------------------------------------- 186s CALCULATION #3 (solvated): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 186s Debye length: 0 A 186s Current memory usage: 61.280 MB total, 122.102 MB high water 186s Using cubic spline charge discretization. 186s Partition overlap fraction = 0.1 186s Processor array = 2 x 2 x 1 186s Grid dimensions: 65 x 65 x 65 186s Grid spacings: 0.112 x 0.112 x 0.188 186s Grid lengths: 7.178 x 7.178 x 12.000 186s Grid center: (2.411, -2.411, 0.000) 186s Multigrid levels: 5 186s Molecule ID: 1 186s Linearized traditional PBE 186s Boundary conditions from focusing 186s 0 ion species (0.000 M ionic strength): 186s Solute dielectric: 1.000 186s Solvent dielectric: 78.540 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 1.485246667424E+03 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #4 (reference): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 186s Debye length: 0 A 186s Current memory usage: 61.207 MB total, 122.102 MB high water 186s Using cubic spline charge discretization. 186s Partition overlap fraction = 0.1 186s Processor array = 2 x 2 x 1 186s Grid dimensions: 65 x 65 x 65 186s Grid spacings: 0.781 x 0.781 x 0.781 186s Grid lengths: 50.000 x 50.000 x 50.000 186s Grid center: (0.000, 0.000, 0.000) 186s Multigrid levels: 5 186s Molecule ID: 1 186s Linearized traditional PBE 186s Multiple Debye-Huckel sphere boundary conditions 186s 0 ion species (0.000 M ionic strength): 186s Solute dielectric: 1.000 186s Solvent dielectric: 1.000 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 2.977178707009E+02 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #5 (reference): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 186s Debye length: 0 A 186s Current memory usage: 61.207 MB total, 122.102 MB high water 186s Using cubic spline charge discretization. 186s Partition overlap fraction = 0.1 186s Processor array = 2 x 2 x 1 186s Grid dimensions: 65 x 65 x 65 186s Grid spacings: 0.296 x 0.296 x 0.383 186s Grid lengths: 18.944 x 18.944 x 24.495 186s Grid center: (2.411, -2.411, 0.000) 186s Multigrid levels: 5 186s Molecule ID: 1 186s Linearized traditional PBE 186s Boundary conditions from focusing 186s 0 ion species (0.000 M ionic strength): 186s Solute dielectric: 1.000 186s Solvent dielectric: 1.000 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 8.799304557588E+02 kJ/mol 186s Calculating forces... 186s [focusFillBound()]: WARNING: 186s Unusually large potential values 186s detected on the focusing boundary! 186s Convergence not guaranteed for NPBE/NRPBE calculations! 186s 186s ---------------------------------------- 186s CALCULATION #6 (reference): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 186s Debye length: 0 A 186s Current memory usage: 61.207 MB total, 122.102 MB high water 186s Using cubic spline charge discretization. 186s Partition overlap fraction = 0.1 186s Processor array = 2 x 2 x 1 186s Grid dimensions: 65 x 65 x 65 186s Grid spacings: 0.112 x 0.112 x 0.188 186s Grid lengths: 7.178 x 7.178 x 12.000 186s Grid center: (2.411, -2.411, 0.000) 186s Multigrid levels: 5 186s Molecule ID: 1 186s Linearized traditional PBE 186s Boundary conditions from focusing 186s 0 ion species (0.000 M ionic strength): 186s Solute dielectric: 1.000 186s Solvent dielectric: 1.000 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 1.542873949131E+03 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s PRINT STATEMENTS 186s 186s print energy 1 (solvated) - 2 (reference) end 186s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 186s Global net ELEC energy = -5.762728170718E+01 kJ/mol 186s ---------------------------------------- 186s CLEANING UP AND SHUTTING DOWN... 186s Destroying force arrays. 186s No energy arrays to destroy. 186s Destroying multigrid structures. 186s Destroying finite element structures. 186s Destroying 1 molecules 186s Final memory usage: 0.001 MB total, 122.102 MB high water 186s 186s 186s Thanks for using APBS! 186s 189s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 189s BINARY: /usr/bin/apbs 189s INPUT: apbs-mol-parallel-PE2.in 189s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 189s asc_getToken: Error occurred (bailing out). 189s Vio_scanf: Format problem with input. 189s 189s 189s ---------------------------------------------------------------------- 189s APBS -- Adaptive Poisson-Boltzmann Solver 189s Version APBS 3.4.1 189s 189s Nathan A. Baker (nathan.baker@pnnl.gov) 189s Pacific Northwest National Laboratory 189s 189s Additional contributing authors listed in the code documentation. 189s 189s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 189s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 189s Northwest Division for the U.S. Department of Energy. 189s 189s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 189s Portions Copyright (c) 2002-2020, Nathan A. Baker. 189s Portions Copyright (c) 1999-2002, The Regents of the University of California. 189s Portions Copyright (c) 1995, Michael Holst. 189s All rights reserved. 189s 189s Redistribution and use in source and binary forms, with or without 189s modification, are permitted provided that the following conditions are met: 189s 189s * Redistributions of source code must retain the above copyright notice, this 189s list of conditions and the following disclaimer. 189s 189s * Redistributions in binary form must reproduce the above copyright notice, 189s this list of conditions and the following disclaimer in the documentation 189s and/or other materials provided with the distribution. 189s 189s * Neither the name of the developer nor the names of its contributors may be 189s used to endorse or promote products derived from this software without 189s specific prior written permission. 189s 189s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 189s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 189s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 189s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 189s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 189s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 189s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 189s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 189s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 189s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 189s ---------------------------------------------------------------------- 189s APBS uses FETK (the Finite Element ToolKit) to solve the 189s Poisson-Boltzmann equation numerically. FETK is a portable collection 189s of finite element modeling class libraries developed by the Michael Holst 189s research group and written in an object-oriented form of C. FEtk is 189s designed to solve general coupled systems of nonlinear partial differential 189s equations using adaptive finite element methods, inexact Newton methods, 189s and algebraic multilevel methods. More information about FEtk may be found 189s at . 189s ---------------------------------------------------------------------- 189s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 189s Aqua is a modified form of the Holst group PMG library 189s which has been modified by Patrice Koehl 189s for improved efficiency and 189s memory usage when solving the Poisson-Boltzmann equation. 189s ---------------------------------------------------------------------- 189s Please cite your use of APBS as: 189s 189s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 189s nanosystems: application to microtubules and the ribosome. Proc. 189s Natl. Acad. Sci. USA 98, 10037-10041 2001. 189s 189s 189s This executable compiled on Jan 3 2025 at 11:01:42 189s 189s Parsing input file apbs-mol-parallel-PE2.in... 189s rank 0 size 1... 189s Parsed input file. 189s Got paths for 1 molecules 189s Reading PQR-format atom data from ion.pqr. 189s 1 atoms 189s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 189s Net charge 1.00e+00 e 189s Preparing to run 6 PBE calculations. 189s ---------------------------------------- 189s CALCULATION #1 (solvated): MULTIGRID 189s Setting up problem... 189s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 189s Debye length: 0 A 189s Current memory usage: 61.280 MB total, 61.280 MB high water 189s Using cubic spline charge discretization. 189s Partition overlap fraction = 0.1 189s Processor array = 2 x 2 x 1 189s Grid dimensions: 65 x 65 x 65 189s Grid spacings: 0.781 x 0.781 x 0.781 189s Grid lengths: 50.000 x 50.000 x 50.000 189s Grid center: (0.000, 0.000, 0.000) 189s Multigrid levels: 5 189s Molecule ID: 1 189s Linearized traditional PBE 189s Multiple Debye-Huckel sphere boundary conditions 189s 0 ion species (0.000 M ionic strength): 189s Solute dielectric: 1.000 189s Solvent dielectric: 78.540 189s Using "molecular" surface definition; no smoothing 189s Solvent probe radius: 1.400 A 189s Temperature: 298.150 K 189s Electrostatic energies will be calculated 189s Total electrostatic energy = 2.401768459091E+02 kJ/mol 189s Calculating forces... 189s ---------------------------------------- 189s CALCULATION #2 (solvated): MULTIGRID 189s Setting up problem... 189s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 189s Debye length: 0 A 189s Current memory usage: 61.280 MB total, 122.102 MB high water 189s Using cubic spline charge discretization. 189s Partition overlap fraction = 0.1 189s Processor array = 2 x 2 x 1 189s Grid dimensions: 65 x 65 x 65 189s Grid spacings: 0.296 x 0.296 x 0.383 189s Grid lengths: 18.944 x 18.944 x 24.495 189s Grid center: (-2.411, 2.411, 0.000) 189s Multigrid levels: 5 189s Molecule ID: 1 189s Linearized traditional PBE 189s Boundary conditions from focusing 189s 0 ion species (0.000 M ionic strength): 189s Solute dielectric: 1.000 189s Solvent dielectric: 78.540 189s Using "molecular" surface definition; no smoothing 189s Solvent probe radius: 1.400 A 189s Temperature: 298.150 K 189s Electrostatic energies will be calculated 189s Total electrostatic energy = 8.142935605695E+02 kJ/mol 189s Calculating forces... 189s [focusFillBound()]: WARNING: 189s Unusually large potential values 189s detected on the focusing boundary! 189s Convergence not guaranteed for NPBE/NRPBE calculations! 189s 189s ---------------------------------------- 189s CALCULATION #3 (solvated): MULTIGRID 189s Setting up problem... 189s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 189s Debye length: 0 A 189s Current memory usage: 61.280 MB total, 122.102 MB high water 189s Using cubic spline charge discretization. 189s Partition overlap fraction = 0.1 189s Processor array = 2 x 2 x 1 189s Grid dimensions: 65 x 65 x 65 189s Grid spacings: 0.112 x 0.112 x 0.188 189s Grid lengths: 7.178 x 7.178 x 12.000 189s Grid center: (-2.411, 2.411, 0.000) 189s Multigrid levels: 5 189s Molecule ID: 1 189s Linearized traditional PBE 189s Boundary conditions from focusing 189s 0 ion species (0.000 M ionic strength): 189s Solute dielectric: 1.000 189s Solvent dielectric: 78.540 189s Using "molecular" surface definition; no smoothing 189s Solvent probe radius: 1.400 A 189s Temperature: 298.150 K 189s Electrostatic energies will be calculated 189s Total electrostatic energy = 1.485255306569E+03 kJ/mol 189s Calculating forces... 189s ---------------------------------------- 189s CALCULATION #4 (reference): MULTIGRID 189s Setting up problem... 189s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 189s Debye length: 0 A 189s Current memory usage: 61.207 MB total, 122.102 MB high water 189s Using cubic spline charge discretization. 189s Partition overlap fraction = 0.1 189s Processor array = 2 x 2 x 1 189s Grid dimensions: 65 x 65 x 65 189s Grid spacings: 0.781 x 0.781 x 0.781 189s Grid lengths: 50.000 x 50.000 x 50.000 189s Grid center: (0.000, 0.000, 0.000) 189s Multigrid levels: 5 189s Molecule ID: 1 189s Linearized traditional PBE 189s Multiple Debye-Huckel sphere boundary conditions 189s 0 ion species (0.000 M ionic strength): 189s Solute dielectric: 1.000 189s Solvent dielectric: 1.000 189s Using "molecular" surface definition; no smoothing 189s Solvent probe radius: 1.400 A 189s Temperature: 298.150 K 189s Electrostatic energies will be calculated 189s Total electrostatic energy = 2.977178707146E+02 kJ/mol 189s Calculating forces... 189s ---------------------------------------- 189s CALCULATION #5 (reference): MULTIGRID 189s Setting up problem... 189s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 189s Debye length: 0 A 189s Current memory usage: 61.207 MB total, 122.102 MB high water 189s Using cubic spline charge discretization. 189s Partition overlap fraction = 0.1 189s Processor array = 2 x 2 x 1 189s Grid dimensions: 65 x 65 x 65 189s Grid spacings: 0.296 x 0.296 x 0.383 189s Grid lengths: 18.944 x 18.944 x 24.495 189s Grid center: (-2.411, 2.411, 0.000) 189s Multigrid levels: 5 189s Molecule ID: 1 189s Linearized traditional PBE 189s Boundary conditions from focusing 189s 0 ion species (0.000 M ionic strength): 189s Solute dielectric: 1.000 189s Solvent dielectric: 1.000 189s Using "molecular" surface definition; no smoothing 189s Solvent probe radius: 1.400 A 189s Temperature: 298.150 K 189s Electrostatic energies will be calculated 189s Total electrostatic energy = 8.799304557596E+02 kJ/mol 189s Calculating forces... 189s [focusFillBound()]: WARNING: 189s Unusually large potential values 189s detected on the focusing boundary! 189s Convergence not guaranteed for NPBE/NRPBE calculations! 189s 189s ---------------------------------------- 189s CALCULATION #6 (reference): MULTIGRID 189s Setting up problem... 189s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 189s Debye length: 0 A 189s Current memory usage: 61.207 MB total, 122.102 MB high water 189s Using cubic spline charge discretization. 189s Partition overlap fraction = 0.1 189s Processor array = 2 x 2 x 1 189s Grid dimensions: 65 x 65 x 65 189s Grid spacings: 0.112 x 0.112 x 0.188 189s Grid lengths: 7.178 x 7.178 x 12.000 189s Grid center: (-2.411, 2.411, 0.000) 189s Multigrid levels: 5 189s Molecule ID: 1 189s Linearized traditional PBE 189s Boundary conditions from focusing 189s 0 ion species (0.000 M ionic strength): 189s Solute dielectric: 1.000 189s Solvent dielectric: 1.000 189s Using "molecular" surface definition; no smoothing 189s Solvent probe radius: 1.400 A 189s Temperature: 298.150 K 189s Electrostatic energies will be calculated 189s Total electrostatic energy = 1.542873949141E+03 kJ/mol 189s Calculating forces... 189s ---------------------------------------- 189s PRINT STATEMENTS 189s 189s print energy 1 (solvated) - 2 (reference) end 189s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 189s Global net ELEC energy = -5.761864257239E+01 kJ/mol 189s ---------------------------------------- 189s CLEANING UP AND SHUTTING DOWN... 189s Destroying force arrays. 189s No energy arrays to destroy. 189s Destroying multigrid structures. 189s Destroying finite element structures. 189s Destroying 1 molecules 189s Final memory usage: 0.001 MB total, 122.102 MB high water 189s 189s 189s Thanks for using APBS! 189s 189s Processor 2 results: 189s 2.401768459091e+02 189s 8.142935605695e+02 189s 1.485255306569e+03 189s 2.977178707146e+02 189s 8.799304557596e+02 189s 1.542873949141e+03 189s -5.761864257239e+01 189s 192s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 192s BINARY: /usr/bin/apbs 192s INPUT: apbs-mol-parallel-PE3.in 192s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 192s asc_getToken: Error occurred (bailing out). 192s Vio_scanf: Format problem with input. 192s 192s 192s ---------------------------------------------------------------------- 192s APBS -- Adaptive Poisson-Boltzmann Solver 192s Version APBS 3.4.1 192s 192s Nathan A. Baker (nathan.baker@pnnl.gov) 192s Pacific Northwest National Laboratory 192s 192s Additional contributing authors listed in the code documentation. 192s 192s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 192s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 192s Northwest Division for the U.S. Department of Energy. 192s 192s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 192s Portions Copyright (c) 2002-2020, Nathan A. Baker. 192s Portions Copyright (c) 1999-2002, The Regents of the University of California. 192s Portions Copyright (c) 1995, Michael Holst. 192s All rights reserved. 192s 192s Redistribution and use in source and binary forms, with or without 192s modification, are permitted provided that the following conditions are met: 192s 192s * Redistributions of source code must retain the above copyright notice, this 192s list of conditions and the following disclaimer. 192s 192s * Redistributions in binary form must reproduce the above copyright notice, 192s this list of conditions and the following disclaimer in the documentation 192s and/or other materials provided with the distribution. 192s 192s * Neither the name of the developer nor the names of its contributors may be 192s used to endorse or promote products derived from this software without 192s specific prior written permission. 192s 192s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 192s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 192s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 192s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 192s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 192s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 192s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 192s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 192s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 192s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 192s ---------------------------------------------------------------------- 192s APBS uses FETK (the Finite Element ToolKit) to solve the 192s Poisson-Boltzmann equation numerically. FETK is a portable collection 192s of finite element modeling class libraries developed by the Michael Holst 192s research group and written in an object-oriented form of C. FEtk is 192s designed to solve general coupled systems of nonlinear partial differential 192s equations using adaptive finite element methods, inexact Newton methods, 192s and algebraic multilevel methods. More information about FEtk may be found 192s at . 192s ---------------------------------------------------------------------- 192s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 192s Aqua is a modified form of the Holst group PMG library 192s which has been modified by Patrice Koehl 192s for improved efficiency and 192s memory usage when solving the Poisson-Boltzmann equation. 192s ---------------------------------------------------------------------- 192s Please cite your use of APBS as: 192s 192s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 192s nanosystems: application to microtubules and the ribosome. Proc. 192s Natl. Acad. Sci. USA 98, 10037-10041 2001. 192s 192s 192s This executable compiled on Jan 3 2025 at 11:01:42 192s 192s Parsing input file apbs-mol-parallel-PE3.in... 192s rank 0 size 1... 192s Parsed input file. 192s Got paths for 1 molecules 192s Reading PQR-format atom data from ion.pqr. 192s 1 atoms 192s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 192s Net charge 1.00e+00 e 192s Preparing to run 6 PBE calculations. 192s ---------------------------------------- 192s CALCULATION #1 (solvated): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 61.280 MB total, 61.280 MB high water 192s Using cubic spline charge discretization. 192s Partition overlap fraction = 0.1 192s Processor array = 2 x 2 x 1 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.781 x 0.781 x 0.781 192s Grid lengths: 50.000 x 50.000 x 50.000 192s Grid center: (0.000, 0.000, 0.000) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Multiple Debye-Huckel sphere boundary conditions 192s 0 ion species (0.000 M ionic strength): 192s Solute dielectric: 1.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 1.400 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 2.401768459091E+02 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s CALCULATION #2 (solvated): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 61.280 MB total, 122.102 MB high water 192s Using cubic spline charge discretization. 192s Partition overlap fraction = 0.1 192s Processor array = 2 x 2 x 1 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.296 x 0.296 x 0.383 192s Grid lengths: 18.944 x 18.944 x 24.495 192s Grid center: (2.411, 2.411, 0.000) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 0 ion species (0.000 M ionic strength): 192s Solute dielectric: 1.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 1.400 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 8.142778325440E+02 kJ/mol 192s Calculating forces... 192s [focusFillBound()]: WARNING: 192s Unusually large potential values 192s detected on the focusing boundary! 192s Convergence not guaranteed for NPBE/NRPBE calculations! 192s 192s ---------------------------------------- 192s CALCULATION #3 (solvated): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 61.280 MB total, 122.102 MB high water 192s Using cubic spline charge discretization. 192s Partition overlap fraction = 0.1 192s Processor array = 2 x 2 x 1 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.112 x 0.112 x 0.188 192s Grid lengths: 7.178 x 7.178 x 12.000 192s Grid center: (2.411, 2.411, 0.000) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 0 ion species (0.000 M ionic strength): 192s Solute dielectric: 1.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 1.400 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 1.485246665692E+03 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s CALCULATION #4 (reference): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 61.207 MB total, 122.102 MB high water 192s Using cubic spline charge discretization. 192s Partition overlap fraction = 0.1 192s Processor array = 2 x 2 x 1 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.781 x 0.781 x 0.781 192s Grid lengths: 50.000 x 50.000 x 50.000 192s Grid center: (0.000, 0.000, 0.000) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Multiple Debye-Huckel sphere boundary conditions 192s 0 ion species (0.000 M ionic strength): 192s Solute dielectric: 1.000 192s Solvent dielectric: 1.000 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 1.400 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 2.977178707146E+02 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s CALCULATION #5 (reference): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 61.207 MB total, 122.102 MB high water 192s Using cubic spline charge discretization. 192s Partition overlap fraction = 0.1 192s Processor array = 2 x 2 x 1 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.296 x 0.296 x 0.383 192s Grid lengths: 18.944 x 18.944 x 24.495 192s Grid center: (2.411, 2.411, 0.000) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 0 ion species (0.000 M ionic strength): 192s Solute dielectric: 1.000 192s Solvent dielectric: 1.000 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 1.400 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 8.799304557596E+02 kJ/mol 192s Calculating forces... 192s [focusFillBound()]: WARNING: 192s Unusually large potential values 192s detected on the focusing boundary! 192s Convergence not guaranteed for NPBE/NRPBE calculations! 192s 192s ---------------------------------------- 192s CALCULATION #6 (reference): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 61.207 MB total, 122.102 MB high water 192s Using cubic spline charge discretization. 192s Partition overlap fraction = 0.1 192s Processor array = 2 x 2 x 1 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.112 x 0.112 x 0.188 192s Grid lengths: 7.178 x 7.178 x 12.000 192s Grid center: (2.411, 2.411, 0.000) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 0 ion species (0.000 M ionic strength): 192s Solute dielectric: 1.000 192s Solvent dielectric: 1.000 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 1.400 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 1.542873949141E+03 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s PRINT STATEMENTS 192s 192s print energy 1 (solvated) - 2 (reference) end 192s Local net energy (PE 0) = -5.762728344953E+01 kJ/mol 192s Global net ELEC energy = -5.762728344953E+01 kJ/mol 192s ---------------------------------------- 192s CLEANING UP AND SHUTTING DOWN... 192s Destroying force arrays. 192s No energy arrays to destroy. 192s Destroying multigrid structures. 192s Destroying finite element structures. 192s Destroying 1 molecules 192s Final memory usage: 0.001 MB total, 122.102 MB high water 192s 192s 192s Thanks for using APBS! 192s 192s Processor 3 results: 192s 2.401768459091e+02 192s 8.142778325440e+02 192s 1.485246665692e+03 192s 2.977178707146e+02 192s 8.799304557596e+02 192s 1.542873949141e+03 192s -5.762728344953e+01 192s 192s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 192s *** PASSED *** 192s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 192s *** PASSED *** 192s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 192s *** PASSED *** 192s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 192s *** PASSED *** 192s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 192s *** PASSED *** 192s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 192s *** PASSED *** 192s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 192s *** PASSED *** 192s Elapsed time: 11.582153 seconds 192s -------------------------------------------------------------------------------- 192s -------------------------------------------------------------------------------- 192s Testing input file apbs-smol-parallel.in 192s 192s Splitting the input file into 4 separate files using the inputgen utility 192s 195s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 195s EXPECTED COMPUTED: 7 195s EXPECTED EXPECTED: 7 195s COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 195s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 195s COMPUTED RESULT 960.7073836226 195s COMPUTED RESULT 3257.1427835730997 195s COMPUTED RESULT 5941.0039478710005 195s COMPUTED RESULT 1190.8714828309999 195s COMPUTED RESULT 3519.7218230368003 195s COMPUTED RESULT 6171.495796544 195s COMPUTED RESULT -230.49184867462003 195s BINARY: /usr/bin/apbs 195s INPUT: apbs-smol-parallel-PE0.in 195s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 195s Processor 0 results: 195s asc_getToken: Error occurred (bailing out). 195s Vio_scanf: Format problem with input. 195s 195s 195s ---------------------------------------------------------------------- 195s APBS -- Adaptive Poisson-Boltzmann Solver 195s Version APBS 3.4.1 195s 195s Nathan A. Baker (nathan.baker@pnnl.gov) 195s Pacific Northwest National Laboratory 195s 195s Additional contributing authors listed in the code documentation. 195s 195s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 195s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 195s Northwest Division for the U.S. Department of Energy. 195s 195s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 195s Portions Copyright (c) 2002-2020, Nathan A. Baker. 195s Portions Copyright (c) 1999-2002, The Regents of the University of California. 195s Portions Copyright (c) 1995, Michael Holst. 195s All rights reserved. 195s 195s Redistribution and use in source and binary forms, with or without 195s modification, are permitted provided that the following conditions are met: 195s 195s * Redistributions of source code must retain the above copyright notice, this 195s list of conditions and the following disclaimer. 195s 195s * Redistributions in binary form must reproduce the above copyright notice, 195s this list of conditions and the following disclaimer in the documentation 195s and/or other materials provided with the distribution. 195s 195s * Neither the name of the developer nor the names of its contributors may be 195s used to endorse or promote products derived from this software without 195s specific prior written permission. 195s 195s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 195s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 195s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 195s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 195s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 195s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 195s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 195s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 195s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 195s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 195s ---------------------------------------------------------------------- 195s APBS uses FETK (the Finite Element ToolKit) to solve the 195s Poisson-Boltzmann equation numerically. FETK is a portable collection 195s of finite element modeling class libraries developed by the Michael Holst 195s research group and written in an object-oriented form of C. FEtk is 195s designed to solve general coupled systems of nonlinear partial differential 195s equations using adaptive finite element methods, inexact Newton methods, 195s and algebraic multilevel methods. More information about FEtk may be found 195s at . 195s ---------------------------------------------------------------------- 195s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 195s Aqua is a modified form of the Holst group PMG library 195s which has been modified by Patrice Koehl 195s for improved efficiency and 195s memory usage when solving the Poisson-Boltzmann equation. 195s ---------------------------------------------------------------------- 195s Please cite your use of APBS as: 195s 195s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 195s nanosystems: application to microtubules and the ribosome. Proc. 195s Natl. Acad. Sci. USA 98, 10037-10041 2001. 195s 195s 195s This executable compiled on Jan 3 2025 at 11:01:42 195s 195s Parsing input file apbs-smol-parallel-PE0.in... 195s rank 0 size 1... 195s Parsed input file. 195s Got paths for 1 molecules 195s Reading PQR-format atom data from ion.pqr. 195s 1 atoms 195s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 195s Net charge 1.00e+00 e 195s Preparing to run 6 PBE calculations. 195s ---------------------------------------- 195s CALCULATION #1 (solvated): MULTIGRID 195s Setting up problem... 195s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 195s Debye length: 0 A 195s Current memory usage: 61.280 MB total, 61.280 MB high water 195s Using cubic spline charge discretization. 195s Partition overlap fraction = 0.1 195s Processor array = 2 x 2 x 1 195s Grid dimensions: 65 x 65 x 65 195s Grid spacings: 0.781 x 0.781 x 0.781 195s Grid lengths: 50.000 x 50.000 x 50.000 195s Grid center: (0.000, 0.000, 0.000) 195s Multigrid levels: 5 195s Molecule ID: 1 195s Linearized traditional PBE 195s Multiple Debye-Huckel sphere boundary conditions 195s 0 ion species (0.000 M ionic strength): 195s Solute dielectric: 1.000 195s Solvent dielectric: 78.540 195s Using "molecular" surface definition;harmonic average smoothing 195s Solvent probe radius: 1.400 A 195s Temperature: 298.150 K 195s Electrostatic energies will be calculated 195s Total electrostatic energy = 2.383232191816E+02 kJ/mol 195s Calculating forces... 195s ---------------------------------------- 195s CALCULATION #2 (solvated): MULTIGRID 195s Setting up problem... 195s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 195s Debye length: 0 A 195s Current memory usage: 61.280 MB total, 122.102 MB high water 195s Using cubic spline charge discretization. 195s Partition overlap fraction = 0.1 195s Processor array = 2 x 2 x 1 195s Grid dimensions: 65 x 65 x 65 195s Grid spacings: 0.296 x 0.296 x 0.383 195s Grid lengths: 18.944 x 18.944 x 24.495 195s Grid center: (-2.411, -2.411, 0.000) 195s Multigrid levels: 5 195s Molecule ID: 1 195s Linearized traditional PBE 195s Boundary conditions from focusing 195s 0 ion species (0.000 M ionic strength): 195s Solute dielectric: 1.000 195s Solvent dielectric: 78.540 195s Using "molecular" surface definition;harmonic average smoothing 195s Solvent probe radius: 1.400 A 195s Temperature: 298.150 K 195s Electrostatic energies will be calculated 195s Total electrostatic energy = 8.145369591602E+02 kJ/mol 195s Calculating forces... 195s [focusFillBound()]: WARNING: 195s Unusually large potential values 195s detected on the focusing boundary! 195s Convergence not guaranteed for NPBE/NRPBE calculations! 195s 195s ---------------------------------------- 195s CALCULATION #3 (solvated): MULTIGRID 195s Setting up problem... 195s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 195s Debye length: 0 A 195s Current memory usage: 61.280 MB total, 122.102 MB high water 195s Using cubic spline charge discretization. 195s Partition overlap fraction = 0.1 195s Processor array = 2 x 2 x 1 195s Grid dimensions: 65 x 65 x 65 195s Grid spacings: 0.112 x 0.112 x 0.188 195s Grid lengths: 7.178 x 7.178 x 12.000 195s Grid center: (-2.411, -2.411, 0.000) 195s Multigrid levels: 5 195s Molecule ID: 1 195s Linearized traditional PBE 195s Boundary conditions from focusing 195s 0 ion species (0.000 M ionic strength): 195s Solute dielectric: 1.000 195s Solvent dielectric: 78.540 195s Using "molecular" surface definition;harmonic average smoothing 195s Solvent probe radius: 1.400 A 195s Temperature: 298.150 K 195s Electrostatic energies will be calculated 195s Total electrostatic energy = 1.485524998001E+03 kJ/mol 195s Calculating forces... 195s ---------------------------------------- 195s CALCULATION #4 (reference): MULTIGRID 195s Setting up problem... 195s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 195s Debye length: 0 A 195s Current memory usage: 61.207 MB total, 122.102 MB high water 195s Using cubic spline charge discretization. 195s Partition overlap fraction = 0.1 195s Processor array = 2 x 2 x 1 195s Grid dimensions: 65 x 65 x 65 195s Grid spacings: 0.781 x 0.781 x 0.781 195s Grid lengths: 50.000 x 50.000 x 50.000 195s Grid center: (0.000, 0.000, 0.000) 195s Multigrid levels: 5 195s Molecule ID: 1 195s Linearized traditional PBE 195s Multiple Debye-Huckel sphere boundary conditions 195s 0 ion species (0.000 M ionic strength): 195s Solute dielectric: 1.000 195s Solvent dielectric: 1.000 195s Using "molecular" surface definition;harmonic average smoothing 195s Solvent probe radius: 1.400 A 195s Temperature: 298.150 K 195s Electrostatic energies will be calculated 195s Total electrostatic energy = 2.977178707009E+02 kJ/mol 195s Calculating forces... 195s ---------------------------------------- 195s CALCULATION #5 (reference): MULTIGRID 195s Setting up problem... 195s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 195s Debye length: 0 A 195s Current memory usage: 61.207 MB total, 122.102 MB high water 195s Using cubic spline charge discretization. 195s Partition overlap fraction = 0.1 195s Processor array = 2 x 2 x 1 195s Grid dimensions: 65 x 65 x 65 195s Grid spacings: 0.296 x 0.296 x 0.383 195s Grid lengths: 18.944 x 18.944 x 24.495 195s Grid center: (-2.411, -2.411, 0.000) 195s Multigrid levels: 5 195s Molecule ID: 1 195s Linearized traditional PBE 195s Boundary conditions from focusing 195s 0 ion species (0.000 M ionic strength): 195s Solute dielectric: 1.000 195s Solvent dielectric: 1.000 195s Using "molecular" surface definition;harmonic average smoothing 195s Solvent probe radius: 1.400 A 195s Temperature: 298.150 K 195s Electrostatic energies will be calculated 195s Total electrostatic energy = 8.799304557588E+02 kJ/mol 195s Calculating forces... 195s [focusFillBound()]: WARNING: 195s Unusually large potential values 195s detected on the focusing boundary! 195s Convergence not guaranteed for NPBE/NRPBE calculations! 195s 195s ---------------------------------------- 195s CALCULATION #6 (reference): MULTIGRID 195s Setting up problem... 195s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 195s Debye length: 0 A 195s Current memory usage: 61.207 MB total, 122.102 MB high water 195s Using cubic spline charge discretization. 195s Partition overlap fraction = 0.1 195s Processor array = 2 x 2 x 1 195s Grid dimensions: 65 x 65 x 65 195s Grid spacings: 0.112 x 0.112 x 0.188 195s Grid lengths: 7.178 x 7.178 x 12.000 195s Grid center: (-2.411, -2.411, 0.000) 195s Multigrid levels: 5 195s Molecule ID: 1 195s Linearized traditional PBE 195s Boundary conditions from focusing 195s 0 ion species (0.000 M ionic strength): 195s Solute dielectric: 1.000 195s Solvent dielectric: 1.000 195s Using "molecular" surface definition;harmonic average smoothing 195s Solvent probe radius: 1.400 A 195s Temperature: 298.150 K 195s Electrostatic energies will be calculated 195s Total electrostatic energy = 1.542873949131E+03 kJ/mol 195s Calculating forces... 195s ---------------------------------------- 195s PRINT STATEMENTS 195s 195s print energy 1 (solvated) - 2 (reference) end 195s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 195s Global net ELEC energy = -5.734895113069E+01 kJ/mol 195s ---------------------------------------- 195s CLEANING UP AND SHUTTING DOWN... 195s Destroying force arrays. 195s No energy arrays to destroy. 195s Destroying multigrid structures. 195s Destroying finite element structures. 195s Destroying 1 molecules 195s Final memory usage: 0.001 MB total, 122.102 MB high water 195s 195s 195s Thanks for using APBS! 195s 195s 2.383232191816e+02 195s 8.145369591602e+02 195s 1.485524998001e+03 195s 2.977178707009e+02 195s 8.799304557588e+02 195s 1.542873949131e+03 195s -5.734895113069e+01 195s 198s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 198s BINARY: /usr/bin/apbs 198s INPUT: apbs-smol-parallel-PE1.in 198s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 198s asc_getToken: Error occurred (bailing out). 198s Vio_scanf: Format problem with input. 198s 198s 198s ---------------------------------------------------------------------- 198s APBS -- Adaptive Poisson-Boltzmann Solver 198s Version APBS 3.4.1 198s 198s Nathan A. Baker (nathan.baker@pnnl.gov) 198s Pacific Northwest National Laboratory 198s 198s Additional contributing authors listed in the code documentation. 198s 198s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 198s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 198s Northwest Division for the U.S. Department of Energy. 198s 198s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 198s Portions Copyright (c) 2002-2020, Nathan A. Baker. 198s Portions Copyright (c) 1999-2002, The Regents of the University of California. 198s Portions Copyright (c) 1995, Michael Holst. 198s All rights reserved. 198s 198s Redistribution and use in source and binary forms, with or without 198s modification, are permitted provided that the following conditions are met: 198s 198s * Redistributions of source code must retain the above copyright notice, this 198s list of conditions and the following disclaimer. 198s 198s * Redistributions in binary form must reproduce the above copyright notice, 198s this list of conditions and the following disclaimer in the documentation 198s and/or other materials provided with the distribution. 198s 198s * Neither the name of the developer nor the names of its contributors may be 198s used to endorse or promote products derived from this software without 198s specific prior written permission. 198s 198s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 198s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 198s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 198s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 198s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 198s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 198s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 198s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 198s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 198s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 198s ---------------------------------------------------------------------- 198s APBS uses FETK (the Finite Element ToolKit) to solve the 198s Poisson-Boltzmann equation numerically. FETK is a portable collection 198s of finite element modeling class libraries developed by the Michael Holst 198s research group and written in an object-oriented form of C. FEtk is 198s designed to solve general coupled systems of nonlinear partial differential 198s equations using adaptive finite element methods, inexact Newton methods, 198s and algebraic multilevel methods. More information about FEtk may be found 198s at . 198s ---------------------------------------------------------------------- 198s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 198s Aqua is a modified form of the Holst group PMG library 198s which has been modified by Patrice Koehl 198s for improved efficiency and 198s memory usage when solving the Poisson-Boltzmann equation. 198s ---------------------------------------------------------------------- 198s Please cite your use of APBS as: 198s 198s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 198s nanosystems: application to microtubules and the ribosome. Proc. 198s Natl. Acad. Sci. USA 98, 10037-10041 2001. 198s 198s 198s This executable compiled on Jan 3 2025 at 11:01:42 198s 198s Parsing input file apbs-smol-parallel-PE1.in... 198s rank 0 size 1... 198s Parsed input file. 198s Got paths for 1 molecules 198s Reading PQR-format atom data from ion.pqr. 198s 1 atoms 198s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 198s Net charge 1.00e+00 e 198s Preparing to run 6 PBE calculations. 198s ---------------------------------------- 198s CALCULATION #1 (solvated): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.280 MB total, 61.280 MB high water 198s Using cubic spline charge discretization. 198s Partition overlap fraction = 0.1 198s Processor array = 2 x 2 x 1 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.781 x 0.781 x 0.781 198s Grid lengths: 50.000 x 50.000 x 50.000 198s Grid center: (0.000, 0.000, 0.000) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 0 ion species (0.000 M ionic strength): 198s Solute dielectric: 1.000 198s Solvent dielectric: 78.540 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 1.400 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 2.383232191816E+02 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #2 (solvated): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.280 MB total, 122.102 MB high water 198s Using cubic spline charge discretization. 198s Partition overlap fraction = 0.1 198s Processor array = 2 x 2 x 1 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.296 x 0.296 x 0.383 198s Grid lengths: 18.944 x 18.944 x 24.495 198s Grid center: (2.411, -2.411, 0.000) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 0 ion species (0.000 M ionic strength): 198s Solute dielectric: 1.000 198s Solvent dielectric: 78.540 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 1.400 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 8.145419898332E+02 kJ/mol 198s Calculating forces... 198s [focusFillBound()]: WARNING: 198s Unusually large potential values 198s detected on the focusing boundary! 198s Convergence not guaranteed for NPBE/NRPBE calculations! 198s 198s ---------------------------------------- 198s CALCULATION #3 (solvated): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.280 MB total, 122.102 MB high water 198s Using cubic spline charge discretization. 198s Partition overlap fraction = 0.1 198s Processor array = 2 x 2 x 1 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.112 x 0.112 x 0.188 198s Grid lengths: 7.178 x 7.178 x 12.000 198s Grid center: (2.411, -2.411, 0.000) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 0 ion species (0.000 M ionic strength): 198s Solute dielectric: 1.000 198s Solvent dielectric: 78.540 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 1.400 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 1.485529328612E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #4 (reference): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.207 MB total, 122.102 MB high water 198s Using cubic spline charge discretization. 198s Partition overlap fraction = 0.1 198s Processor array = 2 x 2 x 1 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.781 x 0.781 x 0.781 198s Grid lengths: 50.000 x 50.000 x 50.000 198s Grid center: (0.000, 0.000, 0.000) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 0 ion species (0.000 M ionic strength): 198s Solute dielectric: 1.000 198s Solvent dielectric: 1.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 1.400 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 2.977178707009E+02 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #5 (reference): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.207 MB total, 122.102 MB high water 198s Using cubic spline charge discretization. 198s Partition overlap fraction = 0.1 198s Processor array = 2 x 2 x 1 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.296 x 0.296 x 0.383 198s Grid lengths: 18.944 x 18.944 x 24.495 198s Grid center: (2.411, -2.411, 0.000) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 0 ion species (0.000 M ionic strength): 198s Solute dielectric: 1.000 198s Solvent dielectric: 1.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 1.400 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 8.799304557588E+02 kJ/mol 198s Calculating forces... 198s [focusFillBound()]: WARNING: 198s Unusually large potential values 198s detected on the focusing boundary! 198s Convergence not guaranteed for NPBE/NRPBE calculations! 198s 198s ---------------------------------------- 198s CALCULATION #6 (reference): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.207 MB total, 122.102 MB high water 198s Using cubic spline charge discretization. 198s Partition overlap fraction = 0.1 198s Processor array = 2 x 2 x 1 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.112 x 0.112 x 0.188 198s Grid lengths: 7.178 x 7.178 x 12.000 198s Grid center: (2.411, -2.411, 0.000) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 0 ion species (0.000 M ionic strength): 198s Solute dielectric: 1.000 198s Solvent dielectric: 1.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 1.400 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 1.542873949131E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s PRINT STATEMENTS 198s 198s print energy 1 (solvated) - 2 (reference) end 198s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 198s Global net ELEC energy = -5.734462051928E+01 kJ/mol 198s ---------------------------------------- 198s CLEANING UP AND SHUTTING DOWN... 198s Destroying force arrays. 198s No energy arrays to destroy. 198s Destroying multigrid structures. 198s Destroying finite element structures. 198s Destroying 1 molecules 198s Final memory usage: 0.001 MB total, 122.102 MB high water 198s 198s 198s Thanks for using APBS! 198s 198s Processor 1 results: 198s 2.383232191816e+02 198s 8.145419898332e+02 198s 1.485529328612e+03 198s 2.977178707009e+02 198s 8.799304557588e+02 198s 1.542873949131e+03 198s -5.734462051928e+01 198s 200s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 200s BINARY: /usr/bin/apbs 200s INPUT: apbs-smol-parallel-PE2.in 200s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 200s asc_getToken: Error occurred (bailing out). 200s Vio_scanf: Format problem with input. 200s 200s 200s ---------------------------------------------------------------------- 200s APBS -- Adaptive Poisson-Boltzmann Solver 200s Version APBS 3.4.1 200s 200s Nathan A. Baker (nathan.baker@pnnl.gov) 200s Pacific Northwest National Laboratory 200s 200s Additional contributing authors listed in the code documentation. 200s 200s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 200s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 200s Northwest Division for the U.S. Department of Energy. 200s 200s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 200s Portions Copyright (c) 2002-2020, Nathan A. Baker. 200s Portions Copyright (c) 1999-2002, The Regents of the University of California. 200s Portions Copyright (c) 1995, Michael Holst. 200s All rights reserved. 200s 200s Redistribution and use in source and binary forms, with or without 200s modification, are permitted provided that the following conditions are met: 200s 200s * Redistributions of source code must retain the above copyright notice, this 200s list of conditions and the following disclaimer. 200s 200s * Redistributions in binary form must reproduce the above copyright notice, 200s this list of conditions and the following disclaimer in the documentation 200s and/or other materials provided with the distribution. 200s 200s * Neither the name of the developer nor the names of its contributors may be 200s used to endorse or promote products derived from this software without 200s specific prior written permission. 200s 200s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 200s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 200s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 200s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 200s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 200s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 200s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 200s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 200s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 200s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 200s ---------------------------------------------------------------------- 200s APBS uses FETK (the Finite Element ToolKit) to solve the 200s Poisson-Boltzmann equation numerically. FETK is a portable collection 200s of finite element modeling class libraries developed by the Michael Holst 200s research group and written in an object-oriented form of C. FEtk is 200s designed to solve general coupled systems of nonlinear partial differential 200s equations using adaptive finite element methods, inexact Newton methods, 200s and algebraic multilevel methods. More information about FEtk may be found 200s at . 200s ---------------------------------------------------------------------- 200s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 200s Aqua is a modified form of the Holst group PMG library 200s which has been modified by Patrice Koehl 200s for improved efficiency and 200s memory usage when solving the Poisson-Boltzmann equation. 200s ---------------------------------------------------------------------- 200s Please cite your use of APBS as: 200s 200s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 200s nanosystems: application to microtubules and the ribosome. Proc. 200s Natl. Acad. Sci. USA 98, 10037-10041 2001. 200s 200s 200s This executable compiled on Jan 3 2025 at 11:01:42 200s 200s Parsing input file apbs-smol-parallel-PE2.in... 200s rank 0 size 1... 200s Parsed input file. 200s Got paths for 1 molecules 200s Reading PQR-format atom data from ion.pqr. 200s 1 atoms 200s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 200s Net charge 1.00e+00 e 200s Preparing to run 6 PBE calculations. 200s ---------------------------------------- 200s CALCULATION #1 (solvated): MULTIGRID 200s Setting up problem... 200s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 200s Debye length: 0 A 200s Current memory usage: 61.280 MB total, 61.280 MB high water 200s Using cubic spline charge discretization. 200s Partition overlap fraction = 0.1 200s Processor array = 2 x 2 x 1 200s Grid dimensions: 65 x 65 x 65 200s Grid spacings: 0.781 x 0.781 x 0.781 200s Grid lengths: 50.000 x 50.000 x 50.000 200s Grid center: (0.000, 0.000, 0.000) 200s Multigrid levels: 5 200s Molecule ID: 1 200s Linearized traditional PBE 200s Multiple Debye-Huckel sphere boundary conditions 200s 0 ion species (0.000 M ionic strength): 200s Solute dielectric: 1.000 200s Solvent dielectric: 78.540 200s Using "molecular" surface definition;harmonic average smoothing 200s Solvent probe radius: 1.400 A 200s Temperature: 298.150 K 200s Electrostatic energies will be calculated 200s Total electrostatic energy = 2.383232191909E+02 kJ/mol 200s Calculating forces... 200s ---------------------------------------- 200s CALCULATION #2 (solvated): MULTIGRID 200s Setting up problem... 200s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 200s Debye length: 0 A 200s Current memory usage: 61.280 MB total, 122.102 MB high water 200s Using cubic spline charge discretization. 200s Partition overlap fraction = 0.1 200s Processor array = 2 x 2 x 1 200s Grid dimensions: 65 x 65 x 65 200s Grid spacings: 0.296 x 0.296 x 0.383 200s Grid lengths: 18.944 x 18.944 x 24.495 200s Grid center: (-2.411, 2.411, 0.000) 200s Multigrid levels: 5 200s Molecule ID: 1 200s Linearized traditional PBE 200s Boundary conditions from focusing 200s 0 ion species (0.000 M ionic strength): 200s Solute dielectric: 1.000 200s Solvent dielectric: 78.540 200s Using "molecular" surface definition;harmonic average smoothing 200s Solvent probe radius: 1.400 A 200s Temperature: 298.150 K 200s Electrostatic energies will be calculated 200s Total electrostatic energy = 8.145369593489E+02 kJ/mol 200s Calculating forces... 200s [focusFillBound()]: WARNING: 200s Unusually large potential values 200s detected on the focusing boundary! 200s Convergence not guaranteed for NPBE/NRPBE calculations! 200s 200s ---------------------------------------- 200s CALCULATION #3 (solvated): MULTIGRID 200s Setting up problem... 200s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 200s Debye length: 0 A 200s Current memory usage: 61.280 MB total, 122.102 MB high water 200s Using cubic spline charge discretization. 200s Partition overlap fraction = 0.1 200s Processor array = 2 x 2 x 1 200s Grid dimensions: 65 x 65 x 65 200s Grid spacings: 0.112 x 0.112 x 0.188 200s Grid lengths: 7.178 x 7.178 x 12.000 200s Grid center: (-2.411, 2.411, 0.000) 200s Multigrid levels: 5 200s Molecule ID: 1 200s Linearized traditional PBE 200s Boundary conditions from focusing 200s 0 ion species (0.000 M ionic strength): 200s Solute dielectric: 1.000 200s Solvent dielectric: 78.540 200s Using "molecular" surface definition;harmonic average smoothing 200s Solvent probe radius: 1.400 A 200s Temperature: 298.150 K 200s Electrostatic energies will be calculated 200s Total electrostatic energy = 1.485524997676E+03 kJ/mol 200s Calculating forces... 200s ---------------------------------------- 200s CALCULATION #4 (reference): MULTIGRID 200s Setting up problem... 200s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 200s Debye length: 0 A 200s Current memory usage: 61.207 MB total, 122.102 MB high water 200s Using cubic spline charge discretization. 200s Partition overlap fraction = 0.1 200s Processor array = 2 x 2 x 1 200s Grid dimensions: 65 x 65 x 65 200s Grid spacings: 0.781 x 0.781 x 0.781 200s Grid lengths: 50.000 x 50.000 x 50.000 200s Grid center: (0.000, 0.000, 0.000) 200s Multigrid levels: 5 200s Molecule ID: 1 200s Linearized traditional PBE 200s Multiple Debye-Huckel sphere boundary conditions 200s 0 ion species (0.000 M ionic strength): 200s Solute dielectric: 1.000 200s Solvent dielectric: 1.000 200s Using "molecular" surface definition;harmonic average smoothing 200s Solvent probe radius: 1.400 A 200s Temperature: 298.150 K 200s Electrostatic energies will be calculated 200s Total electrostatic energy = 2.977178707146E+02 kJ/mol 200s Calculating forces... 200s ---------------------------------------- 200s CALCULATION #5 (reference): MULTIGRID 200s Setting up problem... 200s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 200s Debye length: 0 A 200s Current memory usage: 61.207 MB total, 122.102 MB high water 200s Using cubic spline charge discretization. 200s Partition overlap fraction = 0.1 200s Processor array = 2 x 2 x 1 200s Grid dimensions: 65 x 65 x 65 200s Grid spacings: 0.296 x 0.296 x 0.383 200s Grid lengths: 18.944 x 18.944 x 24.495 200s Grid center: (-2.411, 2.411, 0.000) 200s Multigrid levels: 5 200s Molecule ID: 1 200s Linearized traditional PBE 200s Boundary conditions from focusing 200s 0 ion species (0.000 M ionic strength): 200s Solute dielectric: 1.000 200s Solvent dielectric: 1.000 200s Using "molecular" surface definition;harmonic average smoothing 200s Solvent probe radius: 1.400 A 200s Temperature: 298.150 K 200s Electrostatic energies will be calculated 200s Total electrostatic energy = 8.799304557596E+02 kJ/mol 200s Calculating forces... 200s [focusFillBound()]: WARNING: 200s Unusually large potential values 200s detected on the focusing boundary! 200s Convergence not guaranteed for NPBE/NRPBE calculations! 200s 200s ---------------------------------------- 200s CALCULATION #6 (reference): MULTIGRID 200s Setting up problem... 200s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 200s Debye length: 0 A 200s Current memory usage: 61.207 MB total, 122.102 MB high water 200s Using cubic spline charge discretization. 200s Partition overlap fraction = 0.1 200s Processor array = 2 x 2 x 1 200s Grid dimensions: 65 x 65 x 65 200s Grid spacings: 0.112 x 0.112 x 0.188 200s Grid lengths: 7.178 x 7.178 x 12.000 200s Grid center: (-2.411, 2.411, 0.000) 200s Multigrid levels: 5 200s Molecule ID: 1 200s Linearized traditional PBE 200s Boundary conditions from focusing 200s 0 ion species (0.000 M ionic strength): 200s Solute dielectric: 1.000 200s Solvent dielectric: 1.000 200s Using "molecular" surface definition;harmonic average smoothing 200s Solvent probe radius: 1.400 A 200s Temperature: 298.150 K 200s Electrostatic energies will be calculated 200s Total electrostatic energy = 1.542873949141E+03 kJ/mol 200s Calculating forces... 200s ---------------------------------------- 200s PRINT STATEMENTS 200s 200s print energy 1 (solvated) - 2 (reference) end 200s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 200s Global net ELEC energy = -5.734895146550E+01 kJ/mol 200s ---------------------------------------- 200s CLEANING UP AND SHUTTING DOWN... 200s Destroying force arrays. 200s No energy arrays to destroy. 200s Destroying multigrid structures. 200s Destroying finite element structures. 200s Destroying 1 molecules 200s Final memory usage: 0.001 MB total, 122.102 MB high water 200s 200s 200s Thanks for using APBS! 200s 200s Processor 2 results: 200s 2.383232191909e+02 200s 8.145369593489e+02 200s 1.485524997676e+03 200s 2.977178707146e+02 200s 8.799304557596e+02 200s 1.542873949141e+03 200s -5.734895146550e+01 200s 203s Processor 3 results: 203s 2.383232191909e+02 203s 8.145419900310e+02 203s 1.485529328301e+03 203s 2.977178707146e+02 203s 8.799304557596e+02 203s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 203s BINARY: /usr/bin/apbs 203s INPUT: apbs-smol-parallel-PE3.in 203s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 203s asc_getToken: Error occurred (bailing out). 203s Vio_scanf: Format problem with input. 203s 203s 203s ---------------------------------------------------------------------- 203s APBS -- Adaptive Poisson-Boltzmann Solver 203s Version APBS 3.4.1 203s 203s Nathan A. Baker (nathan.baker@pnnl.gov) 203s Pacific Northwest National Laboratory 203s 203s Additional contributing authors listed in the code documentation. 203s 203s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 203s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 203s Northwest Division for the U.S. Department of Energy. 203s 203s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 203s Portions Copyright (c) 2002-2020, Nathan A. Baker. 203s Portions Copyright (c) 1999-2002, The Regents of the University of California. 203s Portions Copyright (c) 1995, Michael Holst. 203s All rights reserved. 203s 203s Redistribution and use in source and binary forms, with or without 203s modification, are permitted provided that the following conditions are met: 203s 203s * Redistributions of source code must retain the above copyright notice, this 203s list of conditions and the following disclaimer. 203s 203s * Redistributions in binary form must reproduce the above copyright notice, 203s this list of conditions and the following disclaimer in the documentation 203s and/or other materials provided with the distribution. 203s 203s * Neither the name of the developer nor the names of its contributors may be 203s used to endorse or promote products derived from this software without 203s specific prior written permission. 203s 203s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 203s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 203s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 203s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 203s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 203s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 203s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 203s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 203s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 203s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 203s ---------------------------------------------------------------------- 203s APBS uses FETK (the Finite Element ToolKit) to solve the 203s Poisson-Boltzmann equation numerically. FETK is a portable collection 203s of finite element modeling class libraries developed by the Michael Holst 203s research group and written in an object-oriented form of C. FEtk is 203s designed to solve general coupled systems of nonlinear partial differential 203s equations using adaptive finite element methods, inexact Newton methods, 203s and algebraic multilevel methods. More information about FEtk may be found 203s at . 203s ---------------------------------------------------------------------- 203s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 203s Aqua is a modified form of the Holst group PMG library 203s which has been modified by Patrice Koehl 203s for improved efficiency and 203s memory usage when solving the Poisson-Boltzmann equation. 203s ---------------------------------------------------------------------- 203s Please cite your use of APBS as: 203s 203s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 203s nanosystems: application to microtubules and the ribosome. Proc. 203s Natl. Acad. Sci. USA 98, 10037-10041 2001. 203s 203s 203s This executable compiled on Jan 3 2025 at 11:01:42 203s 203s Parsing input file apbs-smol-parallel-PE3.in... 203s rank 0 size 1... 203s Parsed input file. 203s Got paths for 1 molecules 203s Reading PQR-format atom data from ion.pqr. 203s 1 atoms 203s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 203s Net charge 1.00e+00 e 203s Preparing to run 6 PBE calculations. 203s ---------------------------------------- 203s CALCULATION #1 (solvated): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 61.280 MB total, 61.280 MB high water 203s Using cubic spline charge discretization. 203s Partition overlap fraction = 0.1 203s Processor array = 2 x 2 x 1 203s Grid dimensions: 65 x 65 x 65 203s Grid spacings: 0.781 x 0.781 x 0.781 203s Grid lengths: 50.000 x 50.000 x 50.000 203s Grid center: (0.000, 0.000, 0.000) 203s Multigrid levels: 5 203s Molecule ID: 1 203s Linearized traditional PBE 203s Multiple Debye-Huckel sphere boundary conditions 203s 0 ion species (0.000 M ionic strength): 203s Solute dielectric: 1.000 203s Solvent dielectric: 78.540 203s Using "molecular" surface definition;harmonic average smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 2.383232191909E+02 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s CALCULATION #2 (solvated): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 61.280 MB total, 122.102 MB high water 203s Using cubic spline charge discretization. 203s Partition overlap fraction = 0.1 203s Processor array = 2 x 2 x 1 203s Grid dimensions: 65 x 65 x 65 203s Grid spacings: 0.296 x 0.296 x 0.383 203s Grid lengths: 18.944 x 18.944 x 24.495 203s Grid center: (2.411, 2.411, 0.000) 203s Multigrid levels: 5 203s Molecule ID: 1 203s Linearized traditional PBE 203s Boundary conditions from focusing 203s 0 ion species (0.000 M ionic strength): 203s Solute dielectric: 1.000 203s Solvent dielectric: 78.540 203s Using "molecular" surface definition;harmonic average smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 8.145419900310E+02 kJ/mol 203s Calculating forces... 203s [focusFillBound()]: WARNING: 203s Unusually large potential values 203s detected on the focusing boundary! 203s Convergence not guaranteed for NPBE/NRPBE calculations! 203s 203s ---------------------------------------- 203s CALCULATION #3 (solvated): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 61.280 MB total, 122.102 MB high water 203s Using cubic spline charge discretization. 203s Partition overlap fraction = 0.1 203s Processor array = 2 x 2 x 1 203s Grid dimensions: 65 x 65 x 65 203s Grid spacings: 0.112 x 0.112 x 0.188 203s Grid lengths: 7.178 x 7.178 x 12.000 203s Grid center: (2.411, 2.411, 0.000) 203s Multigrid levels: 5 203s Molecule ID: 1 203s Linearized traditional PBE 203s Boundary conditions from focusing 203s 0 ion species (0.000 M ionic strength): 203s Solute dielectric: 1.000 203s Solvent dielectric: 78.540 203s Using "molecular" surface definition;harmonic average smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 1.485529328301E+03 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s CALCULATION #4 (reference): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 61.207 MB total, 122.102 MB high water 203s Using cubic spline charge discretization. 203s Partition overlap fraction = 0.1 203s Processor array = 2 x 2 x 1 203s Grid dimensions: 65 x 65 x 65 203s Grid spacings: 0.781 x 0.781 x 0.781 203s Grid lengths: 50.000 x 50.000 x 50.000 203s Grid center: (0.000, 0.000, 0.000) 203s Multigrid levels: 5 203s Molecule ID: 1 203s Linearized traditional PBE 203s Multiple Debye-Huckel sphere boundary conditions 203s 0 ion species (0.000 M ionic strength): 203s Solute dielectric: 1.000 203s Solvent dielectric: 1.000 203s Using "molecular" surface definition;harmonic average smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 2.977178707146E+02 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s CALCULATION #5 (reference): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 61.207 MB total, 122.102 MB high water 203s Using cubic spline charge discretization. 203s Partition overlap fraction = 0.1 203s Processor array = 2 x 2 x 1 203s Grid dimensions: 65 x 65 x 65 203s Grid spacings: 0.296 x 0.296 x 0.383 203s Grid lengths: 18.944 x 18.944 x 24.495 203s Grid center: (2.411, 2.411, 0.000) 203s Multigrid levels: 5 203s Molecule ID: 1 203s Linearized traditional PBE 203s Boundary conditions from focusing 203s 0 ion species (0.000 M ionic strength): 203s Solute dielectric: 1.000 203s Solvent dielectric: 1.000 203s Using "molecular" surface definition;harmonic average smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 8.799304557596E+02 kJ/mol 203s Calculating forces... 203s [focusFillBound()]: WARNING: 203s Unusually large potential values 203s detected on the focusing boundary! 203s Convergence not guaranteed for NPBE/NRPBE calculations! 203s 203s ---------------------------------------- 203s CALCULATION #6 (reference): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 61.207 MB total, 122.102 MB high water 203s Using cubic spline charge discretization. 203s Partition overlap fraction = 0.1 203s Processor array = 2 x 2 x 1 203s Grid dimensions: 65 x 65 x 65 203s Grid spacings: 0.112 x 0.112 x 0.188 203s Grid lengths: 7.178 x 7.178 x 12.000 203s Grid center: (2.411, 2.411, 0.000) 203s Multigrid levels: 5 203s Molecule ID: 1 203s Linearized traditional PBE 203s Boundary conditions from focusing 203s 0 ion species (0.000 M ionic strength): 203s Solute dielectric: 1.000 203s Solvent dielectric: 1.000 203s Using "molecular" surface definition;harmonic average smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 1.542873949141E+03 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s PRINT STATEMENTS 203s 203s print energy 1 (solvated) - 2 (reference) end 203s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 203s Global net ELEC energy = -5.734462084052E+01 kJ/mol 203s ---------------------------------------- 203s CLEANING UP AND SHUTTING DOWN... 203s Destroying force arrays. 203s No energy arrays to destroy. 203s Destroying multigrid structures. 203s Destroying finite element structures. 203s Destroying 1 molecules 203s Final memory usage: 0.001 MB total, 122.102 MB high water 203s 203s 203s Thanks for using APBS! 203s 203s 1.542873949141e+03 203s -5.734462084052e+01 203s 203s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 203s *** PASSED *** 203s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 203s *** PASSED *** 203s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 203s *** PASSED *** 203s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 203s *** PASSED *** 203s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 203s *** PASSED *** 203s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 203s *** PASSED *** 203s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 203s *** PASSED *** 203s Elapsed time: 11.14466 seconds 203s -------------------------------------------------------------------------------- 203s Total elapsed time: 27.672957 seconds 203s Test results have been logged 203s -------------------------------------------------------------------------------- 203s -------------------------------------------------------------------------------- 203s Testing input file apbs-mol-auto.in 203s 303s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 303s EXPECTED COMPUTED: 7 303s EXPECTED EXPECTED: 7 303s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 303s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 303s COMPUTED RESULT 953.292876745 303s COMPUTED RESULT 3258.1578983732998 303s COMPUTED RESULT 5942.108652589999 303s COMPUTED RESULT 1190.8714828309999 303s COMPUTED RESULT 3519.7218230368003 303s COMPUTED RESULT 6171.495796544 303s COMPUTED RESULT -229.38714395599 303s Running tests for actin-dimer-auto section 303s BINARY: /usr/bin/apbs 303s INPUT: apbs-mol-auto.in 303s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 303s asc_getToken: Error occurred (bailing out). 303s Vio_scanf: Format problem with input. 303s 303s 303s ---------------------------------------------------------------------- 303s APBS -- Adaptive Poisson-Boltzmann Solver 303s Version APBS 3.4.1 303s 303s Nathan A. Baker (nathan.baker@pnnl.gov) 303s Pacific Northwest National Laboratory 303s 303s Additional contributing authors listed in the code documentation. 303s 303s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 303s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 303s Northwest Division for the U.S. Department of Energy. 303s 303s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 303s Portions Copyright (c) 2002-2020, Nathan A. Baker. 303s Portions Copyright (c) 1999-2002, The Regents of the University of California. 303s Portions Copyright (c) 1995, Michael Holst. 303s All rights reserved. 303s 303s Redistribution and use in source and binary forms, with or without 303s modification, are permitted provided that the following conditions are met: 303s 303s * Redistributions of source code must retain the above copyright notice, this 303s list of conditions and the following disclaimer. 303s 303s * Redistributions in binary form must reproduce the above copyright notice, 303s this list of conditions and the following disclaimer in the documentation 303s and/or other materials provided with the distribution. 303s 303s * Neither the name of the developer nor the names of its contributors may be 303s used to endorse or promote products derived from this software without 303s specific prior written permission. 303s 303s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 303s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 303s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 303s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 303s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 303s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 303s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 303s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 303s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 303s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 303s ---------------------------------------------------------------------- 303s APBS uses FETK (the Finite Element ToolKit) to solve the 303s Poisson-Boltzmann equation numerically. FETK is a portable collection 303s of finite element modeling class libraries developed by the Michael Holst 303s research group and written in an object-oriented form of C. FEtk is 303s designed to solve general coupled systems of nonlinear partial differential 303s equations using adaptive finite element methods, inexact Newton methods, 303s and algebraic multilevel methods. More information about FEtk may be found 303s at . 303s ---------------------------------------------------------------------- 303s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 303s Aqua is a modified form of the Holst group PMG library 303s which has been modified by Patrice Koehl 303s for improved efficiency and 303s memory usage when solving the Poisson-Boltzmann equation. 303s ---------------------------------------------------------------------- 303s Please cite your use of APBS as: 303s 303s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 303s nanosystems: application to microtubules and the ribosome. Proc. 303s Natl. Acad. Sci. USA 98, 10037-10041 2001. 303s 303s 303s This executable compiled on Jan 3 2025 at 11:01:42 303s 303s Parsing input file apbs-mol-auto.in... 303s rank 0 size 1... 303s Parsed input file. 303s Got paths for 3 molecules 303s Reading PQR-format atom data from mol1.pqr. 303s asc_getToken: Error occurred (bailing out). 303s Vio_scanf: Format problem with input. 303s 5877 atoms 303s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 303s Net charge -1.20e+01 e 303s Reading PQR-format atom data from mol2.pqr. 303s asc_getToken: Error occurred (bailing out). 303s Vio_scanf: Format problem with input. 303s 5877 atoms 303s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 303s Net charge -1.20e+01 e 303s Reading PQR-format atom data from complex.pqr. 303s 11754 atoms 303s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 303s Net charge -2.40e+01 e 303s Preparing to run 6 PBE calculations. 303s ---------------------------------------- 303s CALCULATION #1 (mol1): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 13.5959 A 303s Current memory usage: 1028.322 MB total, 1028.322 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 161 x 161 x 161 303s Grid spacings: 0.975 x 0.756 x 1.012 303s Grid lengths: 156.000 x 121.000 x 162.000 303s Grid center: (2.518, -2.465, 16.742) 303s Multigrid levels: 4 303s Molecule ID: 1 303s Nonlinear traditional PBE 303s Single Debye-Huckel sphere boundary conditions 303s 2 ion species (0.050 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.400 303s Using "molecular" surface definition; no smoothing 303s Solvent probe radius: 1.400 A 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 1.527617850342E+05 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #2 (mol1): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 13.5959 A 303s Current memory usage: 1028.322 MB total, 2042.113 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 161 x 161 x 161 303s Grid spacings: 0.700 x 0.569 x 0.725 303s Grid lengths: 112.000 x 91.000 x 116.000 303s Grid center: (2.518, -2.465, 16.742) 303s Multigrid levels: 4 303s Molecule ID: 1 303s Nonlinear traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.050 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.400 303s Using "molecular" surface definition; no smoothing 303s Solvent probe radius: 1.400 A 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 2.919510754196E+05 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #3 (mol2): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 13.5959 A 303s Current memory usage: 1030.291 MB total, 2042.113 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 161 x 161 x 161 303s Grid spacings: 0.975 x 0.756 x 1.012 303s Grid lengths: 156.000 x 121.000 x 162.000 303s Grid center: (2.518, -2.465, 16.742) 303s Multigrid levels: 4 303s Molecule ID: 2 303s Nonlinear traditional PBE 303s Single Debye-Huckel sphere boundary conditions 303s 2 ion species (0.050 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.400 303s Using "molecular" surface definition; no smoothing 303s Solvent probe radius: 1.400 A 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 1.527671844880E+05 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #4 (mol2): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 13.5959 A 303s Current memory usage: 1030.291 MB total, 2046.048 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 161 x 161 x 161 303s Grid spacings: 0.700 x 0.569 x 0.725 303s Grid lengths: 112.000 x 91.000 x 116.000 303s Grid center: (2.518, -2.465, 16.742) 303s Multigrid levels: 4 303s Molecule ID: 2 303s Nonlinear traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.050 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.400 303s Using "molecular" surface definition; no smoothing 303s Solvent probe radius: 1.400 A 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 2.915468859278E+05 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #5 (complex): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 13.5959 A 303s Current memory usage: 1046.446 MB total, 2046.048 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 161 x 161 x 161 303s Grid spacings: 0.975 x 0.756 x 1.012 303s Grid lengths: 156.000 x 121.000 x 162.000 303s Grid center: (2.518, -2.465, 16.742) 303s Multigrid levels: 4 303s Molecule ID: 3 303s Nonlinear traditional PBE 303s Single Debye-Huckel sphere boundary conditions 303s 2 ion species (0.050 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.400 303s Using "molecular" surface definition; no smoothing 303s Solvent probe radius: 1.400 A 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 3.056317807611E+05 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #6 (complex): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 13.5959 A 303s Current memory usage: 1046.446 MB total, 2069.492 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 161 x 161 x 161 303s Grid spacings: 0.700 x 0.569 x 0.725 303s Grid lengths: 112.000 x 91.000 x 116.000 303s Grid center: (2.518, -2.465, 16.742) 303s Multigrid levels: 4 303s Molecule ID: 3 303s Nonlinear traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.050 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.400 303s Using "molecular" surface definition; no smoothing 303s Solvent probe radius: 1.400 A 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 5.836028296532E+05 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s PRINT STATEMENTS 303s 303s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 303s Local net energy (PE 0) = 1.048683058621E+02 kJ/mol 303s Global net ELEC energy = 1.048683058621E+02 kJ/mol 303s ---------------------------------------- 303s CLEANING UP AND SHUTTING DOWN... 303s Destroying force arrays. 303s No energy arrays to destroy. 303s Destroying multigrid structures. 303s Destroying finite element structures. 303s Destroying 3 molecules 303s Final memory usage: 0.001 MB total, 2069.492 MB high water 303s 303s 303s Thanks for using APBS! 303s 303s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 303s *** PASSED *** 303s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 303s *** PASSED *** 303s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 303s *** PASSED *** 303s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 303s *** PASSED *** 303s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 303s *** PASSED *** 303s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 303s *** PASSED *** 303s Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) 303s *** PASSED *** 303s Elapsed time: 99.531943 seconds 303s -------------------------------------------------------------------------------- 303s -------------------------------------------------------------------------------- 303s Testing input file apbs-smol-auto.in 303s 373s Checking for intermediate energies in input file apbs-mol-auto.out 373s EXPECTED COMPUTED: 7 373s EXPECTED EXPECTED: 7 373s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] 373s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 373s COMPUTED RESULT 152761.7850342 373s COMPUTED RESULT 291951.0754196 373s COMPUTED RESULT 152767.184488 373s COMPUTED RESULT 291546.8859278 373s COMPUTED RESULT 305631.7807611 373s COMPUTED RESULT 583602.8296532 373s COMPUTED RESULT 104.8683058621 373s BINARY: /usr/bin/apbs 373s INPUT: apbs-smol-auto.in 373s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 373s asc_getToken: Error occurred (bailing out). 373s Vio_scanf: Format problem with input. 373s 373s 373s ---------------------------------------------------------------------- 373s APBS -- Adaptive Poisson-Boltzmann Solver 373s Version APBS 3.4.1 373s 373s Nathan A. Baker (nathan.baker@pnnl.gov) 373s Pacific Northwest National Laboratory 373s 373s Additional contributing authors listed in the code documentation. 373s 373s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 373s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 373s Northwest Division for the U.S. Department of Energy. 373s 373s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 373s Portions Copyright (c) 2002-2020, Nathan A. Baker. 373s Portions Copyright (c) 1999-2002, The Regents of the University of California. 373s Portions Copyright (c) 1995, Michael Holst. 373s All rights reserved. 373s 373s Redistribution and use in source and binary forms, with or without 373s modification, are permitted provided that the following conditions are met: 373s 373s * Redistributions of source code must retain the above copyright notice, this 373s list of conditions and the following disclaimer. 373s 373s * Redistributions in binary form must reproduce the above copyright notice, 373s this list of conditions and the following disclaimer in the documentation 373s and/or other materials provided with the distribution. 373s 373s * Neither the name of the developer nor the names of its contributors may be 373s used to endorse or promote products derived from this software without 373s specific prior written permission. 373s 373s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 373s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 373s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 373s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 373s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 373s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 373s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 373s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 373s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 373s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 373s ---------------------------------------------------------------------- 373s APBS uses FETK (the Finite Element ToolKit) to solve the 373s Poisson-Boltzmann equation numerically. FETK is a portable collection 373s of finite element modeling class libraries developed by the Michael Holst 373s research group and written in an object-oriented form of C. FEtk is 373s designed to solve general coupled systems of nonlinear partial differential 373s equations using adaptive finite element methods, inexact Newton methods, 373s and algebraic multilevel methods. More information about FEtk may be found 373s at . 373s ---------------------------------------------------------------------- 373s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 373s Aqua is a modified form of the Holst group PMG library 373s which has been modified by Patrice Koehl 373s for improved efficiency and 373s memory usage when solving the Poisson-Boltzmann equation. 373s ---------------------------------------------------------------------- 373s Please cite your use of APBS as: 373s 373s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 373s nanosystems: application to microtubules and the ribosome. Proc. 373s Natl. Acad. Sci. USA 98, 10037-10041 2001. 373s 373s 373s This executable compiled on Jan 3 2025 at 11:01:42 373s 373s Parsing input file apbs-smol-auto.in... 373s rank 0 size 1... 373s Parsed input file. 373s Got paths for 3 molecules 373s Reading PQR-format atom data from mol1.pqr. 373s asc_getToken: Error occurred (bailing out). 373s Vio_scanf: Format problem with input. 373s 5877 atoms 373s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 373s Net charge -1.20e+01 e 373s Reading PQR-format atom data from mol2.pqr. 373s asc_getToken: Error occurred (bailing out). 373s Vio_scanf: Format problem with input. 373s 5877 atoms 373s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 373s Net charge -1.20e+01 e 373s Reading PQR-format atom data from complex.pqr. 373s 11754 atoms 373s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 373s Net charge -2.40e+01 e 373s Preparing to run 6 PBE calculations. 373s ---------------------------------------- 373s CALCULATION #1 (mol1): MULTIGRID 373s Setting up problem... 373s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 373s Debye length: 13.5959 A 373s Current memory usage: 1028.322 MB total, 1028.322 MB high water 373s Using linear spline charge discretization. 373s Grid dimensions: 161 x 161 x 161 373s Grid spacings: 0.975 x 0.756 x 1.012 373s Grid lengths: 156.000 x 121.000 x 162.000 373s Grid center: (2.518, -2.465, 16.742) 373s Multigrid levels: 4 373s Molecule ID: 1 373s Nonlinear traditional PBE 373s Single Debye-Huckel sphere boundary conditions 373s 2 ion species (0.050 M ionic strength): 373s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 373s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 373s Solute dielectric: 2.000 373s Solvent dielectric: 78.400 373s Using "molecular" surface definition;harmonic average smoothing 373s Solvent probe radius: 1.400 A 373s Temperature: 298.150 K 373s Electrostatic energies will be calculated 373s Total electrostatic energy = 1.528632421825E+05 kJ/mol 373s Calculating forces... 373s ---------------------------------------- 373s CALCULATION #2 (mol1): MULTIGRID 373s Setting up problem... 373s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 373s Debye length: 13.5959 A 373s Current memory usage: 1028.322 MB total, 2042.113 MB high water 373s Using linear spline charge discretization. 373s Grid dimensions: 161 x 161 x 161 373s Grid spacings: 0.700 x 0.569 x 0.725 373s Grid lengths: 112.000 x 91.000 x 116.000 373s Grid center: (2.518, -2.465, 16.742) 373s Multigrid levels: 4 373s Molecule ID: 1 373s Nonlinear traditional PBE 373s Boundary conditions from focusing 373s 2 ion species (0.050 M ionic strength): 373s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 373s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 373s Solute dielectric: 2.000 373s Solvent dielectric: 78.400 373s Using "molecular" surface definition;harmonic average smoothing 373s Solvent probe radius: 1.400 A 373s Temperature: 298.150 K 373s Electrostatic energies will be calculated 373s Total electrostatic energy = 2.920618662320E+05 kJ/mol 373s Calculating forces... 373s ---------------------------------------- 373s CALCULATION #3 (mol2): MULTIGRID 373s Setting up problem... 373s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 373s Debye length: 13.5959 A 373s Current memory usage: 1030.291 MB total, 2042.113 MB high water 373s Using linear spline charge discretization. 373s Grid dimensions: 161 x 161 x 161 373s Grid spacings: 0.975 x 0.756 x 1.012 373s Grid lengths: 156.000 x 121.000 x 162.000 373s Grid center: (2.518, -2.465, 16.742) 373s Multigrid levels: 4 373s Molecule ID: 2 373s Nonlinear traditional PBE 373s Single Debye-Huckel sphere boundary conditions 373s 2 ion species (0.050 M ionic strength): 373s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 373s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 373s Solute dielectric: 2.000 373s Solvent dielectric: 78.400 373s Using "molecular" surface definition;harmonic average smoothing 373s Solvent probe radius: 1.400 A 373s Temperature: 298.150 K 373s Electrostatic energies will be calculated 373s Total electrostatic energy = 1.529297900572E+05 kJ/mol 373s Calculating forces... 373s ---------------------------------------- 373s CALCULATION #4 (mol2): MULTIGRID 373s Setting up problem... 373s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 373s Debye length: 13.5959 A 373s Current memory usage: 1030.291 MB total, 2046.048 MB high water 373s Using linear spline charge discretization. 373s Grid dimensions: 161 x 161 x 161 373s Grid spacings: 0.700 x 0.569 x 0.725 373s Grid lengths: 112.000 x 91.000 x 116.000 373s Grid center: (2.518, -2.465, 16.742) 373s Multigrid levels: 4 373s Molecule ID: 2 373s Nonlinear traditional PBE 373s Boundary conditions from focusing 373s 2 ion species (0.050 M ionic strength): 373s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 373s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 373s Solute dielectric: 2.000 373s Solvent dielectric: 78.400 373s Using "molecular" surface definition;harmonic average smoothing 373s Solvent probe radius: 1.400 A 373s Temperature: 298.150 K 373s Electrostatic energies will be calculated 373s Total electrostatic energy = 2.916592202835E+05 kJ/mol 373s Calculating forces... 373s ---------------------------------------- 373s CALCULATION #5 (complex): MULTIGRID 373s Setting up problem... 373s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 373s Debye length: 13.5959 A 373s Current memory usage: 1046.446 MB total, 2046.048 MB high water 373s Using linear spline charge discretization. 373s Grid dimensions: 161 x 161 x 161 373s Grid spacings: 0.975 x 0.756 x 1.012 373s Grid lengths: 156.000 x 121.000 x 162.000 373s Grid center: (2.518, -2.465, 16.742) 373s Multigrid levels: 4 373s Molecule ID: 3 373s Nonlinear traditional PBE 373s Single Debye-Huckel sphere boundary conditions 373s 2 ion species (0.050 M ionic strength): 373s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 373s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 373s Solute dielectric: 2.000 373s Solvent dielectric: 78.400 373s Using "molecular" surface definition;harmonic average smoothing 373s Solvent probe radius: 1.400 A 373s Temperature: 298.150 K 373s Electrostatic energies will be calculated 373s Total electrostatic energy = 3.059244262535E+05 kJ/mol 373s Calculating forces... 373s ---------------------------------------- 373s CALCULATION #6 (complex): MULTIGRID 373s Setting up problem... 373s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 373s Debye length: 13.5959 A 373s Current memory usage: 1046.446 MB total, 2069.492 MB high water 373s Using linear spline charge discretization. 373s Grid dimensions: 161 x 161 x 161 373s Grid spacings: 0.700 x 0.569 x 0.725 373s Grid lengths: 112.000 x 91.000 x 116.000 373s Grid center: (2.518, -2.465, 16.742) 373s Multigrid levels: 4 373s Molecule ID: 3 373s Nonlinear traditional PBE 373s Boundary conditions from focusing 373s 2 ion species (0.050 M ionic strength): 373s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 373s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 373s Solute dielectric: 2.000 373s Solvent dielectric: 78.400 373s Using "molecular" surface definition;harmonic average smoothing 373s Solvent probe radius: 1.400 A 373s Temperature: 298.150 K 373s Electrostatic energies will be calculated 373s Total electrostatic energy = 5.838306706232E+05 kJ/mol 373s Calculating forces... 373s ---------------------------------------- 373s PRINT STATEMENTS 373s 373s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 373s Local net energy (PE 0) = 1.095841077688E+02 kJ/mol 373s Global net ELEC energy = 1.095841077688E+02 kJ/mol 373s ---------------------------------------- 373s CLEANING UP AND SHUTTING DOWN... 373s Destroying force arrays. 373s No energy arrays to destroy. 373s Destroying multigrid structures. 373s Destroying finite element structures. 373s Destroying 3 molecules 373s Final memory usage: 0.001 MB total, 2069.492 MB high water 373s 373s 373s Thanks for using APBS! 373s 373s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 373s *** PASSED *** 373s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 373s *** PASSED *** 373s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 373s *** PASSED *** 373s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 373s *** PASSED *** 373s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 373s *** PASSED *** 373s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 373s *** PASSED *** 373s Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) 373s *** PASSED *** 373s Elapsed time: 70.402391 seconds 373s -------------------------------------------------------------------------------- 373s Total elapsed time: 169.934334 seconds 373s Test results have been logged 373s -------------------------------------------------------------------------------- 373s -------------------------------------------------------------------------------- 373s Testing input file alkanes.in 373s 383s Checking for intermediate energies in input file apbs-smol-auto.out 383s EXPECTED COMPUTED: 7 383s EXPECTED EXPECTED: 7 383s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] 383s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 383s COMPUTED RESULT 152863.2421825 383s COMPUTED RESULT 292061.866232 383s COMPUTED RESULT 152929.7900572 383s COMPUTED RESULT 291659.2202835 383s COMPUTED RESULT 305924.4262535 383s COMPUTED RESULT 583830.6706232 383s COMPUTED RESULT 109.5841077688 383s Running tests for alkanes section 383s BINARY: /usr/bin/apbs 383s INPUT: alkanes.in 383s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 383s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 383s *** PASSED *** 383s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 383s *** PASSED *** 383s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 383s *** PASSED *** 383s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 383s *** PASSED *** 383s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 383s *** PASSED *** 383s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 383s *** PASSED *** 383s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 383s *** PASSED *** 383s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 383s *** PASSED *** 383s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 383s *** PASSED *** 383s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 383s *** PASSED *** 383s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 383s *** PASSED *** 383s Elapsed time: 10.409205 seconds 383s -------------------------------------------------------------------------------- 383s Total elapsed time: 10.409205 seconds 383s Test results have been logged 383s -------------------------------------------------------------------------------- 383s -------------------------------------------------------------------------------- 383s Testing input file 1d7h-dmso-mol.in 383s 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 383s 383s ---------------------------------------------------------------------- 383s APBS -- Adaptive Poisson-Boltzmann Solver 383s Version APBS 3.4.1 383s 383s Nathan A. Baker (nathan.baker@pnnl.gov) 383s Pacific Northwest National Laboratory 383s 383s Additional contributing authors listed in the code documentation. 383s 383s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 383s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 383s Northwest Division for the U.S. Department of Energy. 383s 383s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 383s Portions Copyright (c) 2002-2020, Nathan A. Baker. 383s Portions Copyright (c) 1999-2002, The Regents of the University of California. 383s Portions Copyright (c) 1995, Michael Holst. 383s All rights reserved. 383s 383s Redistribution and use in source and binary forms, with or without 383s modification, are permitted provided that the following conditions are met: 383s 383s * Redistributions of source code must retain the above copyright notice, this 383s list of conditions and the following disclaimer. 383s 383s * Redistributions in binary form must reproduce the above copyright notice, 383s this list of conditions and the following disclaimer in the documentation 383s and/or other materials provided with the distribution. 383s 383s * Neither the name of the developer nor the names of its contributors may be 383s used to endorse or promote products derived from this software without 383s specific prior written permission. 383s 383s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 383s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 383s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 383s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 383s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 383s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 383s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 383s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 383s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 383s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 383s ---------------------------------------------------------------------- 383s APBS uses FETK (the Finite Element ToolKit) to solve the 383s Poisson-Boltzmann equation numerically. FETK is a portable collection 383s of finite element modeling class libraries developed by the Michael Holst 383s research group and written in an object-oriented form of C. FEtk is 383s designed to solve general coupled systems of nonlinear partial differential 383s equations using adaptive finite element methods, inexact Newton methods, 383s and algebraic multilevel methods. More information about FEtk may be found 383s at . 383s ---------------------------------------------------------------------- 383s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 383s Aqua is a modified form of the Holst group PMG library 383s which has been modified by Patrice Koehl 383s for improved efficiency and 383s memory usage when solving the Poisson-Boltzmann equation. 383s ---------------------------------------------------------------------- 383s Please cite your use of APBS as: 383s 383s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 383s nanosystems: application to microtubules and the ribosome. Proc. 383s Natl. Acad. Sci. USA 98, 10037-10041 2001. 383s 383s 383s This executable compiled on Jan 3 2025 at 11:01:42 383s 383s Parsing input file alkanes.in... 383s rank 0 size 1... 383s Parsed input file. 383s Reading parameter data from parm.dat. 383s Got paths for 11 molecules 383s Reading PDB-format atom data from 2-methylbutane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 17 atoms 383s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 383s Net charge 4.33e+00 e 383s Reading PDB-format atom data from butane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 14 atoms 383s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 383s Net charge 3.51e+00 e 383s Reading PDB-format atom data from cyclohexane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 18 atoms 383s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 383s Net charge 4.93e+00 e 383s Reading PDB-format atom data from cyclopentane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 13 atoms 383s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 383s Net charge 3.88e+00 e 383s Reading PDB-format atom data from ethane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 8 atoms 383s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 383s Net charge 1.87e+00 e 383s Reading PDB-format atom data from hexane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 20 atoms 383s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 383s Net charge 5.16e+00 e 383s Reading PDB-format atom data from isobutane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 14 atoms 383s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 383s Net charge 3.51e+00 e 383s Reading PDB-format atom data from methane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 5 atoms 383s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 383s Net charge 1.05e+00 e 383s Reading PDB-format atom data from neopentane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 17 atoms 383s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 383s Net charge 4.33e+00 e 383s Reading PDB-format atom data from pentane.pdb. 383s asc_getToken: Error occurred (bailing out). 383s Vio_scanf: Format problem with input. 383s 17 atoms 383s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 383s Net charge 4.33e+00 e 383s Reading PDB-format atom data from propane.pdb. 383s 11 atoms 383s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 383s Net charge 2.69e+00 e 383s Preparing to run 11 PBE calculations. 383s ---------------------------------------- 383s CALCULATION #1 (solvated-2-methylbutane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 3.815624614267E+00 383s SASA for atom 1: 0.000000000000E+00 383s SASA for atom 2: 6.122920124655E-01 383s SASA for atom 3: 3.957497153740E+00 383s SASA for atom 4: 4.308445014544E+00 383s SASA for atom 5: 1.843264951960E+01 383s SASA for atom 6: 1.837011296483E+01 383s SASA for atom 7: 1.666599184724E+01 383s SASA for atom 8: 1.480031796315E+01 383s SASA for atom 9: 1.603020354037E+01 383s SASA for atom 10: 1.473778140838E+01 383s SASA for atom 11: 1.611879699297E+01 383s SASA for atom 12: 1.810954398660E+01 383s SASA for atom 13: 1.420100931324E+01 383s SASA for atom 14: 1.437298483886E+01 383s SASA for atom 15: 1.814081226399E+01 383s SASA for atom 16: 2.152820898091E+01 383s 383s Total solvent accessible surface area: 214.202 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 3.243280922127E-02 383s Surface tension*area energy for atom 1: 0.000000000000E+00 383s Surface tension*area energy for atom 2: 5.204482105957E-03 383s Surface tension*area energy for atom 3: 3.363872580679E-02 383s Surface tension*area energy for atom 4: 3.662178262362E-02 383s Surface tension*area energy for atom 5: 1.566775209166E-01 383s Surface tension*area energy for atom 6: 1.561459602010E-01 383s Surface tension*area energy for atom 7: 1.416609307015E-01 383s Surface tension*area energy for atom 8: 1.258027026868E-01 383s Surface tension*area energy for atom 9: 1.362567300932E-01 383s Surface tension*area energy for atom 10: 1.252711419712E-01 383s Surface tension*area energy for atom 11: 1.370097744402E-01 383s Surface tension*area energy for atom 12: 1.539311238861E-01 383s Surface tension*area energy for atom 13: 1.207085791625E-01 383s Surface tension*area energy for atom 14: 1.221703711303E-01 383s Surface tension*area energy for atom 15: 1.541969042439E-01 383s Surface tension*area energy for atom 16: 1.829897763377E-01 383s 383s Total surface tension energy: 1.82072 kJ/mol 383s 383s Total solvent accessible volume: 253.665 A^3 383s 383s Total pressure*volume energy: 60.7274 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.271287875274E+00 383s WCA energy for atom 1: -5.600872869478E+00 383s WCA energy for atom 2: -5.773775123943E+00 383s WCA energy for atom 3: -6.072801488986E+00 383s WCA energy for atom 4: -6.378470721845E+00 383s WCA energy for atom 5: -1.573474558351E+00 383s WCA energy for atom 6: -1.582338715648E+00 383s WCA energy for atom 7: -1.504044838266E+00 383s WCA energy for atom 8: -1.351002262819E+00 383s WCA energy for atom 9: -1.437367175239E+00 383s WCA energy for atom 10: -1.384626257493E+00 383s WCA energy for atom 11: -1.468867560891E+00 383s WCA energy for atom 12: -1.557005662832E+00 383s WCA energy for atom 13: -1.473759654043E+00 383s WCA energy for atom 14: -1.502261431335E+00 383s WCA energy for atom 15: -1.550940901474E+00 383s WCA energy for atom 16: -1.667828659696E+00 383s 383s Total WCA energy: -48.1507 kJ/mol 383s 383s Total non-polar energy = 1.439739455792E+01 kJ/mol 383s ---------------------------------------- 383s CALCULATION #2 (solvated-butane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 4.405515699447E+00 383s SASA for atom 1: 8.213673337951E-01 383s SASA for atom 2: 8.064333822716E-01 383s SASA for atom 3: 4.375647796400E+00 383s SASA for atom 4: 1.855251124959E+01 383s SASA for atom 5: 2.147609518526E+01 383s SASA for atom 6: 1.852645435176E+01 383s SASA for atom 7: 1.660345529247E+01 383s SASA for atom 8: 1.658782115377E+01 383s SASA for atom 9: 1.658260977421E+01 383s SASA for atom 10: 1.658260977421E+01 383s SASA for atom 11: 2.145003828744E+01 383s SASA for atom 12: 1.852124297220E+01 383s SASA for atom 13: 1.856293400871E+01 383s 383s Total solvent accessible surface area: 193.855 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 3.744688344530E-02 383s Surface tension*area energy for atom 1: 6.981622337259E-03 383s Surface tension*area energy for atom 2: 6.854683749309E-03 383s Surface tension*area energy for atom 3: 3.719300626940E-02 383s Surface tension*area energy for atom 4: 1.576963456215E-01 383s Surface tension*area energy for atom 5: 1.825468090747E-01 383s Surface tension*area energy for atom 6: 1.574748619900E-01 383s Surface tension*area energy for atom 7: 1.411293699860E-01 383s Surface tension*area energy for atom 8: 1.409964798071E-01 383s Surface tension*area energy for atom 9: 1.409521830808E-01 383s Surface tension*area energy for atom 10: 1.409521830808E-01 383s Surface tension*area energy for atom 11: 1.823253254433E-01 383s Surface tension*area energy for atom 12: 1.574305652637E-01 383s Surface tension*area energy for atom 13: 1.577849390741E-01 383s 383s Total surface tension energy: 1.64777 kJ/mol 383s 383s Total solvent accessible volume: 217.863 A^3 383s 383s Total pressure*volume energy: 52.1564 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.728858147814E+00 383s WCA energy for atom 1: -6.204037472587E+00 383s WCA energy for atom 2: -6.202937735018E+00 383s WCA energy for atom 3: -6.728762249931E+00 383s WCA energy for atom 4: -1.623549989062E+00 383s WCA energy for atom 5: -1.709092300778E+00 383s WCA energy for atom 6: -1.625196457114E+00 383s WCA energy for atom 7: -1.484289341167E+00 383s WCA energy for atom 8: -1.485410538626E+00 383s WCA energy for atom 9: -1.485593139015E+00 383s WCA energy for atom 10: -1.484878734279E+00 383s WCA energy for atom 11: -1.708585062695E+00 383s WCA energy for atom 12: -1.625094916482E+00 383s WCA energy for atom 13: -1.624416805392E+00 383s 383s Total WCA energy: -41.7207 kJ/mol 383s 383s Total non-polar energy = 1.208346456826E+01 kJ/mol 383s ---------------------------------------- 383s CALCULATION #3 (solvated-cyclohexane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 7.840324549863E-01 383s SASA for atom 1: 8.064333822716E-01 383s SASA for atom 2: 8.288343095569E-01 383s SASA for atom 3: 7.840324549863E-01 383s SASA for atom 4: 7.989664065098E-01 383s SASA for atom 5: 8.363012853187E-01 383s SASA for atom 6: 2.001169752764E+01 383s SASA for atom 7: 1.616048802948E+01 383s SASA for atom 8: 2.001169752764E+01 383s SASA for atom 9: 1.619175630687E+01 383s SASA for atom 10: 1.616048802948E+01 383s SASA for atom 11: 1.993352683418E+01 383s SASA for atom 12: 2.001169752764E+01 383s SASA for atom 13: 1.618133354774E+01 383s SASA for atom 14: 1.617091078861E+01 383s SASA for atom 15: 2.001690890721E+01 383s SASA for atom 16: 1.993873821374E+01 383s SASA for atom 17: 1.617091078861E+01 383s 383s Total solvent accessible surface area: 221.799 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 6.664275867383E-03 383s Surface tension*area energy for atom 1: 6.854683749309E-03 383s Surface tension*area energy for atom 2: 7.045091631234E-03 383s Surface tension*area energy for atom 3: 6.664275867383E-03 383s Surface tension*area energy for atom 4: 6.791214455333E-03 383s Surface tension*area energy for atom 5: 7.108560925209E-03 383s Surface tension*area energy for atom 6: 1.700994289850E-01 383s Surface tension*area energy for atom 7: 1.373641482506E-01 383s Surface tension*area energy for atom 8: 1.700994289850E-01 383s Surface tension*area energy for atom 9: 1.376299286084E-01 383s Surface tension*area energy for atom 10: 1.373641482506E-01 383s Surface tension*area energy for atom 11: 1.694349780905E-01 383s Surface tension*area energy for atom 12: 1.700994289850E-01 383s Surface tension*area energy for atom 13: 1.375413351558E-01 383s Surface tension*area energy for atom 14: 1.374527417032E-01 383s Surface tension*area energy for atom 15: 1.701437257113E-01 383s Surface tension*area energy for atom 16: 1.694792748168E-01 383s Surface tension*area energy for atom 17: 1.374527417032E-01 383s 383s Total surface tension energy: 1.88529 kJ/mol 383s 383s Total solvent accessible volume: 267.435 A^3 383s 383s Total pressure*volume energy: 64.0239 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -5.793234697241E+00 383s WCA energy for atom 1: -5.784370526583E+00 383s WCA energy for atom 2: -5.791799130412E+00 383s WCA energy for atom 3: -5.788504399087E+00 383s WCA energy for atom 4: -5.797319672490E+00 383s WCA energy for atom 5: -5.787358035342E+00 383s WCA energy for atom 6: -1.523887929614E+00 383s WCA energy for atom 7: -1.413678912317E+00 383s WCA energy for atom 8: -1.521751604392E+00 383s WCA energy for atom 9: -1.414741802525E+00 383s WCA energy for atom 10: -1.413367854344E+00 383s WCA energy for atom 11: -1.523407238081E+00 383s WCA energy for atom 12: -1.523000623583E+00 383s WCA energy for atom 13: -1.413922068538E+00 383s WCA energy for atom 14: -1.416316744211E+00 383s WCA energy for atom 15: -1.524577474659E+00 383s WCA energy for atom 16: -1.523300410052E+00 383s WCA energy for atom 17: -1.414522566061E+00 383s 383s Total WCA energy: -52.3691 kJ/mol 383s 383s Total non-polar energy = 1.354016672221E+01 kJ/mol 383s ---------------------------------------- 383s CALCULATION #4 (solvated-cyclopentane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 9.490526193215E+00 383s SASA for atom 1: 9.512927120500E+00 383s SASA for atom 2: 2.299828534626E+00 383s SASA for atom 3: 1.919012770776E+00 383s SASA for atom 4: 2.307295510388E+00 383s SASA for atom 5: 2.325838699632E+01 383s SASA for atom 6: 2.325838699632E+01 383s SASA for atom 7: 2.045987617019E+01 383s SASA for atom 8: 2.067875411190E+01 383s SASA for atom 9: 2.028790064456E+01 383s SASA for atom 10: 1.897463299431E+01 383s SASA for atom 11: 2.048593306801E+01 383s SASA for atom 12: 2.070481100972E+01 383s 383s Total solvent accessible surface area: 193.638 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 8.066947264233E-02 383s Surface tension*area energy for atom 1: 8.085988052425E-02 383s Surface tension*area energy for atom 2: 1.954854254432E-02 383s Surface tension*area energy for atom 3: 1.631160855160E-02 383s Surface tension*area energy for atom 4: 1.961201183830E-02 383s Surface tension*area energy for atom 5: 1.976962894687E-01 383s Surface tension*area energy for atom 6: 1.976962894687E-01 383s Surface tension*area energy for atom 7: 1.739089474466E-01 383s Surface tension*area energy for atom 8: 1.757694099511E-01 383s Surface tension*area energy for atom 9: 1.724471554788E-01 383s Surface tension*area energy for atom 10: 1.612843804516E-01 383s Surface tension*area energy for atom 11: 1.741304310781E-01 383s Surface tension*area energy for atom 12: 1.759908935826E-01 383s 383s Total surface tension energy: 1.64593 kJ/mol 383s 383s Total solvent accessible volume: 217.998 A^3 383s 383s Total pressure*volume energy: 52.1887 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.343496616804E+00 383s WCA energy for atom 1: -6.327869601807E+00 383s WCA energy for atom 2: -6.334858040579E+00 383s WCA energy for atom 3: -6.296075406417E+00 383s WCA energy for atom 4: -6.345600816761E+00 383s WCA energy for atom 5: -1.663697465126E+00 383s WCA energy for atom 6: -1.662444032853E+00 383s WCA energy for atom 7: -1.572325104493E+00 383s WCA energy for atom 8: -1.604626551065E+00 383s WCA energy for atom 9: -1.586431484963E+00 383s WCA energy for atom 10: -1.554291291374E+00 383s WCA energy for atom 11: -1.574315220751E+00 383s WCA energy for atom 12: -1.604941679892E+00 383s 383s Total WCA energy: -44.471 kJ/mol 383s 383s Total non-polar energy = 9.363673200142E+00 kJ/mol 383s ---------------------------------------- 383s CALCULATION #5 (solvated-ethane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 5.995981536705E+00 383s SASA for atom 1: 5.966113633657E+00 383s SASA for atom 2: 2.121552620704E+01 383s SASA for atom 3: 2.124158310486E+01 383s SASA for atom 4: 2.125200586399E+01 383s SASA for atom 5: 2.123116034573E+01 383s SASA for atom 6: 2.125200586399E+01 383s SASA for atom 7: 2.127285138225E+01 383s 383s Total solvent accessible surface area: 139.427 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 5.096584306199E-02 383s Surface tension*area energy for atom 1: 5.071196588609E-02 383s Surface tension*area energy for atom 2: 1.803319727598E-01 383s Surface tension*area energy for atom 3: 1.805534563913E-01 383s Surface tension*area energy for atom 4: 1.806420498439E-01 383s Surface tension*area energy for atom 5: 1.804648629387E-01 383s Surface tension*area energy for atom 6: 1.806420498439E-01 383s Surface tension*area energy for atom 7: 1.808192367491E-01 383s 383s Total surface tension energy: 1.18513 kJ/mol 383s 383s Total solvent accessible volume: 140.346 A^3 383s 383s Total pressure*volume energy: 33.5988 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -7.360066353115E+00 383s WCA energy for atom 1: -7.355483516201E+00 383s WCA energy for atom 2: -1.776106201066E+00 383s WCA energy for atom 3: -1.773973940651E+00 383s WCA energy for atom 4: -1.775401936843E+00 383s WCA energy for atom 5: -1.773464835521E+00 383s WCA energy for atom 6: -1.774382856097E+00 383s WCA energy for atom 7: -1.772366599434E+00 383s 383s Total WCA energy: -25.3612 kJ/mol 383s 383s Total non-polar energy = 9.422717598546E+00 kJ/mol 383s ---------------------------------------- 383s CALCULATION #6 (solvated-hexane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 4.405515699447E+00 383s SASA for atom 1: 8.213673337951E-01 383s SASA for atom 2: 3.285469335181E-01 383s SASA for atom 3: 2.986790304710E-01 383s SASA for atom 4: 1.855251124959E+01 383s SASA for atom 5: 2.147609518526E+01 383s SASA for atom 6: 1.852645435176E+01 383s SASA for atom 7: 1.655655287639E+01 383s SASA for atom 8: 1.655134149682E+01 383s SASA for atom 9: 1.360170066332E+01 383s SASA for atom 10: 1.357043238593E+01 383s SASA for atom 11: 1.381536722546E+01 383s SASA for atom 12: 1.384142412329E+01 383s SASA for atom 13: 7.765654792245E-01 383s SASA for atom 14: 1.684839013200E+01 383s SASA for atom 15: 1.682233323417E+01 383s SASA for atom 16: 4.166572475070E+00 383s SASA for atom 17: 2.179398933870E+01 383s SASA for atom 18: 1.877660057086E+01 383s SASA for atom 19: 1.876096643216E+01 383s 383s Total solvent accessible surface area: 250.291 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 3.744688344530E-02 383s Surface tension*area energy for atom 1: 6.981622337259E-03 383s Surface tension*area energy for atom 2: 2.792648934903E-03 383s Surface tension*area energy for atom 3: 2.538771759003E-03 383s Surface tension*area energy for atom 4: 1.576963456215E-01 383s Surface tension*area energy for atom 5: 1.825468090747E-01 383s Surface tension*area energy for atom 6: 1.574748619900E-01 383s Surface tension*area energy for atom 7: 1.407306994493E-01 383s Surface tension*area energy for atom 8: 1.406864027230E-01 383s Surface tension*area energy for atom 9: 1.156144556382E-01 383s Surface tension*area energy for atom 10: 1.153486752804E-01 383s Surface tension*area energy for atom 11: 1.174306214164E-01 383s Surface tension*area energy for atom 12: 1.176521050479E-01 383s Surface tension*area energy for atom 13: 6.600806573408E-03 383s Surface tension*area energy for atom 14: 1.432113161220E-01 383s Surface tension*area energy for atom 15: 1.429898324905E-01 383s Surface tension*area energy for atom 16: 3.541586603809E-02 383s Surface tension*area energy for atom 17: 1.852489093789E-01 383s Surface tension*area energy for atom 18: 1.596011048523E-01 383s Surface tension*area energy for atom 19: 1.594682146734E-01 383s 383s Total surface tension energy: 2.12748 kJ/mol 383s 383s Total solvent accessible volume: 298.053 A^3 383s 383s Total pressure*volume energy: 71.3539 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.635406071935E+00 383s WCA energy for atom 1: -5.957247427848E+00 383s WCA energy for atom 2: -5.524801144538E+00 383s WCA energy for atom 3: -5.522294168859E+00 383s WCA energy for atom 4: -1.605314409440E+00 383s WCA energy for atom 5: -1.701051761776E+00 383s WCA energy for atom 6: -1.606669162773E+00 383s WCA energy for atom 7: -1.442505934938E+00 383s WCA energy for atom 8: -1.443059002759E+00 383s WCA energy for atom 9: -1.328947132810E+00 383s WCA energy for atom 10: -1.328906972440E+00 383s WCA energy for atom 11: -1.331566344214E+00 383s WCA energy for atom 12: -1.328041776815E+00 383s WCA energy for atom 13: -5.937562025661E+00 383s WCA energy for atom 14: -1.442277774427E+00 383s WCA energy for atom 15: -1.442777091510E+00 383s WCA energy for atom 16: -6.602262542378E+00 383s WCA energy for atom 17: -1.698172146664E+00 383s WCA energy for atom 18: -1.600970858835E+00 383s WCA energy for atom 19: -1.600841970217E+00 383s 383s Total WCA energy: -57.0807 kJ/mol 383s 383s Total non-polar energy = 1.640068943201E+01 kJ/mol 383s ---------------------------------------- 383s CALCULATION #7 (solvated-isobutane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 3.464676753463E+00 383s SASA for atom 1: 1.984493338158E+01 383s SASA for atom 2: 1.778643845361E+01 383s SASA for atom 3: 1.671289426332E+01 383s SASA for atom 4: 0.000000000000E+00 383s SASA for atom 5: 3.531879535319E+00 383s SASA for atom 6: 1.673895116114E+01 383s SASA for atom 7: 1.793756846098E+01 383s SASA for atom 8: 1.973549441072E+01 383s SASA for atom 9: 1.710895911022E+01 383s SASA for atom 10: 4.599657069253E+00 383s SASA for atom 11: 1.937069784121E+01 383s SASA for atom 12: 1.654613011726E+01 383s SASA for atom 13: 1.936548646165E+01 383s 383s Total solvent accessible surface area: 192.744 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 2.944975240444E-02 383s Surface tension*area energy for atom 1: 1.686819337434E-01 383s Surface tension*area energy for atom 2: 1.511847268556E-01 383s Surface tension*area energy for atom 3: 1.420596012382E-01 383s Surface tension*area energy for atom 4: 0.000000000000E+00 383s Surface tension*area energy for atom 5: 3.002097605021E-02 383s Surface tension*area energy for atom 6: 1.422810848697E-01 383s Surface tension*area energy for atom 7: 1.524693319183E-01 383s Surface tension*area energy for atom 8: 1.677517024912E-01 383s Surface tension*area energy for atom 9: 1.454261524369E-01 383s Surface tension*area energy for atom 10: 3.909708508865E-02 383s Surface tension*area energy for atom 11: 1.646509316503E-01 383s Surface tension*area energy for atom 12: 1.406421059967E-01 383s Surface tension*area energy for atom 13: 1.646066349240E-01 383s 383s Total surface tension energy: 1.63832 kJ/mol 383s 383s Total solvent accessible volume: 218.943 A^3 383s 383s Total pressure*volume energy: 52.415 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.381016335247E+00 383s WCA energy for atom 1: -1.612317964554E+00 383s WCA energy for atom 2: -1.588013719598E+00 383s WCA energy for atom 3: -1.532162371190E+00 383s WCA energy for atom 4: -5.987950445279E+00 383s WCA energy for atom 5: -6.393089030861E+00 383s WCA energy for atom 6: -1.533454887042E+00 383s WCA energy for atom 7: -1.587650918485E+00 383s WCA energy for atom 8: -1.614083521570E+00 383s WCA energy for atom 9: -1.442402031577E+00 383s WCA energy for atom 10: -6.408813541353E+00 383s WCA energy for atom 11: -1.605830214390E+00 383s WCA energy for atom 12: -1.529385873788E+00 383s WCA energy for atom 13: -1.605662490385E+00 383s 383s Total WCA energy: -40.8218 kJ/mol 383s 383s Total non-polar energy = 1.323144287435E+01 kJ/mol 383s ---------------------------------------- 383s CALCULATION #8 (solvated-methane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 1.231304303117E+01 383s SASA for atom 1: 2.323233009850E+01 383s SASA for atom 2: 2.345641941977E+01 383s SASA for atom 3: 2.377431357320E+01 383s SASA for atom 4: 2.264344420771E+01 383s 383s Total solvent accessible surface area: 105.42 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 1.046608657649E-01 383s Surface tension*area energy for atom 1: 1.974748058372E-01 383s Surface tension*area energy for atom 2: 1.993795650680E-01 383s Surface tension*area energy for atom 3: 2.020816653722E-01 383s Surface tension*area energy for atom 4: 1.924692757655E-01 383s 383s Total surface tension energy: 0.896066 kJ/mol 383s 383s Total solvent accessible volume: 95.985 A^3 383s 383s Total pressure*volume energy: 22.9788 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -8.133807570805E+00 383s WCA energy for atom 1: -1.962181541765E+00 383s WCA energy for atom 2: -1.964078319162E+00 383s WCA energy for atom 3: -1.963015006647E+00 383s WCA energy for atom 4: -1.957425549100E+00 383s 383s Total WCA energy: -15.9805 kJ/mol 383s 383s Total non-polar energy = 7.894367190329E+00 kJ/mol 383s ---------------------------------------- 383s CALCULATION #9 (solvated-neopentane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 2.441701074100E+00 383s SASA for atom 1: 1.663993494942E+01 383s SASA for atom 2: 1.715586152630E+01 383s SASA for atom 3: 1.645753666466E+01 383s SASA for atom 4: 0.000000000000E+00 383s SASA for atom 5: 2.389432243768E+00 383s SASA for atom 6: 1.638457735076E+01 383s SASA for atom 7: 1.667641460637E+01 383s SASA for atom 8: 1.721839808108E+01 383s SASA for atom 9: 2.419300146815E+00 383s SASA for atom 10: 1.640021148945E+01 383s SASA for atom 11: 1.666599184724E+01 383s SASA for atom 12: 1.719234118325E+01 383s SASA for atom 13: 2.449168049862E+00 383s SASA for atom 14: 1.723403221977E+01 383s SASA for atom 15: 1.639500010989E+01 383s SASA for atom 16: 1.663472356985E+01 383s 383s Total solvent accessible surface area: 210.755 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 2.075445912985E-02 383s Surface tension*area energy for atom 1: 1.414394470700E-01 383s Surface tension*area energy for atom 2: 1.458248229736E-01 383s Surface tension*area energy for atom 3: 1.398890616496E-01 383s Surface tension*area energy for atom 4: 0.000000000000E+00 383s Surface tension*area energy for atom 5: 2.031017407203E-02 383s Surface tension*area energy for atom 6: 1.392689074814E-01 383s Surface tension*area energy for atom 7: 1.417495241541E-01 383s Surface tension*area energy for atom 8: 1.463563836891E-01 383s Surface tension*area energy for atom 9: 2.056405124793E-02 383s Surface tension*area energy for atom 10: 1.394017976603E-01 383s Surface tension*area energy for atom 11: 1.416609307015E-01 383s Surface tension*area energy for atom 12: 1.461349000577E-01 383s Surface tension*area energy for atom 13: 2.081792842383E-02 383s Surface tension*area energy for atom 14: 1.464892738680E-01 383s Surface tension*area energy for atom 15: 1.393575009340E-01 383s Surface tension*area energy for atom 16: 1.413951503437E-01 383s 383s Total surface tension energy: 1.79141 kJ/mol 383s 383s Total solvent accessible volume: 251.127 A^3 383s 383s Total pressure*volume energy: 60.1198 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.011082520236E+00 383s WCA energy for atom 1: -1.497367782613E+00 383s WCA energy for atom 2: -1.498546483218E+00 383s WCA energy for atom 3: -1.492562171495E+00 383s WCA energy for atom 4: -5.447325863939E+00 383s WCA energy for atom 5: -6.004516149175E+00 383s WCA energy for atom 6: -1.492776531092E+00 383s WCA energy for atom 7: -1.496078170066E+00 383s WCA energy for atom 8: -1.501529655270E+00 383s WCA energy for atom 9: -5.996267554365E+00 383s WCA energy for atom 10: -1.492194267752E+00 383s WCA energy for atom 11: -1.496027211216E+00 383s WCA energy for atom 12: -1.500561393960E+00 383s WCA energy for atom 13: -6.000218612907E+00 383s WCA energy for atom 14: -1.500859921426E+00 383s WCA energy for atom 15: -1.492908499790E+00 383s WCA energy for atom 16: -1.494057174414E+00 383s 383s Total WCA energy: -47.4149 kJ/mol 383s 383s Total non-polar energy = 1.449633815052E+01 kJ/mol 383s ---------------------------------------- 383s CALCULATION #10 (solvated-pentane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 4.405515699447E+00 383s SASA for atom 1: 8.213673337951E-01 383s SASA for atom 2: 3.285469335181E-01 383s SASA for atom 3: 7.466975761774E-01 383s SASA for atom 4: 1.855251124959E+01 383s SASA for atom 5: 2.147609518526E+01 383s SASA for atom 6: 1.852645435176E+01 383s SASA for atom 7: 1.655655287639E+01 383s SASA for atom 8: 1.655134149682E+01 383s SASA for atom 9: 1.360170066332E+01 383s SASA for atom 10: 1.357043238593E+01 383s SASA for atom 11: 1.685881289113E+01 383s SASA for atom 12: 1.687444702982E+01 383s SASA for atom 13: 4.196440378117E+00 383s SASA for atom 14: 1.881308022781E+01 383s SASA for atom 15: 1.882350298694E+01 383s SASA for atom 16: 2.182004623652E+01 383s 383s Total solvent accessible surface area: 222.524 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 3.744688344530E-02 383s Surface tension*area energy for atom 1: 6.981622337259E-03 383s Surface tension*area energy for atom 2: 2.792648934903E-03 383s Surface tension*area energy for atom 3: 6.346929397508E-03 383s Surface tension*area energy for atom 4: 1.576963456215E-01 383s Surface tension*area energy for atom 5: 1.825468090747E-01 383s Surface tension*area energy for atom 6: 1.574748619900E-01 383s Surface tension*area energy for atom 7: 1.407306994493E-01 383s Surface tension*area energy for atom 8: 1.406864027230E-01 383s Surface tension*area energy for atom 9: 1.156144556382E-01 383s Surface tension*area energy for atom 10: 1.153486752804E-01 383s Surface tension*area energy for atom 11: 1.432999095746E-01 383s Surface tension*area energy for atom 12: 1.434327997535E-01 383s Surface tension*area energy for atom 13: 3.566974321399E-02 383s Surface tension*area energy for atom 14: 1.599111819364E-01 383s Surface tension*area energy for atom 15: 1.599997753890E-01 383s Surface tension*area energy for atom 16: 1.854703930104E-01 383s 383s Total surface tension energy: 1.89145 kJ/mol 383s 383s Total solvent accessible volume: 258.93 A^3 383s 383s Total pressure*volume energy: 61.9878 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.655804319869E+00 383s WCA energy for atom 1: -6.027315962813E+00 383s WCA energy for atom 2: -5.696430965386E+00 383s WCA energy for atom 3: -6.016749084714E+00 383s WCA energy for atom 4: -1.608595384643E+00 383s WCA energy for atom 5: -1.703300955380E+00 383s WCA energy for atom 6: -1.609931495887E+00 383s WCA energy for atom 7: -1.457107525189E+00 383s WCA energy for atom 8: -1.457741620594E+00 383s WCA energy for atom 9: -1.354235498709E+00 383s WCA energy for atom 10: -1.354106470090E+00 383s WCA energy for atom 11: -1.456736412636E+00 383s WCA energy for atom 12: -1.455995435596E+00 383s WCA energy for atom 13: -6.633650611186E+00 383s WCA energy for atom 14: -1.605996088477E+00 383s WCA energy for atom 15: -1.606549890103E+00 383s WCA energy for atom 16: -1.700042300035E+00 383s 383s Total WCA energy: -49.4003 kJ/mol 383s 383s Total non-polar energy = 1.447900211546E+01 kJ/mol 383s ---------------------------------------- 383s CALCULATION #11 (solvated-propane): APOLAR 383s 383s Solvent Accessible Surface Area (SASA) for each atom: 383s SASA for atom 0: 3.173464698754E+00 383s SASA for atom 1: 1.931858404557E+01 383s SASA for atom 2: 2.014198201675E+01 383s SASA for atom 3: 2.149694070352E+01 383s SASA for atom 4: 1.904078819252E+00 383s SASA for atom 5: 2.067354273233E+01 383s SASA for atom 6: 1.937590922077E+01 383s SASA for atom 7: 3.098794941136E+00 383s SASA for atom 8: 1.942802301642E+01 383s SASA for atom 9: 1.973028303116E+01 383s SASA for atom 10: 2.204934693736E+01 383s 383s Total solvent accessible surface area: 170.391 A^2 383s 383s Surface tension*area energies (gamma * SASA) for each atom: 383s Surface tension*area energy for atom 0: 2.697444993941E-02 383s Surface tension*area energy for atom 1: 1.642079643873E-01 383s Surface tension*area energy for atom 2: 1.712068471424E-01 383s Surface tension*area energy for atom 3: 1.827239959799E-01 383s Surface tension*area energy for atom 4: 1.618466996365E-02 383s Surface tension*area energy for atom 5: 1.757251132248E-01 383s Surface tension*area energy for atom 6: 1.646952283766E-01 383s Surface tension*area energy for atom 7: 2.633975699966E-02 383s Surface tension*area energy for atom 8: 1.651381956396E-01 383s Surface tension*area energy for atom 9: 1.677074057649E-01 383s Surface tension*area energy for atom 10: 1.874194489675E-01 383s 383s Total surface tension energy: 1.44832 kJ/mol 383s 383s Total solvent accessible volume: 183.573 A^3 383s 383s Total pressure*volume energy: 43.9474 kJ/mol 383s 383s WCA dispersion Energies for each atom: 383s WCA energy for atom 0: -6.818670105515E+00 383s WCA energy for atom 1: -1.641297645338E+00 383s WCA energy for atom 2: -1.649584120441E+00 383s WCA energy for atom 3: -1.711408141255E+00 383s WCA energy for atom 4: -6.624720142882E+00 383s WCA energy for atom 5: -1.610117050515E+00 383s WCA energy for atom 6: -1.596858009746E+00 383s WCA energy for atom 7: -6.816460624835E+00 383s WCA energy for atom 8: -1.642782751806E+00 383s WCA energy for atom 9: -1.645779566650E+00 383s WCA energy for atom 10: -1.714436154542E+00 383s 383s Total WCA energy: -33.4721 kJ/mol 383s 383s Total non-polar energy = 1.192358496286E+01 kJ/mol 383s ---------------------------------------- 383s PRINT STATEMENTS 383s 383s print APOL energy 1 (solvated-2-methylbutane) end 383s Global net APOL energy = 1.439739455792E+01 kJ/mol 383s 383s print APOL energy 2 (solvated-butane) end 383s Global net APOL energy = 1.208346456826E+01 kJ/mol 383s 383s print APOL energy 3 (solvated-cyclohexane) end 383s Global net APOL energy = 1.354016672221E+01 kJ/mol 383s 383s print APOL energy 4 (solvated-cyclopentane) end 383s Global net APOL energy = 9.363673200142E+00 kJ/mol 383s 383s print APOL energy 5 (solvated-ethane) end 383s Global net APOL energy = 9.422717598546E+00 kJ/mol 383s 383s print APOL energy 6 (solvated-hexane) end 383s Global net APOL energy = 1.640068943201E+01 kJ/mol 383s 383s print APOL energy 7 (solvated-isobutane) end 383s Global net APOL energy = 1.323144287435E+01 kJ/mol 383s 383s print APOL energy 8 (solvated-methane) end 383s Global net APOL energy = 7.894367190329E+00 kJ/mol 383s 383s print APOL energy 9 (solvated-neopentane) end 383s Global net APOL energy = 1.449633815052E+01 kJ/mol 383s 383s print APOL energy 10 (solvated-pentane) end 383s Global net APOL energy = 1.447900211546E+01 kJ/mol 383s 383s print APOL energy 11 (solvated-propane) end 383s Global net APOL energy = 1.192358496286E+01 kJ/mol 383s ---------------------------------------- 383s CLEANING UP AND SHUTTING DOWN... 383s Destroying force arrays. 383s No energy arrays to destroy. 383s Destroying multigrid structures. 383s Destroying finite element structures. 383s Destroying 11 molecules 383s Final memory usage: 0.001 MB total, 2.267 MB high water 383s 383s 383s Thanks for using APBS! 383s 394s Checking for intermediate energies in input file alkanes.out 394s EXPECTED COMPUTED: 11 394s EXPECTED EXPECTED: 11 394s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 394s 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'] 394s COMPUTED RESULT 14.39739455792 394s COMPUTED RESULT 12.08346456826 394s COMPUTED RESULT 13.54016672221 394s COMPUTED RESULT 9.363673200142 394s COMPUTED RESULT 9.422717598546 394s COMPUTED RESULT 16.40068943201 394s COMPUTED RESULT 13.23144287435 394s COMPUTED RESULT 7.894367190329 394s COMPUTED RESULT 14.49633815052 394s COMPUTED RESULT 14.47900211546 394s COMPUTED RESULT 11.92358496286 394s Running tests for FKBP section 394s BINARY: /usr/bin/apbs 394s INPUT: 1d7h-dmso-mol.in 394s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 394s 394s ---------------------------------------------------------------------- 394s APBS -- Adaptive Poisson-Boltzmann Solver 394s Version APBS 3.4.1 394s 394s Nathan A. Baker (nathan.baker@pnnl.gov) 394s Pacific Northwest National Laboratory 394s 394s Additional contributing authors listed in the code documentation. 394s 394s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 394s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 394s Northwest Division for the U.S. Department of Energy. 394s 394s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 394s Portions Copyright (c) 2002-2020, Nathan A. Baker. 394s Portions Copyright (c) 1999-2002, The Regents of the University of California. 394s Portions Copyright (c) 1995, Michael Holst. 394s All rights reserved. 394s 394s Redistribution and use in source and binary forms, with or without 394s modification, are permitted provided that the following conditions are met: 394s 394s * Redistributions of source code must retain the above copyright notice, this 394s list of conditions and the following disclaimer. 394s 394s * Redistributions in binary form must reproduce the above copyright notice, 394s this list of conditions and the following disclaimer in the documentation 394s and/or other materials provided with the distribution. 394s 394s * Neither the name of the developer nor the names of its contributors may be 394s used to endorse or promote products derived from this software without 394s specific prior written permission. 394s 394s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 394s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 394s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 394s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 394s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 394s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 394s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 394s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 394s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 394s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 394s ---------------------------------------------------------------------- 394s APBS uses FETK (the Finite Element ToolKit) to solve the 394s Poisson-Boltzmann equation numerically. FETK is a portable collection 394s of finite element modeling class libraries developed by the Michael Holst 394s research group and written in an object-oriented form of C. FEtk is 394s designed to solve general coupled systems of nonlinear partial differential 394s equations using adaptive finite element methods, inexact Newton methods, 394s and algebraic multilevel methods. More information about FEtk may be found 394s at . 394s ---------------------------------------------------------------------- 394s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 394s Aqua is a modified form of the Holst group PMG library 394s which has been modified by Patrice Koehl 394s for improved efficiency and 394s memory usage when solving the Poisson-Boltzmann equation. 394s ---------------------------------------------------------------------- 394s Please cite your use of APBS as: 394s 394s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 394s nanosystems: application to microtubules and the ribosome. Proc. 394s Natl. Acad. Sci. USA 98, 10037-10041 2001. 394s 394s 394s This executable compiled on Jan 3 2025 at 11:01:42 394s 394s Parsing input file 1d7h-dmso-mol.in... 394s rank 0 size 1... 394s Parsed input file. 394s Got paths for 3 molecules 394s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 1673 atoms 394s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 394s Net charge 9.91e-01 e 394s Reading PQR-format atom data from dmso-min.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 10 atoms 394s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 394s Net charge 2.78e-17 e 394s Reading PQR-format atom data from 1d7h-min.pqr. 394s 1663 atoms 394s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 394s Net charge 9.91e-01 e 394s Preparing to run 12 PBE calculations. 394s ---------------------------------------- 394s CALCULATION #1 (complex-solv-coarse): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 30.4176 A 394s Current memory usage: 122.059 MB total, 122.059 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 1.500 x 1.500 x 1.500 394s Grid lengths: 96.000 x 96.000 x 96.000 394s Grid center: (25.875, 18.349, 19.112) 394s Multigrid levels: 5 394s Molecule ID: 1 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 78.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 1.060899690259E+04 kJ/mol 394s Calculating forces... 394s [focusFillBound()]: WARNING: 394s Unusually large potential values 394s detected on the focusing boundary! 394s Convergence not guaranteed for NPBE/NRPBE calculations! 394s 394s ---------------------------------------- 394s CALCULATION #2 (complex-solv-fine): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 30.4176 A 394s Current memory usage: 122.059 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.225 x 0.225 x 0.225 394s Grid lengths: 14.400 x 14.400 x 14.400 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 1 394s Linearized traditional PBE 394s Boundary conditions from focusing 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 78.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 4.276523673491E+04 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #3 (complex-ref-coarse): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 4.87072 A 394s Current memory usage: 122.059 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 1.500 x 1.500 x 1.500 394s Grid lengths: 96.000 x 96.000 x 96.000 394s Grid center: (25.875, 18.349, 19.112) 394s Multigrid levels: 5 394s Molecule ID: 1 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 2.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 1.399234956777E+04 kJ/mol 394s Calculating forces... 394s [focusFillBound()]: WARNING: 394s Unusually large potential values 394s detected on the focusing boundary! 394s Convergence not guaranteed for NPBE/NRPBE calculations! 394s 394s ---------------------------------------- 394s CALCULATION #4 (complex-ref-fine): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 4.87072 A 394s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 394s *** PASSED *** 394s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 394s *** PASSED *** 394s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 394s *** PASSED *** 394s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 394s *** PASSED *** 394s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 394s *** PASSED *** 394s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 394s *** PASSED *** 394s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 394s *** PASSED *** 394s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 394s *** PASSED *** 394s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 394s *** PASSED *** 394s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 394s *** PASSED *** 394s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 394s *** PASSED *** 394s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 394s *** PASSED *** 394s Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) 394s *** PASSED *** 394s Elapsed time: 10.866486 seconds 394s -------------------------------------------------------------------------------- 394s -------------------------------------------------------------------------------- 394s Testing input file 1d7h-dmso-smol.in 394s 394s Current memory usage: 122.059 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.225 x 0.225 x 0.225 394s Grid lengths: 14.400 x 14.400 x 14.400 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 1 394s Linearized traditional PBE 394s Boundary conditions from focusing 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 2.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 4.610066575192E+04 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 30.4176 A 394s Current memory usage: 62.428 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 1.500 x 1.500 x 1.500 394s Grid lengths: 96.000 x 96.000 x 96.000 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 2 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 78.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 3.961107503213E+01 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #6 (dmso-solv-fine): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 30.4176 A 394s Current memory usage: 62.428 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.225 x 0.225 x 0.225 394s Grid lengths: 14.400 x 14.400 x 14.400 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 2 394s Linearized traditional PBE 394s Boundary conditions from focusing 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 78.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 7.121048606059E+02 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 4.87072 A 394s Current memory usage: 62.428 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 1.500 x 1.500 x 1.500 394s Grid lengths: 96.000 x 96.000 x 96.000 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 2 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 2.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 6.751571424823E+01 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #8 (dmso-ref-fine): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 4.87072 A 394s Current memory usage: 62.428 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.225 x 0.225 x 0.225 394s Grid lengths: 14.400 x 14.400 x 14.400 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 2 394s Linearized traditional PBE 394s Boundary conditions from focusing 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 2.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 7.339101343121E+02 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 30.4176 A 394s Current memory usage: 121.736 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 1.500 x 1.500 x 1.500 394s Grid lengths: 96.000 x 96.000 x 96.000 394s Grid center: (25.875, 18.349, 19.112) 394s Multigrid levels: 5 394s Molecule ID: 3 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 78.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 1.058410584089E+04 kJ/mol 394s Calculating forces... 394s [focusFillBound()]: WARNING: 394s Unusually large potential values 394s detected on the focusing boundary! 394s Convergence not guaranteed for NPBE/NRPBE calculations! 394s 394s ---------------------------------------- 394s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 30.4176 A 394s Current memory usage: 121.736 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.225 x 0.225 x 0.225 394s Grid lengths: 14.400 x 14.400 x 14.400 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 3 394s Linearized traditional PBE 394s Boundary conditions from focusing 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 78.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 4.205385249581E+04 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 4.87072 A 394s Current memory usage: 121.736 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 1.500 x 1.500 x 1.500 394s Grid lengths: 96.000 x 96.000 x 96.000 394s Grid center: (25.875, 18.349, 19.112) 394s Multigrid levels: 5 394s Molecule ID: 3 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 2.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 1.395961902233E+04 kJ/mol 394s Calculating forces... 394s [focusFillBound()]: WARNING: 394s Unusually large potential values 394s detected on the focusing boundary! 394s Convergence not guaranteed for NPBE/NRPBE calculations! 394s 394s ---------------------------------------- 394s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 394s Debye length: 4.87072 A 394s Current memory usage: 121.736 MB total, 221.696 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.225 x 0.225 x 0.225 394s Grid lengths: 14.400 x 14.400 x 14.400 394s Grid center: (17.751, 17.770, 20.492) 394s Multigrid levels: 5 394s Molecule ID: 3 394s Linearized traditional PBE 394s Boundary conditions from focusing 394s 2 ion species (0.010 M ionic strength): 394s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 394s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 394s Solute dielectric: 2.000 394s Solvent dielectric: 2.000 394s Using "molecular" surface definition; no smoothing 394s Solvent probe radius: 0.000 A 394s Temperature: 300.000 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 4.538248433997E+04 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s PRINT STATEMENTS 394s 394s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 394s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 394s Global net ELEC energy = -3.335429017008E+03 kJ/mol 394s 394s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 394s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 394s Global net ELEC energy = -2.180527370616E+01 kJ/mol 394s 394s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 394s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 394s Global net ELEC energy = -3.328631844166E+03 kJ/mol 394s 394s 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 394s Local net energy (PE 0) = 1.500810086373E+01 kJ/mol 394s Global net ELEC energy = 1.500810086373E+01 kJ/mol 394s ---------------------------------------- 394s CLEANING UP AND SHUTTING DOWN... 394s Destroying force arrays. 394s No energy arrays to destroy. 394s Destroying multigrid structures. 394s Destroying finite element structures. 394s Destroying 3 molecules 394s Final memory usage: 0.001 MB total, 221.696 MB high water 394s 394s 394s Thanks for using APBS! 394s 404s Checking for intermediate energies in input file 1d7h-dmso-mol.out 404s EXPECTED COMPUTED: 16 404s EXPECTED EXPECTED: 16 404s 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] 404s 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'] 404s COMPUTED RESULT 10608.99690259 404s COMPUTED RESULT 42765.23673491 404s COMPUTED RESULT 13992.34956777 404s COMPUTED RESULT 46100.66575192 404s COMPUTED RESULT 39.61107503213 404s COMPUTED RESULT 712.1048606059 404s COMPUTED RESULT 67.51571424823 404s COMPUTED RESULT 733.9101343121 404s COMPUTED RESULT 10584.10584089 404s COMPUTED RESULT 42053.85249581 404s COMPUTED RESULT 13959.61902233 404s COMPUTED RESULT 45382.48433997 404s COMPUTED RESULT -3335.429017008 404s COMPUTED RESULT -21.80527370616 404s COMPUTED RESULT -3328.631844166 404s COMPUTED RESULT 15.00810086373 404s BINARY: /usr/bin/apbs 404s INPUT: 1d7h-dmso-smol.in 404s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 404s asc_getToken: Error occurred (bailing out). 404s Vio_scanf: Format problem with input. 404s 404s 404s ---------------------------------------------------------------------- 404s APBS -- Adaptive Poisson-Boltzmann Solver 404s Version APBS 3.4.1 404s 404s Nathan A. Baker (nathan.baker@pnnl.gov) 404s Pacific Northwest National Laboratory 404s 404s Additional contributing authors listed in the code documentation. 404s 404s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 404s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 404s Northwest Division for the U.S. Department of Energy. 404s 404s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 404s Portions Copyright (c) 2002-2020, Nathan A. Baker. 404s Portions Copyright (c) 1999-2002, The Regents of the University of California. 404s Portions Copyright (c) 1995, Michael Holst. 404s All rights reserved. 404s 404s Redistribution and use in source and binary forms, with or without 404s modification, are permitted provided that the following conditions are met: 404s 404s * Redistributions of source code must retain the above copyright notice, this 404s list of conditions and the following disclaimer. 404s 404s * Redistributions in binary form must reproduce the above copyright notice, 404s this list of conditions and the following disclaimer in the documentation 404s and/or other materials provided with the distribution. 404s 404s * Neither the name of the developer nor the names of its contributors may be 404s used to endorse or promote products derived from this software without 404s specific prior written permission. 404s 404s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 404s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 404s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 404s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 404s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 404s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 404s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 404s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 404s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 404s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 404s ---------------------------------------------------------------------- 404s APBS uses FETK (the Finite Element ToolKit) to solve the 404s Poisson-Boltzmann equation numerically. FETK is a portable collection 404s of finite element modeling class libraries developed by the Michael Holst 404s research group and written in an object-oriented form of C. FEtk is 404s designed to solve general coupled systems of nonlinear partial differential 404s equations using adaptive finite element methods, inexact Newton methods, 404s and algebraic multilevel methods. More information about FEtk may be found 404s at . 404s ---------------------------------------------------------------------- 404s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 404s Aqua is a modified form of the Holst group PMG library 404s which has been modified by Patrice Koehl 404s for improved efficiency and 404s memory usage when solving the Poisson-Boltzmann equation. 404s ---------------------------------------------------------------------- 404s Please cite your use of APBS as: 404s 404s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 404s nanosystems: application to microtubules and the ribosome. Proc. 404s Natl. Acad. Sci. USA 98, 10037-10041 2001. 404s 404s 404s This executable compiled on Jan 3 2025 at 11:01:42 404s 404s Parsing input file 1d7h-dmso-smol.in... 404s rank 0 size 1... 404s Parsed input file. 404s Got paths for 3 molecules 404s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 404s asc_getToken: Error occurred (bailing out). 404s Vio_scanf: Format problem with input. 404s 1673 atoms 404s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 404s Net charge 9.91e-01 e 404s Reading PQR-format atom data from dmso-min.pqr. 404s asc_getToken: Error occurred (bailing out). 404s Vio_scanf: Format problem with input. 404s 10 atoms 404s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 404s Net charge 2.78e-17 e 404s Reading PQR-format atom data from 1d7h-min.pqr. 404s 1663 atoms 404s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 404s Net charge 9.91e-01 e 404s Preparing to run 12 PBE calculations. 404s ---------------------------------------- 404s CALCULATION #1 (complex-solv-coarse): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 30.4176 A 404s Current memory usage: 122.059 MB total, 122.059 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 1.500 x 1.500 x 1.500 404s Grid lengths: 96.000 x 96.000 x 96.000 404s Grid center: (25.875, 18.349, 19.112) 404s Multigrid levels: 5 404s Molecule ID: 1 404s Linearized traditional PBE 404s Multiple Debye-Huckel sphere boundary conditions 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 78.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 1.074948704824E+04 kJ/mol 404s Calculating forces... 404s [focusFillBound()]: WARNING: 404s Unusually large potential values 404s detected on the focusing boundary! 404s Convergence not guaranteed for NPBE/NRPBE calculations! 404s 404s ---------------------------------------- 404s CALCULATION #2 (complex-solv-fine): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 30.4176 A 404s Current memory usage: 122.059 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 0.225 x 0.225 x 0.225 404s Grid lengths: 14.400 x 14.400 x 14.400 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 1 404s Linearized traditional PBE 404s Boundary conditions from focusing 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 78.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 4.289487256481E+04 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s CALCULATION #3 (complex-ref-coarse): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 4.87072 A 404s Current memory usage: 122.059 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 1.500 x 1.500 x 1.500 404s Grid lengths: 96.000 x 96.000 x 96.000 404s Grid center: (25.875, 18.349, 19.112) 404s Multigrid levels: 5 404s Molecule ID: 1 404s Linearized traditional PBE 404s Multiple Debye-Huckel sphere boundary conditions 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 2.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 1.399234956777E+04 kJ/mol 404s Calculating forces... 404s [focusFillBound()]: WARNING: 404s Unusually large potential values 404s detected on the focusing boundary! 404s Convergence not guaranteed for NPBE/NRPBE calculations! 404s 404s ---------------------------------------- 404s CALCULATION #4 (complex-ref-fine): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 4.87072 A 404s Current memory usage: 122.059 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 0.225 x 0.225 x 0.225 404s Grid lengths: 14.400 x 14.400 x 14.400 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 1 404s Linearized traditional PBE 404s Boundary conditions from focusing 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 2.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 4.610066575192E+04 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 30.4176 A 404s Current memory usage: 62.428 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 1.500 x 1.500 x 1.500 404s Grid lengths: 96.000 x 96.000 x 96.000 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 2 404s Linearized traditional PBE 404s Multiple Debye-Huckel sphere boundary conditions 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 78.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 3.719709905887E+01 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s CALCULATION #6 (dmso-solv-fine): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 30.4176 A 404s Current memory usage: 62.428 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 0.225 x 0.225 x 0.225 404s Grid lengths: 14.400 x 14.400 x 14.400 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 2 404s Linearized traditional PBE 404s Boundary conditions from focusing 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 78.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 7.125747080979E+02 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 4.87072 A 404s Current memory usage: 62.428 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 1.500 x 1.500 x 1.500 404s Grid lengths: 96.000 x 96.000 x 96.000 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 2 404s Linearized traditional PBE 404s Multiple Debye-Huckel sphere boundary conditions 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 2.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 6.751571424823E+01 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s CALCULATION #8 (dmso-ref-fine): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 4.87072 A 404s Current memory usage: 62.428 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 0.225 x 0.225 x 0.225 404s Grid lengths: 14.400 x 14.400 x 14.400 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 2 404s Linearized traditional PBE 404s Boundary conditions from focusing 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 2.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 7.339101343121E+02 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 30.4176 A 404s Current memory usage: 121.736 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 1.500 x 1.500 x 1.500 404s Grid lengths: 96.000 x 96.000 x 96.000 404s Grid center: (25.875, 18.349, 19.112) 404s Multigrid levels: 5 404s Molecule ID: 3 404s Linearized traditional PBE 404s Multiple Debye-Huckel sphere boundary conditions 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 78.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 1.071654753674E+04 kJ/mol 404s Calculating forces... 404s [focusFillBound()]: WARNING: 404s Unusually large potential values 404s detected on the focusing boundary! 404s Convergence not guaranteed for NPBE/NRPBE calculations! 404s 404s ---------------------------------------- 404s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 30.4176 A 404s Current memory usage: 121.736 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 0.225 x 0.225 x 0.225 404s Grid lengths: 14.400 x 14.400 x 14.400 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 3 404s Linearized traditional PBE 404s Boundary conditions from focusing 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 78.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 4.218178203716E+04 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 4.87072 A 404s Current memory usage: 121.736 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 1.500 x 1.500 x 1.500 404s Grid lengths: 96.000 x 96.000 x 96.000 404s Grid center: (25.875, 18.349, 19.112) 404s Multigrid levels: 5 404s Molecule ID: 3 404s Linearized traditional PBE 404s Multiple Debye-Huckel sphere boundary conditions 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 2.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 1.395961902233E+04 kJ/mol 404s Calculating forces... 404s [focusFillBound()]: WARNING: 404s Unusually large potential values 404s detected on the focusing boundary! 404s Convergence not guaranteed for NPBE/NRPBE calculations! 404s 404s ---------------------------------------- 404s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 404s Setting up problem... 404s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 404s Debye length: 4.87072 A 404s Current memory usage: 121.736 MB total, 221.696 MB high water 404s Using linear spline charge discretization. 404s Grid dimensions: 65 x 65 x 65 404s Grid spacings: 0.225 x 0.225 x 0.225 404s Grid lengths: 14.400 x 14.400 x 14.400 404s Grid center: (17.751, 17.770, 20.492) 404s Multigrid levels: 5 404s Molecule ID: 3 404s Linearized traditional PBE 404s Boundary conditions from focusing 404s 2 ion species (0.010 M ionic strength): 404s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 404s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 404s Solute dielectric: 2.000 404s Solvent dielectric: 2.000 404s Using "molecular" surface definition;harmonic average smoothing 404s Solvent probe radius: 0.000 A 404s Temperature: 300.000 K 404s Electrostatic energies will be calculated 404s Total electrostatic energy = 4.538248433997E+04 kJ/mol 404s Calculating forces... 404s ---------------------------------------- 404s PRINT STATEMENTS 404s 404s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 404s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 404s Global net ELEC energy = -3.205793187109E+03 kJ/mol 404s 404s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 404s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 404s Global net ELEC energy = -2.133542621421E+01 kJ/mol 404s 404s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 404s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 404s Global net ELEC energy = -3.200702302816E+03 kJ/mol 404s 404s 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 404s Local net energy (PE 0) = 1.624454192074E+01 kJ/mol 404s Global net ELEC energy = 1.624454192074E+01 kJ/mol 404s ---------------------------------------- 404s CLEANING UP AND SHUTTING DOWN... 404s Destroying force arrays. 404s No energy arrays to destroy. 404s Destroying multigrid structures. 404s Destroying finite element structures. 404s Destroying 3 molecules 404s Final memory usage: 0.001 MB total, 221.696 MB high water 404s 404s 404s Thanks for using APBS! 404s 404s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 404s *** PASSED *** 404s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 404s *** PASSED *** 404s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 404s *** PASSED *** 404s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 404s *** PASSED *** 404s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 404s *** PASSED *** 404s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 404s *** PASSED *** 404s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 404s *** PASSED *** 404s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 404s *** PASSED *** 404s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 404s *** PASSED *** 404s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 404s *** PASSED *** 404s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 404s *** PASSED *** 404s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 404s *** PASSED *** 404s Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) 404s *** PASSED *** 404s Elapsed time: 9.520768 seconds 404s -------------------------------------------------------------------------------- 404s -------------------------------------------------------------------------------- 404s Testing input file 1d7i-dss-mol.in 404s 415s Checking for intermediate energies in input file 1d7h-dmso-smol.out 415s EXPECTED COMPUTED: 16 415s EXPECTED EXPECTED: 16 415s 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] 415s 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'] 415s COMPUTED RESULT 10749.48704824 415s COMPUTED RESULT 42894.87256481 415s COMPUTED RESULT 13992.34956777 415s COMPUTED RESULT 46100.66575192 415s COMPUTED RESULT 37.19709905887 415s COMPUTED RESULT 712.5747080979 415s COMPUTED RESULT 67.51571424823 415s COMPUTED RESULT 733.9101343121 415s COMPUTED RESULT 10716.54753674 415s COMPUTED RESULT 42181.78203716 415s COMPUTED RESULT 13959.61902233 415s COMPUTED RESULT 45382.48433997 415s COMPUTED RESULT -3205.793187109 415s COMPUTED RESULT -21.33542621421 415s COMPUTED RESULT -3200.702302816 415s COMPUTED RESULT 16.24454192074 415s BINARY: /usr/bin/apbs 415s INPUT: 1d7i-dss-mol.in 415s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 415s asc_getToken: Error occurred (bailing out). 415s Vio_scanf: Format problem with input. 415s 415s 415s ---------------------------------------------------------------------- 415s APBS -- Adaptive Poisson-Boltzmann Solver 415s Version APBS 3.4.1 415s 415s Nathan A. Baker (nathan.baker@pnnl.gov) 415s Pacific Northwest National Laboratory 415s 415s Additional contributing authors listed in the code documentation. 415s 415s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 415s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 415s Northwest Division for the U.S. Department of Energy. 415s 415s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 415s Portions Copyright (c) 2002-2020, Nathan A. Baker. 415s Portions Copyright (c) 1999-2002, The Regents of the University of California. 415s Portions Copyright (c) 1995, Michael Holst. 415s All rights reserved. 415s 415s Redistribution and use in source and binary forms, with or without 415s modification, are permitted provided that the following conditions are met: 415s 415s * Redistributions of source code must retain the above copyright notice, this 415s list of conditions and the following disclaimer. 415s 415s * Redistributions in binary form must reproduce the above copyright notice, 415s this list of conditions and the following disclaimer in the documentation 415s and/or other materials provided with the distribution. 415s 415s * Neither the name of the developer nor the names of its contributors may be 415s used to endorse or promote products derived from this software without 415s specific prior written permission. 415s 415s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 415s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 415s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 415s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 415s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 415s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 415s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 415s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 415s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 415s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 415s ---------------------------------------------------------------------- 415s APBS uses FETK (the Finite Element ToolKit) to solve the 415s Poisson-Boltzmann equation numerically. FETK is a portable collection 415s of finite element modeling class libraries developed by the Michael Holst 415s research group and written in an object-oriented form of C. FEtk is 415s designed to solve general coupled systems of nonlinear partial differential 415s equations using adaptive finite element methods, inexact Newton methods, 415s and algebraic multilevel methods. More information about FEtk may be found 415s at . 415s ---------------------------------------------------------------------- 415s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 415s Aqua is a modified form of the Holst group PMG library 415s which has been modified by Patrice Koehl 415s for improved efficiency and 415s memory usage when solving the Poisson-Boltzmann equation. 415s ---------------------------------------------------------------------- 415s Please cite your use of APBS as: 415s 415s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 415s nanosystems: application to microtubules and the ribosome. Proc. 415s Natl. Acad. Sci. USA 98, 10037-10041 2001. 415s 415s 415s This executable compiled on Jan 3 2025 at 11:01:42 415s 415s Parsing input file 1d7i-dss-mol.in... 415s rank 0 size 1... 415s Parsed input file. 415s Got paths for 3 molecules 415s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 415s asc_getToken: Error occurred (bailing out). 415s Vio_scanf: Format problem with input. 415s 1677 atoms 415s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 415s Net charge 9.91e-01 e 415s Reading PQR-format atom data from dss-min.pqr. 415s asc_getToken: Error occurred (bailing out). 415s Vio_scanf: Format problem with input. 415s 14 atoms 415s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 415s Net charge -8.33e-17 e 415s Reading PQR-format atom data from 1d7i-min.pqr. 415s 1663 atoms 415s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 415s Net charge 9.91e-01 e 415s Preparing to run 12 PBE calculations. 415s ---------------------------------------- 415s CALCULATION #1 (complex-solv-coarse): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 30.4176 A 415s Current memory usage: 122.425 MB total, 122.425 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 1.500 x 1.500 x 1.500 415s Grid lengths: 96.000 x 96.000 x 96.000 415s Grid center: (25.264, 18.988, 19.122) 415s Multigrid levels: 5 415s Molecule ID: 1 415s Linearized traditional PBE 415s Multiple Debye-Huckel sphere boundary conditions 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 78.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 9.160578033846E+03 kJ/mol 415s Calculating forces... 415s [focusFillBound()]: WARNING: 415s Unusually large potential values 415s detected on the focusing boundary! 415s Convergence not guaranteed for NPBE/NRPBE calculations! 415s 415s ---------------------------------------- 415s CALCULATION #2 (complex-solv-fine): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 30.4176 A 415s Current memory usage: 122.425 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 0.225 x 0.225 x 0.225 415s Grid lengths: 14.400 x 14.400 x 14.400 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 1 415s Linearized traditional PBE 415s Boundary conditions from focusing 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 78.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 3.955701871716E+04 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s CALCULATION #3 (complex-ref-coarse): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 4.87072 A 415s Current memory usage: 122.425 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 1.500 x 1.500 x 1.500 415s Grid lengths: 96.000 x 96.000 x 96.000 415s Grid center: (25.264, 18.988, 19.122) 415s Multigrid levels: 5 415s Molecule ID: 1 415s Linearized traditional PBE 415s Multiple Debye-Huckel sphere boundary conditions 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 2.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 1.264965939588E+04 kJ/mol 415s Calculating forces... 415s [focusFillBound()]: WARNING: 415s Unusually large potential values 415s detected on the focusing boundary! 415s Convergence not guaranteed for NPBE/NRPBE calculations! 415s 415s ---------------------------------------- 415s CALCULATION #4 (complex-ref-fine): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 4.87072 A 415s Current memory usage: 122.425 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 0.225 x 0.225 x 0.225 415s Grid lengths: 14.400 x 14.400 x 14.400 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 1 415s Linearized traditional PBE 415s Boundary conditions from focusing 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 2.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 4.301801664829E+04 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s CALCULATION #5 (dss-solv-coarse): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 30.4176 A 415s Current memory usage: 62.528 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 1.500 x 1.500 x 1.500 415s Grid lengths: 96.000 x 96.000 x 96.000 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 2 415s Linearized traditional PBE 415s Multiple Debye-Huckel sphere boundary conditions 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 78.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 9.431133325426E+01 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s CALCULATION #6 (dss-solv-fine): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 30.4176 A 415s Current memory usage: 62.528 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 0.225 x 0.225 x 0.225 415s Grid lengths: 14.400 x 14.400 x 14.400 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 2 415s Linearized traditional PBE 415s Boundary conditions from focusing 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 78.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 1.677348113184E+03 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s CALCULATION #7 (dss-ref-coarse): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 4.87072 A 415s Current memory usage: 62.528 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 1.500 x 1.500 x 1.500 415s Grid lengths: 96.000 x 96.000 x 96.000 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 2 415s Linearized traditional PBE 415s Multiple Debye-Huckel sphere boundary conditions 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 2.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 1.171079106781E+02 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s CALCULATION #8 (dss-ref-fine): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 4.87072 A 415s Current memory usage: 62.528 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 0.225 x 0.225 x 0.225 415s Grid lengths: 14.400 x 14.400 x 14.400 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 2 415s Linearized traditional PBE 415s Boundary conditions from focusing 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 2.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 1.697869784185E+03 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 30.4176 A 415s Current memory usage: 121.977 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 1.500 x 1.500 x 1.500 415s Grid lengths: 96.000 x 96.000 x 96.000 415s Grid center: (25.264, 18.988, 19.122) 415s Multigrid levels: 5 415s Molecule ID: 3 415s Linearized traditional PBE 415s Multiple Debye-Huckel sphere boundary conditions 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 78.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 9.040108332204E+03 kJ/mol 415s Calculating forces... 415s [focusFillBound()]: WARNING: 415s Unusually large potential values 415s detected on the focusing boundary! 415s Convergence not guaranteed for NPBE/NRPBE calculations! 415s 415s ---------------------------------------- 415s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 30.4176 A 415s Current memory usage: 121.977 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 0.225 x 0.225 x 0.225 415s Grid lengths: 14.400 x 14.400 x 14.400 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 3 415s Linearized traditional PBE 415s Boundary conditions from focusing 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 78.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 3.787747796627E+04 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 4.87072 A 415s Current memory usage: 121.977 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 1.500 x 1.500 x 1.500 415s Grid lengths: 96.000 x 96.000 x 96.000 415s Grid center: (25.264, 18.988, 19.122) 415s Multigrid levels: 5 415s Molecule ID: 3 415s Linearized traditional PBE 415s Multiple Debye-Huckel sphere boundary conditions 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 2.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 1.252495566243E+04 kJ/mol 415s Calculating forces... 415s [focusFillBound()]: WARNING: 415s Unusually large potential values 415s detected on the focusing boundary! 415s Convergence not guaranteed for NPBE/NRPBE calculations! 415s 415s ---------------------------------------- 415s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 415s Setting up problem... 415s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 415s Debye length: 4.87072 A 415s Current memory usage: 121.977 MB total, 222.305 MB high water 415s Using linear spline charge discretization. 415s Grid dimensions: 65 x 65 x 65 415s Grid spacings: 0.225 x 0.225 x 0.225 415s Grid lengths: 14.400 x 14.400 x 14.400 415s Grid center: (17.340, 19.211, 20.503) 415s Multigrid levels: 5 415s Molecule ID: 3 415s Linearized traditional PBE 415s Boundary conditions from focusing 415s 2 ion species (0.010 M ionic strength): 415s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 415s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 415s Solute dielectric: 2.000 415s Solvent dielectric: 2.000 415s Using "molecular" surface definition; no smoothing 415s Solvent probe radius: 0.000 A 415s Temperature: 300.000 K 415s Electrostatic energies will be calculated 415s Total electrostatic energy = 4.133237922574E+04 kJ/mol 415s Calculating forces... 415s ---------------------------------------- 415s PRINT STATEMENTS 415s 415s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 415s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 415s Global net ELEC energy = -3.460997931137E+03 kJ/mol 415s 415s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 415s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 415s Global net ELEC energy = -2.052167100108E+01 kJ/mol 415s 415s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 415s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 415s Global net ELEC energy = -3.454901259473E+03 kJ/mol 415s 415s 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 415s Local net energy (PE 0) = 1.442499933664E+01 kJ/mol 415s Global net ELEC energy = 1.442499933664E+01 kJ/mol 415s ---------------------------------------- 415s CLEANING UP AND SHUTTING DOWN... 415s Destroying force arrays. 415s No energy arrays to destroy. 415s Destroying multigrid structures. 415s Destroying finite element structures. 415s Destroying 3 molecules 415s Final memory usage: 0.001 MB total, 222.305 MB high water 415s 415s 415s Thanks for using APBS! 415s 415s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 415s *** PASSED *** 415s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 415s *** PASSED *** 415s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 415s *** PASSED *** 415s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 415s *** PASSED *** 415s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 415s *** PASSED *** 415s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 415s *** PASSED *** 415s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 415s *** PASSED *** 415s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 415s *** PASSED *** 415s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 415s *** PASSED *** 415s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 415s *** PASSED *** 415s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 415s *** PASSED *** 415s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 415s *** PASSED *** 415s Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) 415s *** PASSED *** 415s Elapsed time: 10.96035 seconds 415s -------------------------------------------------------------------------------- 415s -------------------------------------------------------------------------------- 415s Testing input file 1d7i-dss-smol.in 415s 425s Checking for intermediate energies in input file 1d7i-dss-mol.out 425s EXPECTED COMPUTED: 16 425s EXPECTED EXPECTED: 16 425s 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] 425s 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'] 425s COMPUTED RESULT 9160.578033846 425s COMPUTED RESULT 39557.01871716 425s COMPUTED RESULT 12649.65939588 425s COMPUTED RESULT 43018.01664829 425s COMPUTED RESULT 94.31133325426 425s COMPUTED RESULT 1677.348113184 425s COMPUTED RESULT 117.1079106781 425s COMPUTED RESULT 1697.869784185 425s COMPUTED RESULT 9040.108332204 425s COMPUTED RESULT 37877.47796627 425s COMPUTED RESULT 12524.95566243 425s COMPUTED RESULT 41332.37922574 425s COMPUTED RESULT -3460.997931137 425s COMPUTED RESULT -20.52167100108 425s COMPUTED RESULT -3454.901259473 425s COMPUTED RESULT 14.42499933664 425s BINARY: /usr/bin/apbs 425s INPUT: 1d7i-dss-smol.in 425s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 425s asc_getToken: Error occurred (bailing out). 425s Vio_scanf: Format problem with input. 425s 425s 425s ---------------------------------------------------------------------- 425s APBS -- Adaptive Poisson-Boltzmann Solver 425s Version APBS 3.4.1 425s 425s Nathan A. Baker (nathan.baker@pnnl.gov) 425s Pacific Northwest National Laboratory 425s 425s Additional contributing authors listed in the code documentation. 425s 425s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 425s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 425s Northwest Division for the U.S. Department of Energy. 425s 425s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 425s Portions Copyright (c) 2002-2020, Nathan A. Baker. 425s Portions Copyright (c) 1999-2002, The Regents of the University of California. 425s Portions Copyright (c) 1995, Michael Holst. 425s All rights reserved. 425s 425s Redistribution and use in source and binary forms, with or without 425s modification, are permitted provided that the following conditions are met: 425s 425s * Redistributions of source code must retain the above copyright notice, this 425s list of conditions and the following disclaimer. 425s 425s * Redistributions in binary form must reproduce the above copyright notice, 425s this list of conditions and the following disclaimer in the documentation 425s and/or other materials provided with the distribution. 425s 425s * Neither the name of the developer nor the names of its contributors may be 425s used to endorse or promote products derived from this software without 425s specific prior written permission. 425s 425s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 425s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 425s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 425s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 425s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 425s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 425s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 425s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 425s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 425s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 425s ---------------------------------------------------------------------- 425s APBS uses FETK (the Finite Element ToolKit) to solve the 425s Poisson-Boltzmann equation numerically. FETK is a portable collection 425s of finite element modeling class libraries developed by the Michael Holst 425s research group and written in an object-oriented form of C. FEtk is 425s designed to solve general coupled systems of nonlinear partial differential 425s equations using adaptive finite element methods, inexact Newton methods, 425s and algebraic multilevel methods. More information about FEtk may be found 425s at . 425s ---------------------------------------------------------------------- 425s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 425s Aqua is a modified form of the Holst group PMG library 425s which has been modified by Patrice Koehl 425s for improved efficiency and 425s memory usage when solving the Poisson-Boltzmann equation. 425s ---------------------------------------------------------------------- 425s Please cite your use of APBS as: 425s 425s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 425s nanosystems: application to microtubules and the ribosome. Proc. 425s Natl. Acad. Sci. USA 98, 10037-10041 2001. 425s 425s 425s This executable compiled on Jan 3 2025 at 11:01:42 425s 425s Parsing input file 1d7i-dss-smol.in... 425s rank 0 size 1... 425s Parsed input file. 425s Got paths for 3 molecules 425s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 425s asc_getToken: Error occurred (bailing out). 425s Vio_scanf: Format problem with input. 425s 1677 atoms 425s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 425s Net charge 9.91e-01 e 425s Reading PQR-format atom data from dss-min.pqr. 425s asc_getToken: Error occurred (bailing out). 425s Vio_scanf: Format problem with input. 425s 14 atoms 425s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 425s Net charge -8.33e-17 e 425s Reading PQR-format atom data from 1d7i-min.pqr. 425s 1663 atoms 425s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 425s Net charge 9.91e-01 e 425s Preparing to run 12 PBE calculations. 425s ---------------------------------------- 425s CALCULATION #1 (complex-solv-coarse): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 30.4176 A 425s Current memory usage: 122.425 MB total, 122.425 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 1.500 x 1.500 x 1.500 425s Grid lengths: 96.000 x 96.000 x 96.000 425s Grid center: (25.264, 18.988, 19.122) 425s Multigrid levels: 5 425s Molecule ID: 1 425s Linearized traditional PBE 425s Multiple Debye-Huckel sphere boundary conditions 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 78.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 9.634884642408E+03 kJ/mol 425s Calculating forces... 425s [focusFillBound()]: WARNING: 425s Unusually large potential values 425s detected on the focusing boundary! 425s Convergence not guaranteed for NPBE/NRPBE calculations! 425s 425s ---------------------------------------- 425s CALCULATION #2 (complex-solv-fine): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 30.4176 A 425s Current memory usage: 122.425 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 0.225 x 0.225 x 0.225 425s Grid lengths: 14.400 x 14.400 x 14.400 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 1 425s Linearized traditional PBE 425s Boundary conditions from focusing 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 78.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 4.003177540425E+04 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s CALCULATION #3 (complex-ref-coarse): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 4.87072 A 425s Current memory usage: 122.425 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 1.500 x 1.500 x 1.500 425s Grid lengths: 96.000 x 96.000 x 96.000 425s Grid center: (25.264, 18.988, 19.122) 425s Multigrid levels: 5 425s Molecule ID: 1 425s Linearized traditional PBE 425s Multiple Debye-Huckel sphere boundary conditions 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 2.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 1.264965939588E+04 kJ/mol 425s Calculating forces... 425s [focusFillBound()]: WARNING: 425s Unusually large potential values 425s detected on the focusing boundary! 425s Convergence not guaranteed for NPBE/NRPBE calculations! 425s 425s ---------------------------------------- 425s CALCULATION #4 (complex-ref-fine): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 4.87072 A 425s Current memory usage: 122.425 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 0.225 x 0.225 x 0.225 425s Grid lengths: 14.400 x 14.400 x 14.400 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 1 425s Linearized traditional PBE 425s Boundary conditions from focusing 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 2.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 4.301801664829E+04 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s CALCULATION #5 (dss-solv-coarse): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 30.4176 A 425s Current memory usage: 62.528 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 1.500 x 1.500 x 1.500 425s Grid lengths: 96.000 x 96.000 x 96.000 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 2 425s Linearized traditional PBE 425s Multiple Debye-Huckel sphere boundary conditions 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 78.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 7.942232645345E+01 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s CALCULATION #6 (dss-solv-fine): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 30.4176 A 425s Current memory usage: 62.528 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 0.225 x 0.225 x 0.225 425s Grid lengths: 14.400 x 14.400 x 14.400 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 2 425s Linearized traditional PBE 425s Boundary conditions from focusing 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 78.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 1.677798535473E+03 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s CALCULATION #7 (dss-ref-coarse): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 4.87072 A 425s Current memory usage: 62.528 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 1.500 x 1.500 x 1.500 425s Grid lengths: 96.000 x 96.000 x 96.000 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 2 425s Linearized traditional PBE 425s Multiple Debye-Huckel sphere boundary conditions 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 2.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 1.171079106781E+02 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s CALCULATION #8 (dss-ref-fine): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 4.87072 A 425s Current memory usage: 62.528 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 0.225 x 0.225 x 0.225 425s Grid lengths: 14.400 x 14.400 x 14.400 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 2 425s Linearized traditional PBE 425s Boundary conditions from focusing 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 2.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 1.697869784185E+03 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 30.4176 A 425s Current memory usage: 121.977 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 1.500 x 1.500 x 1.500 425s Grid lengths: 96.000 x 96.000 x 96.000 425s Grid center: (25.264, 18.988, 19.122) 425s Multigrid levels: 5 425s Molecule ID: 3 425s Linearized traditional PBE 425s Multiple Debye-Huckel sphere boundary conditions 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 78.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 9.507068451372E+03 kJ/mol 425s Calculating forces... 425s [focusFillBound()]: WARNING: 425s Unusually large potential values 425s detected on the focusing boundary! 425s Convergence not guaranteed for NPBE/NRPBE calculations! 425s 425s ---------------------------------------- 425s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 30.4176 A 425s Current memory usage: 121.977 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 0.225 x 0.225 x 0.225 425s Grid lengths: 14.400 x 14.400 x 14.400 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 3 425s Linearized traditional PBE 425s Boundary conditions from focusing 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 78.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 3.835075772299E+04 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 4.87072 A 425s Current memory usage: 121.977 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 1.500 x 1.500 x 1.500 425s Grid lengths: 96.000 x 96.000 x 96.000 425s Grid center: (25.264, 18.988, 19.122) 425s Multigrid levels: 5 425s Molecule ID: 3 425s Linearized traditional PBE 425s Multiple Debye-Huckel sphere boundary conditions 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 2.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 1.252495566243E+04 kJ/mol 425s Calculating forces... 425s [focusFillBound()]: WARNING: 425s Unusually large potential values 425s detected on the focusing boundary! 425s Convergence not guaranteed for NPBE/NRPBE calculations! 425s 425s ---------------------------------------- 425s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 425s Setting up problem... 425s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 425s Debye length: 4.87072 A 425s Current memory usage: 121.977 MB total, 222.305 MB high water 425s Using linear spline charge discretization. 425s Grid dimensions: 65 x 65 x 65 425s Grid spacings: 0.225 x 0.225 x 0.225 425s Grid lengths: 14.400 x 14.400 x 14.400 425s Grid center: (17.340, 19.211, 20.503) 425s Multigrid levels: 5 425s Molecule ID: 3 425s Linearized traditional PBE 425s Boundary conditions from focusing 425s 2 ion species (0.010 M ionic strength): 425s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 425s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 425s Solute dielectric: 2.000 425s Solvent dielectric: 2.000 425s Using "molecular" surface definition;harmonic average smoothing 425s Solvent probe radius: 0.000 A 425s Temperature: 300.000 K 425s Electrostatic energies will be calculated 425s Total electrostatic energy = 4.133237922574E+04 kJ/mol 425s Calculating forces... 425s ---------------------------------------- 425s PRINT STATEMENTS 425s 425s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 425s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 425s Global net ELEC energy = -2.986241244040E+03 kJ/mol 425s 425s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 425s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 425s Global net ELEC energy = -2.007124871262E+01 kJ/mol 425s 425s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 425s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 425s Global net ELEC energy = -2.981621502756E+03 kJ/mol 425s 425s 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 425s Local net energy (PE 0) = 1.545150742843E+01 kJ/mol 425s Global net ELEC energy = 1.545150742843E+01 kJ/mol 425s ---------------------------------------- 425s CLEANING UP AND SHUTTING DOWN... 425s Destroying force arrays. 425s No energy arrays to destroy. 425s Destroying multigrid structures. 425s Destroying finite element structures. 425s Destroying 3 molecules 425s Final memory usage: 0.001 MB total, 222.305 MB high water 425s 425s 425s Thanks for using APBS! 425s 425s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 425s *** PASSED *** 425s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 425s *** PASSED *** 425s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 425s *** PASSED *** 425s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 425s *** PASSED *** 425s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 425s *** PASSED *** 425s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 425s *** PASSED *** 425s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 425s *** PASSED *** 425s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 425s *** PASSED *** 425s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 425s *** PASSED *** 425s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 425s *** PASSED *** 425s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 425s *** PASSED *** 425s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 425s *** PASSED *** 425s Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) 425s *** PASSED *** 425s Elapsed time: 9.733941 seconds 425s -------------------------------------------------------------------------------- 425s Total elapsed time: 41.081545 seconds 425s Test results have been logged 425s -------------------------------------------------------------------------------- 425s -------------------------------------------------------------------------------- 425s Testing input file apbs-mol.in 425s 434s Checking for intermediate energies in input file 1d7i-dss-smol.out 434s EXPECTED COMPUTED: 16 434s EXPECTED EXPECTED: 16 434s 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] 434s 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'] 434s COMPUTED RESULT 9634.884642408 434s COMPUTED RESULT 40031.77540425 434s COMPUTED RESULT 12649.65939588 434s COMPUTED RESULT 43018.01664829 434s COMPUTED RESULT 79.42232645345 434s COMPUTED RESULT 1677.798535473 434s COMPUTED RESULT 117.1079106781 434s COMPUTED RESULT 1697.869784185 434s COMPUTED RESULT 9507.068451372 434s COMPUTED RESULT 38350.75772299 434s COMPUTED RESULT 12524.95566243 434s COMPUTED RESULT 41332.37922574 434s COMPUTED RESULT -2986.24124404 434s COMPUTED RESULT -20.07124871262 434s COMPUTED RESULT -2981.621502756 434s COMPUTED RESULT 15.45150742843 434s Running tests for hca-bind section 434s BINARY: /usr/bin/apbs 434s INPUT: apbs-mol.in 434s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 434s asc_getToken: Error occurred (bailing out). 434s Vio_scanf: Format problem with input. 434s 434s 434s ---------------------------------------------------------------------- 434s APBS -- Adaptive Poisson-Boltzmann Solver 434s Version APBS 3.4.1 434s 434s Nathan A. Baker (nathan.baker@pnnl.gov) 434s Pacific Northwest National Laboratory 434s 434s Additional contributing authors listed in the code documentation. 434s 434s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 434s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 434s Northwest Division for the U.S. Department of Energy. 434s 434s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 434s Portions Copyright (c) 2002-2020, Nathan A. Baker. 434s Portions Copyright (c) 1999-2002, The Regents of the University of California. 434s Portions Copyright (c) 1995, Michael Holst. 434s All rights reserved. 434s 434s Redistribution and use in source and binary forms, with or without 434s modification, are permitted provided that the following conditions are met: 434s 434s * Redistributions of source code must retain the above copyright notice, this 434s list of conditions and the following disclaimer. 434s 434s * Redistributions in binary form must reproduce the above copyright notice, 434s this list of conditions and the following disclaimer in the documentation 434s and/or other materials provided with the distribution. 434s 434s * Neither the name of the developer nor the names of its contributors may be 434s used to endorse or promote products derived from this software without 434s specific prior written permission. 434s 434s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 434s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 434s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 434s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 434s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 434s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 434s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 434s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 434s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 434s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 434s ---------------------------------------------------------------------- 434s APBS uses FETK (the Finite Element ToolKit) to solve the 434s Poisson-Boltzmann equation numerically. FETK is a portable collection 434s of finite element modeling class libraries developed by the Michael Holst 434s research group and written in an object-oriented form of C. FEtk is 434s designed to solve general coupled systems of nonlinear partial differential 434s equations using adaptive finite element methods, inexact Newton methods, 434s and algebraic multilevel methods. More information about FEtk may be found 434s at . 434s ---------------------------------------------------------------------- 434s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 434s Aqua is a modified form of the Holst group PMG library 434s which has been modified by Patrice Koehl 434s for improved efficiency and 434s memory usage when solving the Poisson-Boltzmann equation. 434s ---------------------------------------------------------------------- 434s Please cite your use of APBS as: 434s 434s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 434s nanosystems: application to microtubules and the ribosome. Proc. 434s Natl. Acad. Sci. USA 98, 10037-10041 2001. 434s 434s 434s This executable compiled on Jan 3 2025 at 11:01:42 434s 434s Parsing input file apbs-mol.in... 434s rank 0 size 1... 434s Parsed input file. 434s Got paths for 3 molecules 434s Reading PQR-format atom data from acet.pqr. 434s asc_getToken: Error occurred (bailing out). 434s Vio_scanf: Format problem with input. 434s 18 atoms 434s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 434s Net charge -1.00e+00 e 434s Reading PQR-format atom data from hca.pqr. 434s asc_getToken: Error occurred (bailing out). 434s Vio_scanf: Format problem with input. 434s 2482 atoms 434s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 434s Net charge 1.00e+00 e 434s Reading PQR-format atom data from complex.pqr. 434s 2500 atoms 434s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 434s Net charge -1.02e-14 e 434s Preparing to run 9 PBE calculations. 434s ---------------------------------------- 434s CALCULATION #1 (acet): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 62.727 MB total, 62.727 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 1.500 x 1.500 x 1.500 434s Grid lengths: 96.000 x 96.000 x 96.000 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 1 434s Linearized traditional PBE 434s Single Debye-Huckel sphere boundary conditions 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 2.213600726771E+02 kJ/mol 434s Calculating forces... 434s ---------------------------------------- 434s CALCULATION #2 (acet): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 62.727 MB total, 123.701 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 0.581 x 0.581 x 0.581 434s Grid lengths: 37.181 x 37.181 x 37.181 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 1 434s Linearized traditional PBE 434s Boundary conditions from focusing 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 1.825764811255E+03 kJ/mol 434s Calculating forces... 434s ---------------------------------------- 434s CALCULATION #3 (acet): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 62.727 MB total, 123.701 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 0.225 x 0.225 x 0.225 434s Grid lengths: 14.400 x 14.400 x 14.400 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 1 434s Linearized traditional PBE 434s Boundary conditions from focusing 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 6.458471211905E+03 kJ/mol 434s Calculating forces... 434s ---------------------------------------- 434s CALCULATION #4 (hca): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 146.516 MB total, 146.516 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 1.500 x 1.500 x 1.500 434s Grid lengths: 96.000 x 96.000 x 96.000 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 2 434s Linearized traditional PBE 434s Single Debye-Huckel sphere boundary conditions 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 2.093606095527E+04 kJ/mol 434s Calculating forces... 434s [focusFillBound()]: WARNING: 434s Unusually large potential values 434s detected on the focusing boundary! 434s Convergence not guaranteed for NPBE/NRPBE calculations! 434s 434s ---------------------------------------- 434s CALCULATION #5 (hca): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 146.516 MB total, 245.092 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 0.581 x 0.581 x 0.581 434s Grid lengths: 37.181 x 37.181 x 37.181 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 2 434s Linearized traditional PBE 434s Boundary conditions from focusing 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 1.515433544464E+05 kJ/mol 434s Calculating forces... 434s [focusFillBound()]: WARNING: 434s Unusually large potential values 434s detected on the focusing boundary! 434s Convergence not guaranteed for NPBE/NRPBE calculations! 434s 434s ---------------------------------------- 434s CALCULATION #6 (hca): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 146.516 MB total, 245.092 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 0.225 x 0.225 x 0.225 434s Grid lengths: 14.400 x 14.400 x 14.400 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 2 434s Linearized traditional PBE 434s Boundary conditions from focusing 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 1.786369323561E+05 kJ/mol 434s Calculating forces... 434s ---------------------------------------- 434s CALCULATION #7 (complex): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 146.926 MB total, 245.092 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 1.500 x 1.500 x 1.500 434s Grid lengths: 96.000 x 96.000 x 96.000 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 3 434s Linearized traditional PBE 434s Single Debye-Huckel sphere boundary conditions 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 2.105322784838E+04 kJ/mol 434s Calculating forces... 434s [focusFillBound()]: WARNING: 434s Unusually large potential values 434s detected on the focusing boundary! 434s Convergence not guaranteed for NPBE/NRPBE calculations! 434s 434s ---------------------------------------- 434s CALCULATION #8 (complex): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 146.926 MB total, 245.725 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 0.581 x 0.581 x 0.581 434s Grid lengths: 37.181 x 37.181 x 37.181 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 3 434s Linearized traditional PBE 434s Boundary conditions from focusing 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 1.533304996252E+05 kJ/mol 434s Calculating forces... 434s [focusFillBound()]: WARNING: 434s Unusually large potential values 434s detected on the focusing boundary! 434s Convergence not guaranteed for NPBE/NRPBE calculations! 434s 434s ---------------------------------------- 434s CALCULATION #9 (complex): MULTIGRID 434s Setting up problem... 434s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 434s Debye length: 0 A 434s Current memory usage: 146.926 MB total, 245.725 MB high water 434s Using linear spline charge discretization. 434s Grid dimensions: 65 x 65 x 65 434s Grid spacings: 0.225 x 0.225 x 0.225 434s Grid lengths: 14.400 x 14.400 x 14.400 434s Grid center: (-6.028, 3.898, 15.179) 434s Multigrid levels: 5 434s Molecule ID: 3 434s Linearized traditional PBE 434s Boundary conditions from focusing 434s 2 ion species (0.000 M ionic strength): 434s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 434s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 434s Solute dielectric: 2.000 434s Solvent dielectric: 78.540 434s Using "molecular" surface definition; no smoothing 434s Solvent probe radius: 0.000 A 434s Temperature: 298.150 K 434s Electrostatic energies will be calculated 434s Total electrostatic energy = 1.850429388099E+05 kJ/mol 434s Calculating forces... 434s ---------------------------------------- 434s PRINT STATEMENTS 434s 434s print energy 3 (complex) - 1 (acet) - 2 (hca) end 434s Local net energy (PE 0) = -5.246475812684E+01 kJ/mol 434s Global net ELEC energy = -5.246475812684E+01 kJ/mol 434s ---------------------------------------- 434s CLEANING UP AND SHUTTING DOWN... 434s Destroying force arrays. 434s No energy arrays to destroy. 434s Destroying multigrid structures. 434s Destroying finite element structures. 434s Destroying 3 molecules 434s Final memory usage: 0.001 MB total, 245.725 MB high water 434s 434s 434s Thanks for using APBS! 434s 434s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 434s *** PASSED *** 434s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 434s *** PASSED *** 434s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 434s *** PASSED *** 434s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 434s *** PASSED *** 434s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 434s *** PASSED *** 434s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 434s *** PASSED *** 434s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 434s *** PASSED *** 434s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 434s *** PASSED *** 434s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 434s *** PASSED *** 434s Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) 434s *** PASSED *** 434s Elapsed time: 9.787112 seconds 434s -------------------------------------------------------------------------------- 434s -------------------------------------------------------------------------------- 434s Testing input file apbs-smol.in 434s 442s Checking for intermediate energies in input file apbs-mol.out 442s EXPECTED COMPUTED: 10 442s EXPECTED EXPECTED: 10 442s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] 442s 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'] 442s COMPUTED RESULT 221.3600726771 442s COMPUTED RESULT 1825.764811255 442s COMPUTED RESULT 6458.471211905 442s COMPUTED RESULT 20936.06095527 442s COMPUTED RESULT 151543.3544464 442s COMPUTED RESULT 178636.9323561 442s COMPUTED RESULT 21053.22784838 442s COMPUTED RESULT 153330.4996252 442s COMPUTED RESULT 185042.9388099 442s COMPUTED RESULT -52.46475812684 442s BINARY: /usr/bin/apbs 442s INPUT: apbs-smol.in 442s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 442s asc_getToken: Error occurred (bailing out). 442s Vio_scanf: Format problem with input. 442s 442s 442s ---------------------------------------------------------------------- 442s APBS -- Adaptive Poisson-Boltzmann Solver 442s Version APBS 3.4.1 442s 442s Nathan A. Baker (nathan.baker@pnnl.gov) 442s Pacific Northwest National Laboratory 442s 442s Additional contributing authors listed in the code documentation. 442s 442s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 442s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 442s Northwest Division for the U.S. Department of Energy. 442s 442s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 442s Portions Copyright (c) 2002-2020, Nathan A. Baker. 442s Portions Copyright (c) 1999-2002, The Regents of the University of California. 442s Portions Copyright (c) 1995, Michael Holst. 442s All rights reserved. 442s 442s Redistribution and use in source and binary forms, with or without 442s modification, are permitted provided that the following conditions are met: 442s 442s * Redistributions of source code must retain the above copyright notice, this 442s list of conditions and the following disclaimer. 442s 442s * Redistributions in binary form must reproduce the above copyright notice, 442s this list of conditions and the following disclaimer in the documentation 442s and/or other materials provided with the distribution. 442s 442s * Neither the name of the developer nor the names of its contributors may be 442s used to endorse or promote products derived from this software without 442s specific prior written permission. 442s 442s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 442s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 442s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 442s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 442s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 442s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 442s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 442s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 442s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 442s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 442s ---------------------------------------------------------------------- 442s APBS uses FETK (the Finite Element ToolKit) to solve the 442s Poisson-Boltzmann equation numerically. FETK is a portable collection 442s of finite element modeling class libraries developed by the Michael Holst 442s research group and written in an object-oriented form of C. FEtk is 442s designed to solve general coupled systems of nonlinear partial differential 442s equations using adaptive finite element methods, inexact Newton methods, 442s and algebraic multilevel methods. More information about FEtk may be found 442s at . 442s ---------------------------------------------------------------------- 442s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 442s Aqua is a modified form of the Holst group PMG library 442s which has been modified by Patrice Koehl 442s for improved efficiency and 442s memory usage when solving the Poisson-Boltzmann equation. 442s ---------------------------------------------------------------------- 442s Please cite your use of APBS as: 442s 442s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 442s nanosystems: application to microtubules and the ribosome. Proc. 442s Natl. Acad. Sci. USA 98, 10037-10041 2001. 442s 442s 442s This executable compiled on Jan 3 2025 at 11:01:42 442s 442s Parsing input file apbs-smol.in... 442s rank 0 size 1... 442s Parsed input file. 442s Got paths for 3 molecules 442s Reading PQR-format atom data from acet.pqr. 442s asc_getToken: Error occurred (bailing out). 442s Vio_scanf: Format problem with input. 442s 18 atoms 442s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 442s Net charge -1.00e+00 e 442s Reading PQR-format atom data from hca.pqr. 442s asc_getToken: Error occurred (bailing out). 442s Vio_scanf: Format problem with input. 442s 2482 atoms 442s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 442s Net charge 1.00e+00 e 442s Reading PQR-format atom data from complex.pqr. 442s 2500 atoms 442s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 442s Net charge -1.02e-14 e 442s Preparing to run 9 PBE calculations. 442s ---------------------------------------- 442s CALCULATION #1 (acet): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 62.727 MB total, 62.727 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 1.500 x 1.500 x 1.500 442s Grid lengths: 96.000 x 96.000 x 96.000 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 1 442s Linearized traditional PBE 442s Single Debye-Huckel sphere boundary conditions 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 1.884888131017E+02 kJ/mol 442s Calculating forces... 442s ---------------------------------------- 442s CALCULATION #2 (acet): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 62.727 MB total, 123.701 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 0.581 x 0.581 x 0.581 442s Grid lengths: 37.181 x 37.181 x 37.181 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 1 442s Linearized traditional PBE 442s Boundary conditions from focusing 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 1.820045922544E+03 kJ/mol 442s Calculating forces... 442s ---------------------------------------- 442s CALCULATION #3 (acet): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 62.727 MB total, 123.701 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 0.225 x 0.225 x 0.225 442s Grid lengths: 14.400 x 14.400 x 14.400 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 1 442s Linearized traditional PBE 442s Boundary conditions from focusing 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 6.460002606908E+03 kJ/mol 442s Calculating forces... 442s ---------------------------------------- 442s CALCULATION #4 (hca): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 146.516 MB total, 146.516 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 1.500 x 1.500 x 1.500 442s Grid lengths: 96.000 x 96.000 x 96.000 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 2 442s Linearized traditional PBE 442s Single Debye-Huckel sphere boundary conditions 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 2.189161497021E+04 kJ/mol 442s Calculating forces... 442s [focusFillBound()]: WARNING: 442s Unusually large potential values 442s detected on the focusing boundary! 442s Convergence not guaranteed for NPBE/NRPBE calculations! 442s 442s ---------------------------------------- 442s CALCULATION #5 (hca): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 146.516 MB total, 245.092 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 0.581 x 0.581 x 0.581 442s Grid lengths: 37.181 x 37.181 x 37.181 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 2 442s Linearized traditional PBE 442s Boundary conditions from focusing 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 1.520000494925E+05 kJ/mol 442s Calculating forces... 442s [focusFillBound()]: WARNING: 442s Unusually large potential values 442s detected on the focusing boundary! 442s Convergence not guaranteed for NPBE/NRPBE calculations! 442s 442s ---------------------------------------- 442s CALCULATION #6 (hca): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 146.516 MB total, 245.092 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 0.225 x 0.225 x 0.225 442s Grid lengths: 14.400 x 14.400 x 14.400 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 2 442s Linearized traditional PBE 442s Boundary conditions from focusing 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 1.790436191580E+05 kJ/mol 442s Calculating forces... 442s ---------------------------------------- 442s CALCULATION #7 (complex): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 146.926 MB total, 245.092 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 1.500 x 1.500 x 1.500 442s Grid lengths: 96.000 x 96.000 x 96.000 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 3 442s Linearized traditional PBE 442s Single Debye-Huckel sphere boundary conditions 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 2.195842512312E+04 kJ/mol 442s Calculating forces... 442s [focusFillBound()]: WARNING: 442s Unusually large potential values 442s detected on the focusing boundary! 442s Convergence not guaranteed for NPBE/NRPBE calculations! 442s 442s ---------------------------------------- 442s CALCULATION #8 (complex): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 146.926 MB total, 245.725 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 0.581 x 0.581 x 0.581 442s Grid lengths: 37.181 x 37.181 x 37.181 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 3 442s Linearized traditional PBE 442s Boundary conditions from focusing 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 1.537771604355E+05 kJ/mol 442s Calculating forces... 442s [focusFillBound()]: WARNING: 442s Unusually large potential values 442s detected on the focusing boundary! 442s Convergence not guaranteed for NPBE/NRPBE calculations! 442s 442s ---------------------------------------- 442s CALCULATION #9 (complex): MULTIGRID 442s Setting up problem... 442s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 442s Debye length: 0 A 442s Current memory usage: 146.926 MB total, 245.725 MB high water 442s Using linear spline charge discretization. 442s Grid dimensions: 65 x 65 x 65 442s Grid spacings: 0.225 x 0.225 x 0.225 442s Grid lengths: 14.400 x 14.400 x 14.400 442s Grid center: (-6.028, 3.898, 15.179) 442s Multigrid levels: 5 442s Molecule ID: 3 442s Linearized traditional PBE 442s Boundary conditions from focusing 442s 2 ion species (0.000 M ionic strength): 442s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 442s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 442s Solute dielectric: 2.000 442s Solvent dielectric: 78.540 442s Using "molecular" surface definition;harmonic average smoothing 442s Solvent probe radius: 0.000 A 442s Temperature: 298.150 K 442s Electrostatic energies will be calculated 442s Total electrostatic energy = 1.854495619747E+05 kJ/mol 442s Calculating forces... 442s ---------------------------------------- 442s PRINT STATEMENTS 442s 442s print energy 3 (complex) - 1 (acet) - 2 (hca) end 442s Local net energy (PE 0) = -5.405979017059E+01 kJ/mol 442s Global net ELEC energy = -5.405979017059E+01 kJ/mol 442s ---------------------------------------- 442s CLEANING UP AND SHUTTING DOWN... 442s Destroying force arrays. 442s No energy arrays to destroy. 442s Destroying multigrid structures. 442s Destroying finite element structures. 442s Destroying 3 molecules 442s Final memory usage: 0.001 MB total, 245.725 MB high water 442s 442s 442s Thanks for using APBS! 442s 442s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 442s *** PASSED *** 442s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 442s *** PASSED *** 442s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 442s *** PASSED *** 442s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 442s *** PASSED *** 442s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 442s *** PASSED *** 442s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 442s *** PASSED *** 442s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 442s *** PASSED *** 442s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 442s *** PASSED *** 442s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 442s *** PASSED *** 442s Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) 442s *** PASSED *** 442s Elapsed time: 7.971157 seconds 442s -------------------------------------------------------------------------------- 442s Total elapsed time: 17.758269 seconds 442s Test results have been logged 442s -------------------------------------------------------------------------------- 442s -------------------------------------------------------------------------------- 442s Testing input file apbs-mol.in 442s 447s Checking for intermediate energies in input file apbs-smol.out 447s EXPECTED COMPUTED: 10 447s EXPECTED EXPECTED: 10 447s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] 447s 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'] 447s COMPUTED RESULT 188.4888131017 447s COMPUTED RESULT 1820.045922544 447s COMPUTED RESULT 6460.002606908 447s COMPUTED RESULT 21891.61497021 447s COMPUTED RESULT 152000.0494925 447s COMPUTED RESULT 179043.619158 447s COMPUTED RESULT 21958.42512312 447s COMPUTED RESULT 153777.1604355 447s COMPUTED RESULT 185449.5619747 447s COMPUTED RESULT -54.05979017059 447s Running tests for ionize 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 3 molecules 447s Reading PQR-format atom data from acetic-acid.pqr. 447s asc_getToken: Error occurred (bailing out). 447s Vio_scanf: Format problem with input. 447s 8 atoms 447s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 447s Net charge -1.67e-16 e 447s Reading PQR-format atom data from acetate.pqr. 447s asc_getToken: Error occurred (bailing out). 447s Vio_scanf: Format problem with input. 447s 8 atoms 447s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 447s Net charge -1.00e+00 e 447s Reading PQR-format atom data from proton.pqr. 447s 1 atoms 447s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 447s Net charge 1.00e+00 e 447s Preparing to run 12 PBE calculations. 447s ---------------------------------------- 447s CALCULATION #1 (acetic-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 7.76163 A 447s Current memory usage: 61.598 MB total, 61.598 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.188 x 0.188 x 0.188 447s Grid lengths: 12.000 x 12.000 x 12.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 1 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.150 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 5.823898055191E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #2 (acetic-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 7.76163 A 447s Current memory usage: 61.598 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.094 x 0.094 x 0.094 447s Grid lengths: 6.000 x 6.000 x 6.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 1 447s Linearized traditional PBE 447s Boundary conditions from focusing 447s 2 ion species (0.150 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 9.793274462353E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #3 (acetic-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: 61.422 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.188 x 0.188 x 0.188 447s Grid lengths: 12.000 x 12.000 x 12.000 447s Grid center: (0.000, -0.154, 1.287) 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: 2.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 5.846917564309E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #4 (acetic-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: 61.422 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.094 x 0.094 x 0.094 447s Grid lengths: 6.000 x 6.000 x 6.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 1 447s Linearized traditional PBE 447s Boundary conditions from focusing 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: 2.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 9.815953282539E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #5 (acetate-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 7.76163 A 447s Current memory usage: 61.598 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.188 x 0.188 x 0.188 447s Grid lengths: 12.000 x 12.000 x 12.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 2 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.150 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 8.219846763777E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #6 (acetate-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 7.76163 A 447s Current memory usage: 61.598 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.094 x 0.094 x 0.094 447s Grid lengths: 6.000 x 6.000 x 6.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 2 447s Linearized traditional PBE 447s Boundary conditions from focusing 447s 2 ion species (0.150 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 1.392741988698E+04 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #7 (acetate-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: 61.422 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.188 x 0.188 x 0.188 447s Grid lengths: 12.000 x 12.000 x 12.000 447s Grid center: (0.000, -0.154, 1.287) 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: 2.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 8.420373979905E+03 kJ/mol 447s Calculating forces... 447s [focusFillBound()]: WARNING: 447s Unusually large potential values 447s detected on the focusing boundary! 447s Convergence not guaranteed for NPBE/NRPBE calculations! 447s 447s ---------------------------------------- 447s CALCULATION #8 (acetate-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: 61.422 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.094 x 0.094 x 0.094 447s Grid lengths: 6.000 x 6.000 x 6.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 2 447s Linearized traditional PBE 447s Boundary conditions from focusing 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: 2.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 1.412716615065E+04 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #9 (proton-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 7.76163 A 447s Current memory usage: 61.412 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.188 x 0.188 x 0.188 447s Grid lengths: 12.000 x 12.000 x 12.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 3 447s Linearized traditional PBE 447s Multiple Debye-Huckel sphere boundary conditions 447s 2 ion species (0.150 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 3.862359524598E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #10 (proton-solv): MULTIGRID 447s Setting up problem... 447s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 447s Debye length: 7.76163 A 447s Current memory usage: 61.412 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.094 x 0.094 x 0.094 447s Grid lengths: 6.000 x 6.000 x 6.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 3 447s Linearized traditional PBE 447s Boundary conditions from focusing 447s 2 ion species (0.150 M ionic strength): 447s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 447s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 6.288156251610E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s CALCULATION #11 (proton-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: 61.373 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.188 x 0.188 x 0.188 447s Grid lengths: 12.000 x 12.000 x 12.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 3 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: 2.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 4.162533113906E+03 kJ/mol 447s Calculating forces... 447s [focusFillBound()]: WARNING: 447s Unusually large potential values 447s detected on the focusing boundary! 447s Convergence not guaranteed for NPBE/NRPBE calculations! 447s 447s ---------------------------------------- 447s CALCULATION #12 (proton-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: 61.373 MB total, 122.404 MB high water 447s Using linear spline charge discretization. 447s Grid dimensions: 65 x 65 x 65 447s Grid spacings: 0.094 x 0.094 x 0.094 447s Grid lengths: 6.000 x 6.000 x 6.000 447s Grid center: (0.000, -0.154, 1.287) 447s Multigrid levels: 5 447s Molecule ID: 3 447s Linearized traditional PBE 447s Boundary conditions from focusing 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: 2.000 447s Using "molecular" surface definition; no smoothing 447s Solvent probe radius: 0.000 A 447s Temperature: 293.000 K 447s Electrostatic energies will be calculated 447s Total electrostatic energy = 6.585616091973E+03 kJ/mol 447s Calculating forces... 447s ---------------------------------------- 447s PRINT STATEMENTS 447s 447s print energy 1 (acetic-solv) - 2 (acetic-ref) end 447s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 447s Global net ELEC energy = -2.267882018629E+01 kJ/mol 447s 447s print energy 3 (acetate-solv) - 4 (acetate-ref) end 447s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 447s Global net ELEC energy = -1.997462636633E+02 kJ/mol 447s 447s print energy 5 (proton-solv) - 6 (proton-ref) end 447s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 447s Global net ELEC energy = -2.974598403628E+02 kJ/mol 447s 447s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 447s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 447s Global net ELEC energy = -4.745272838398E+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 3 molecules 447s Final memory usage: 0.001 MB total, 122.404 MB high water 447s 447s 447s Thanks for using APBS! 447s 447s Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 447s *** PASSED *** 447s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 447s *** PASSED *** 447s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 447s *** PASSED *** 447s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 447s *** PASSED *** 447s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 447s *** PASSED *** 447s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 447s *** PASSED *** 447s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 447s *** PASSED *** 447s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 447s *** PASSED *** 447s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 447s *** PASSED *** 447s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 447s *** PASSED *** 447s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 447s *** PASSED *** 447s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 447s *** PASSED *** 447s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 447s *** PASSED *** 447s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 447s *** PASSED *** 447s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 447s *** PASSED *** 447s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 447s *** PASSED *** 447s Elapsed time: 4.548194 seconds 447s -------------------------------------------------------------------------------- 447s -------------------------------------------------------------------------------- 447s Testing input file apbs-smol.in 447s 451s Checking for intermediate energies in input file apbs-mol.out 451s EXPECTED COMPUTED: 16 451s EXPECTED EXPECTED: 16 451s 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] 451s 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'] 451s COMPUTED RESULT 5823.898055191 451s COMPUTED RESULT 9793.274462353 451s COMPUTED RESULT 5846.917564309 451s COMPUTED RESULT 9815.953282539 451s COMPUTED RESULT 8219.846763777 451s COMPUTED RESULT 13927.41988698 451s COMPUTED RESULT 8420.373979905 451s COMPUTED RESULT 14127.16615065 451s COMPUTED RESULT 3862.359524598 451s COMPUTED RESULT 6288.15625161 451s COMPUTED RESULT 4162.533113906 451s COMPUTED RESULT 6585.616091973 451s COMPUTED RESULT -22.67882018629 451s COMPUTED RESULT -199.7462636633 451s COMPUTED RESULT -297.4598403628 451s COMPUTED RESULT -474.5272838398 451s BINARY: /usr/bin/apbs 451s INPUT: apbs-smol.in 451s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 451s asc_getToken: Error occurred (bailing out). 451s Vio_scanf: Format problem with input. 451s 451s 451s ---------------------------------------------------------------------- 451s APBS -- Adaptive Poisson-Boltzmann Solver 451s Version APBS 3.4.1 451s 451s Nathan A. Baker (nathan.baker@pnnl.gov) 451s Pacific Northwest National Laboratory 451s 451s Additional contributing authors listed in the code documentation. 451s 451s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 451s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 451s Northwest Division for the U.S. Department of Energy. 451s 451s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 451s Portions Copyright (c) 2002-2020, Nathan A. Baker. 451s Portions Copyright (c) 1999-2002, The Regents of the University of California. 451s Portions Copyright (c) 1995, Michael Holst. 451s All rights reserved. 451s 451s Redistribution and use in source and binary forms, with or without 451s modification, are permitted provided that the following conditions are met: 451s 451s * Redistributions of source code must retain the above copyright notice, this 451s list of conditions and the following disclaimer. 451s 451s * Redistributions in binary form must reproduce the above copyright notice, 451s this list of conditions and the following disclaimer in the documentation 451s and/or other materials provided with the distribution. 451s 451s * Neither the name of the developer nor the names of its contributors may be 451s used to endorse or promote products derived from this software without 451s specific prior written permission. 451s 451s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 451s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 451s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 451s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 451s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 451s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 451s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 451s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 451s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 451s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 451s ---------------------------------------------------------------------- 451s APBS uses FETK (the Finite Element ToolKit) to solve the 451s Poisson-Boltzmann equation numerically. FETK is a portable collection 451s of finite element modeling class libraries developed by the Michael Holst 451s research group and written in an object-oriented form of C. FEtk is 451s designed to solve general coupled systems of nonlinear partial differential 451s equations using adaptive finite element methods, inexact Newton methods, 451s and algebraic multilevel methods. More information about FEtk may be found 451s at . 451s ---------------------------------------------------------------------- 451s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 451s Aqua is a modified form of the Holst group PMG library 451s which has been modified by Patrice Koehl 451s for improved efficiency and 451s memory usage when solving the Poisson-Boltzmann equation. 451s ---------------------------------------------------------------------- 451s Please cite your use of APBS as: 451s 451s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 451s nanosystems: application to microtubules and the ribosome. Proc. 451s Natl. Acad. Sci. USA 98, 10037-10041 2001. 451s 451s 451s This executable compiled on Jan 3 2025 at 11:01:42 451s 451s Parsing input file apbs-smol.in... 451s rank 0 size 1... 451s Parsed input file. 451s Got paths for 3 molecules 451s Reading PQR-format atom data from acetic-acid.pqr. 451s asc_getToken: Error occurred (bailing out). 451s Vio_scanf: Format problem with input. 451s 8 atoms 451s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 451s Net charge -1.67e-16 e 451s Reading PQR-format atom data from acetate.pqr. 451s asc_getToken: Error occurred (bailing out). 451s Vio_scanf: Format problem with input. 451s 8 atoms 451s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 451s Net charge -1.00e+00 e 451s Reading PQR-format atom data from proton.pqr. 451s 1 atoms 451s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 451s Net charge 1.00e+00 e 451s Preparing to run 12 PBE calculations. 451s ---------------------------------------- 451s CALCULATION #1 (acetic-solv): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 7.76163 A 451s Current memory usage: 61.598 MB total, 61.598 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.188 x 0.188 x 0.188 451s Grid lengths: 12.000 x 12.000 x 12.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 1 451s Linearized traditional PBE 451s Multiple Debye-Huckel sphere boundary conditions 451s 2 ion species (0.150 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 78.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 5.824172730822E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #2 (acetic-solv): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 7.76163 A 451s Current memory usage: 61.598 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.094 x 0.094 x 0.094 451s Grid lengths: 6.000 x 6.000 x 6.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 1 451s Linearized traditional PBE 451s Boundary conditions from focusing 451s 2 ion species (0.150 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 78.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 9.793622759239E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #3 (acetic-ref): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 0 A 451s Current memory usage: 61.422 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.188 x 0.188 x 0.188 451s Grid lengths: 12.000 x 12.000 x 12.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 1 451s Linearized traditional PBE 451s Multiple Debye-Huckel sphere boundary conditions 451s 2 ion species (0.000 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 2.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 5.846917564309E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #4 (acetic-ref): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 0 A 451s Current memory usage: 61.422 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.094 x 0.094 x 0.094 451s Grid lengths: 6.000 x 6.000 x 6.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 1 451s Linearized traditional PBE 451s Boundary conditions from focusing 451s 2 ion species (0.000 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 2.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 9.815953282539E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #5 (acetate-solv): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 7.76163 A 451s Current memory usage: 61.598 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.188 x 0.188 x 0.188 451s Grid lengths: 12.000 x 12.000 x 12.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 2 451s Linearized traditional PBE 451s Multiple Debye-Huckel sphere boundary conditions 451s 2 ion species (0.150 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 78.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 8.221328580569E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #6 (acetate-solv): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 7.76163 A 451s Current memory usage: 61.598 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.094 x 0.094 x 0.094 451s Grid lengths: 6.000 x 6.000 x 6.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 2 451s Linearized traditional PBE 451s Boundary conditions from focusing 451s 2 ion species (0.150 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 78.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 1.392867783119E+04 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #7 (acetate-ref): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 0 A 451s Current memory usage: 61.422 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.188 x 0.188 x 0.188 451s Grid lengths: 12.000 x 12.000 x 12.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 2 451s Linearized traditional PBE 451s Multiple Debye-Huckel sphere boundary conditions 451s 2 ion species (0.000 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 2.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 8.420373979905E+03 kJ/mol 451s Calculating forces... 451s [focusFillBound()]: WARNING: 451s Unusually large potential values 451s detected on the focusing boundary! 451s Convergence not guaranteed for NPBE/NRPBE calculations! 451s 451s ---------------------------------------- 451s CALCULATION #8 (acetate-ref): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 0 A 451s Current memory usage: 61.422 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.094 x 0.094 x 0.094 451s Grid lengths: 6.000 x 6.000 x 6.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 2 451s Linearized traditional PBE 451s Boundary conditions from focusing 451s 2 ion species (0.000 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 2.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 1.412716615065E+04 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #9 (proton-solv): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 7.76163 A 451s Current memory usage: 61.412 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.188 x 0.188 x 0.188 451s Grid lengths: 12.000 x 12.000 x 12.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 3 451s Linearized traditional PBE 451s Multiple Debye-Huckel sphere boundary conditions 451s 2 ion species (0.150 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 78.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 3.863066835285E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #10 (proton-solv): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 7.76163 A 451s Current memory usage: 61.412 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.094 x 0.094 x 0.094 451s Grid lengths: 6.000 x 6.000 x 6.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 3 451s Linearized traditional PBE 451s Boundary conditions from focusing 451s 2 ion species (0.150 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 78.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 6.289649216644E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s CALCULATION #11 (proton-ref): MULTIGRID 451s Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 451s *** PASSED *** 451s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 451s *** PASSED *** 451s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 451s *** PASSED *** 451s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 451s *** PASSED *** 451s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 451s *** PASSED *** 451s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 451s *** PASSED *** 451s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 451s *** PASSED *** 451s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 451s *** PASSED *** 451s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 451s *** PASSED *** 451s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 451s *** PASSED *** 451s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 451s *** PASSED *** 451s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 451s *** PASSED *** 451s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 451s *** PASSED *** 451s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 451s *** PASSED *** 451s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 451s *** PASSED *** 451s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 451s *** PASSED *** 451s Elapsed time: 4.194861 seconds 451s -------------------------------------------------------------------------------- 451s Total elapsed time: 8.743055 seconds 451s Test results have been logged 451s -------------------------------------------------------------------------------- 451s -------------------------------------------------------------------------------- 451s Testing input file ion-pmf.in 451s 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 0 A 451s Current memory usage: 61.373 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.188 x 0.188 x 0.188 451s Grid lengths: 12.000 x 12.000 x 12.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 3 451s Linearized traditional PBE 451s Multiple Debye-Huckel sphere boundary conditions 451s 2 ion species (0.000 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 2.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 4.162533113906E+03 kJ/mol 451s Calculating forces... 451s [focusFillBound()]: WARNING: 451s Unusually large potential values 451s detected on the focusing boundary! 451s Convergence not guaranteed for NPBE/NRPBE calculations! 451s 451s ---------------------------------------- 451s CALCULATION #12 (proton-ref): MULTIGRID 451s Setting up problem... 451s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 451s Debye length: 0 A 451s Current memory usage: 61.373 MB total, 122.404 MB high water 451s Using linear spline charge discretization. 451s Grid dimensions: 65 x 65 x 65 451s Grid spacings: 0.094 x 0.094 x 0.094 451s Grid lengths: 6.000 x 6.000 x 6.000 451s Grid center: (0.000, -0.154, 1.287) 451s Multigrid levels: 5 451s Molecule ID: 3 451s Linearized traditional PBE 451s Boundary conditions from focusing 451s 2 ion species (0.000 M ionic strength): 451s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 451s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 451s Solute dielectric: 2.000 451s Solvent dielectric: 2.000 451s Using "molecular" surface definition;harmonic average smoothing 451s Solvent probe radius: 0.000 A 451s Temperature: 293.000 K 451s Electrostatic energies will be calculated 451s Total electrostatic energy = 6.585616091973E+03 kJ/mol 451s Calculating forces... 451s ---------------------------------------- 451s PRINT STATEMENTS 451s 451s print energy 1 (acetic-solv) - 2 (acetic-ref) end 451s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 451s Global net ELEC energy = -2.233052329981E+01 kJ/mol 451s 451s print energy 3 (acetate-solv) - 4 (acetate-ref) end 451s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 451s Global net ELEC energy = -1.984883194538E+02 kJ/mol 451s 451s print energy 5 (proton-solv) - 6 (proton-ref) end 451s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 451s Global net ELEC energy = -2.959668753288E+02 kJ/mol 451s 451s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 451s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 451s Global net ELEC energy = -4.721246714828E+02 kJ/mol 451s ---------------------------------------- 451s CLEANING UP AND SHUTTING DOWN... 451s Destroying force arrays. 451s No energy arrays to destroy. 451s Destroying multigrid structures. 451s Destroying finite element structures. 451s Destroying 3 molecules 451s Final memory usage: 0.001 MB total, 122.404 MB high water 451s 451s 451s Thanks for using APBS! 451s 458s Checking for intermediate energies in input file apbs-smol.out 458s EXPECTED COMPUTED: 16 458s EXPECTED EXPECTED: 16 458s 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] 458s 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'] 458s COMPUTED RESULT 5824.172730822 458s COMPUTED RESULT 9793.622759239 458s COMPUTED RESULT 5846.917564309 458s COMPUTED RESULT 9815.953282539 458s COMPUTED RESULT 8221.328580569 458s COMPUTED RESULT 13928.67783119 458s COMPUTED RESULT 8420.373979905 458s COMPUTED RESULT 14127.16615065 458s COMPUTED RESULT 3863.066835285 458s COMPUTED RESULT 6289.649216644 458s COMPUTED RESULT 4162.533113906 458s COMPUTED RESULT 6585.616091973 458s COMPUTED RESULT -22.33052329981 458s COMPUTED RESULT -198.4883194538 458s COMPUTED RESULT -295.9668753288 458s COMPUTED RESULT -472.1246714828 458s Running tests for ion-pmf section 458s BINARY: /usr/bin/apbs 458s INPUT: ion-pmf.in 458s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 458s asc_getToken: Error occurred (bailing out). 458s Vio_scanf: Format problem with input. 458s asc_getToken: Error occurred (bailing out). 458s Vio_scanf: Format problem with input. 458s 458s 458s ---------------------------------------------------------------------- 458s APBS -- Adaptive Poisson-Boltzmann Solver 458s Version APBS 3.4.1 458s 458s Nathan A. Baker (nathan.baker@pnnl.gov) 458s Pacific Northwest National Laboratory 458s 458s Additional contributing authors listed in the code documentation. 458s 458s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 458s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 458s Northwest Division for the U.S. Department of Energy. 458s 458s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 458s Portions Copyright (c) 2002-2020, Nathan A. Baker. 458s Portions Copyright (c) 1999-2002, The Regents of the University of California. 458s Portions Copyright (c) 1995, Michael Holst. 458s All rights reserved. 458s 458s Redistribution and use in source and binary forms, with or without 458s modification, are permitted provided that the following conditions are met: 458s 458s * Redistributions of source code must retain the above copyright notice, this 458s list of conditions and the following disclaimer. 458s 458s * Redistributions in binary form must reproduce the above copyright notice, 458s this list of conditions and the following disclaimer in the documentation 458s and/or other materials provided with the distribution. 458s 458s * Neither the name of the developer nor the names of its contributors may be 458s used to endorse or promote products derived from this software without 458s specific prior written permission. 458s 458s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 458s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 458s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 458s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 458s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 458s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 458s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 458s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 458s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 458s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 458s ---------------------------------------------------------------------- 458s APBS uses FETK (the Finite Element ToolKit) to solve the 458s Poisson-Boltzmann equation numerically. FETK is a portable collection 458s of finite element modeling class libraries developed by the Michael Holst 458s research group and written in an object-oriented form of C. FEtk is 458s designed to solve general coupled systems of nonlinear partial differential 458s equations using adaptive finite element methods, inexact Newton methods, 458s and algebraic multilevel methods. More information about FEtk may be found 458s at . 458s ---------------------------------------------------------------------- 458s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 458s Aqua is a modified form of the Holst group PMG library 458s which has been modified by Patrice Koehl 458s for improved efficiency and 458s memory usage when solving the Poisson-Boltzmann equation. 458s ---------------------------------------------------------------------- 458s Please cite your use of APBS as: 458s 458s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 458s nanosystems: application to microtubules and the ribosome. Proc. 458s Natl. Acad. Sci. USA 98, 10037-10041 2001. 458s 458s 458s This executable compiled on Jan 3 2025 at 11:01:42 458s 458s Parsing input file ion-pmf.in... 458s rank 0 size 1... 458s Parsed input file. 458s Reading parameter data from parm.dat. 458s Got paths for 1 molecules 458s Reading PDB-format atom data from ion-pmf.pdb. 458s Vpmg_ibForce: No force for zero ionic strength! 458s Vpmg_ibForce: No force for zero ionic strength! 458s 2 atoms 458s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 458s Net charge 2.00e+00 e 458s Preparing to run 3 PBE calculations. 458s ---------------------------------------- 458s CALCULATION #1 (solv): MULTIGRID 458s Setting up problem... 458s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 458s Debye length: 0 A 458s Current memory usage: 61.106 MB total, 61.106 MB high water 458s Using cubic spline charge discretization. 458s Grid dimensions: 65 x 65 x 65 458s Grid spacings: 0.210 x 0.210 x 0.210 458s Grid lengths: 13.440 x 13.440 x 13.440 458s Grid center: (0.000, 0.000, 0.000) 458s Multigrid levels: 5 458s Molecule ID: 1 458s Linearized traditional PBE 458s Multiple Debye-Huckel sphere boundary conditions 458s 0 ion species (0.000 M ionic strength): 458s Solute dielectric: 1.000 458s Solvent dielectric: 78.540 458s Using spline-based surface definition;window = 0.300 458s Temperature: 298.150 K 458s Electrostatic energies will be calculated 458s All-atom solvent forces will be calculated 458s Total electrostatic energy = 7.839535983197E+03 kJ/mol 458s Calculating forces... 458s Printing per-atom forces for molecule 1 (kJ/mol/A) 458s Legend: 458s tot n -- total force for atom n 458s qf n -- fixed charge force for atom n 458s db n -- dielectric boundary force for atom n 458s ib n -- ionic boundary force for atom n 458s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 458s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 458s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 458s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 458s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 458s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 458s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 458s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 458s Vpmg_ibForce: No force for zero ionic strength! 458s Vpmg_ibForce: No force for zero ionic strength! 458s ---------------------------------------- 458s CALCULATION #2 (ref): MULTIGRID 458s Setting up problem... 458s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 458s Debye length: 0 A 458s Current memory usage: 61.106 MB total, 61.155 MB high water 458s Using cubic spline charge discretization. 458s Grid dimensions: 65 x 65 x 65 458s Grid spacings: 0.210 x 0.210 x 0.210 458s Grid lengths: 13.440 x 13.440 x 13.440 458s Grid center: (0.000, 0.000, 0.000) 458s Multigrid levels: 5 458s Molecule ID: 1 458s Linearized traditional PBE 458s Multiple Debye-Huckel sphere boundary conditions 458s 0 ion species (0.000 M ionic strength): 458s Solute dielectric: 1.000 458s Solvent dielectric: 1.000 458s Using spline-based surface definition;window = 0.300 458s Temperature: 298.150 K 458s Electrostatic energies will be calculated 458s All-atom solvent forces will be calculated 458s Total electrostatic energy = 8.964727588811E+03 kJ/mol 458s Calculating forces... 458s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 458s *** PASSED *** 458s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 458s Printing per-atom forces for molecule 1 (kJ/mol/A) 458s Legend: 458s tot n -- total force for atom n 458s qf n -- fixed charge force for atom n 458s db n -- dielectric boundary force for atom n 458s ib n -- ionic boundary force for atom n 458s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 458s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 458s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 458s mgF db 0 0.000e+00 0.000e+00 0.000e+00 458s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 458s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 458s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 458s mgF db 1 0.000e+00 0.000e+00 0.000e+00 458s ---------------------------------------- 458s CALCULATION #3 (asolv): APOLAR 458s Printing per atom forces (kJ/mol/A) 458s Legend: 458s tot n -- Total force for atom n 458s sasa n -- SASA force for atom n 458s sav n -- SAV force for atom n 458s wca n -- WCA force for atom n 458s 458s gamma 0.000720 458s pressure 0.000000 458s bconc 0.033000 458s 458s tot 0 2.715e-02 9.130e-07 9.128e-07 458s sasa 0 -1.100e+01 0.000e+00 0.000e+00 458s sav 0 0.000e+00 0.000e+00 0.000e+00 458s wca 0 -5.827e-01 -2.767e-05 -2.766e-05 458s tot 1 -2.723e-02 9.131e-07 9.134e-07 458s sasa 1 1.112e+01 0.000e+00 0.000e+00 458s sav 1 0.000e+00 0.000e+00 0.000e+00 458s wca 1 5.827e-01 -2.767e-05 -2.768e-05 458s 458s 458s Solvent Accessible Surface Area (SASA) for each atom: 458s SASA for atom 0: 1.153275282828E+02 458s SASA for atom 1: 1.153114143344E+02 458s 458s Total solvent accessible surface area: 230.639 A^2 458s 458s Surface tension*area energies (gamma * SASA) for each atom: 458s Surface tension*area energy for atom 0: 8.303582036361E-02 458s Surface tension*area energy for atom 1: 8.302421832080E-02 458s 458s Total surface tension energy: 0.16606 kJ/mol 458s 458s Total solvent accessible volume: 0 A^3 458s 458s Total pressure*volume energy: 0 kJ/mol 458s 458s WCA dispersion Energies for each atom: 458s WCA energy for atom 0: -6.909718345777E+00 458s WCA energy for atom 1: -6.909411348230E+00 458s 458s Total WCA energy: -13.8191 kJ/mol 458s 458s Total non-polar energy = -1.365306965532E+01 kJ/mol 458s ---------------------------------------- 458s PRINT STATEMENTS 458s 458s print energy 1 (solv) - 2 (ref) end 458s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 458s Global net ELEC energy = -1.125191605614E+03 kJ/mol 458s print force 1 (solv) - 2 (ref) end 458s Printing per-atom forces (kJ/mol/A). 458s Legend: 458s tot n -- Total force for atom n 458s qf n -- Fixed charge force for atom n 458s db n -- Dielectric boundary force for atom n 458s ib n -- Ionic boundary force for atom n 458s tot all -- Total force for system 458s qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 458s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 458s db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 458s tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 458s qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 458s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 458s db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 458s tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 458s tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 458s 458s print APOL energy 1 (asolv) end 458s Global net APOL energy = -1.365306965532E+01 kJ/mol 458s 458s print APOL force 1 (asolv) end 458s Printing per atom forces (kJ/mol/A) 458s Legend: 458s tot n -- Total force for atom n 458s sasa n -- SASA force for atom n 458s sav n -- SAV force for atom n 458s wca n -- WCA force for atom n 458s tot all -- Total force for system 458s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 458s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 458s wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 458s tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 458s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 458s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 458s wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 458s tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 458s tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 458s ---------------------------------------- 458s CLEANING UP AND SHUTTING DOWN... 458s Destroying force arrays. 458s No energy arrays to destroy. 458s Destroying multigrid structures. 458s Destroying finite element structures. 458s Destroying 1 molecules 458s Final memory usage: 60.711 MB total, 62.250 MB high water 458s 458s 458s Thanks for using APBS! 458s 458s *** PASSED *** 458s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 458s *** PASSED *** 458s Elapsed time: 6.51907 seconds 458s -------------------------------------------------------------------------------- 458s Total elapsed time: 6.51907 seconds 458s Test results have been logged 458s -------------------------------------------------------------------------------- 458s -------------------------------------------------------------------------------- 458s Testing input file apbs-mol-vdw.in 458s 474s Checking for intermediate energies in input file ion-pmf.out 474s EXPECTED COMPUTED: 4 474s EXPECTED EXPECTED: 4 474s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] 474s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 474s COMPUTED RESULT 7839.535983197 474s COMPUTED RESULT 8964.727588811 474s COMPUTED RESULT -1125.191605614 474s COMPUTED RESULT -13.65306965532 474s Running tests for pka-lig section 474s BINARY: /usr/bin/apbs 474s INPUT: apbs-mol-vdw.in 474s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 474s asc_getToken: Error occurred (bailing out). 474s Vio_scanf: Format problem with input. 474s 474s 474s ---------------------------------------------------------------------- 474s APBS -- Adaptive Poisson-Boltzmann Solver 474s Version APBS 3.4.1 474s 474s Nathan A. Baker (nathan.baker@pnnl.gov) 474s Pacific Northwest National Laboratory 474s 474s Additional contributing authors listed in the code documentation. 474s 474s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 474s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 474s Northwest Division for the U.S. Department of Energy. 474s 474s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 474s Portions Copyright (c) 2002-2020, Nathan A. Baker. 474s Portions Copyright (c) 1999-2002, The Regents of the University of California. 474s Portions Copyright (c) 1995, Michael Holst. 474s All rights reserved. 474s 474s Redistribution and use in source and binary forms, with or without 474s modification, are permitted provided that the following conditions are met: 474s 474s * Redistributions of source code must retain the above copyright notice, this 474s list of conditions and the following disclaimer. 474s 474s * Redistributions in binary form must reproduce the above copyright notice, 474s this list of conditions and the following disclaimer in the documentation 474s and/or other materials provided with the distribution. 474s 474s * Neither the name of the developer nor the names of its contributors may be 474s used to endorse or promote products derived from this software without 474s specific prior written permission. 474s 474s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 474s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 474s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 474s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 474s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 474s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 474s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 474s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 474s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 474s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 474s ---------------------------------------------------------------------- 474s APBS uses FETK (the Finite Element ToolKit) to solve the 474s Poisson-Boltzmann equation numerically. FETK is a portable collection 474s of finite element modeling class libraries developed by the Michael Holst 474s research group and written in an object-oriented form of C. FEtk is 474s designed to solve general coupled systems of nonlinear partial differential 474s equations using adaptive finite element methods, inexact Newton methods, 474s and algebraic multilevel methods. More information about FEtk may be found 474s at . 474s ---------------------------------------------------------------------- 474s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 474s Aqua is a modified form of the Holst group PMG library 474s which has been modified by Patrice Koehl 474s for improved efficiency and 474s memory usage when solving the Poisson-Boltzmann equation. 474s ---------------------------------------------------------------------- 474s Please cite your use of APBS as: 474s 474s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 474s nanosystems: application to microtubules and the ribosome. Proc. 474s Natl. Acad. Sci. USA 98, 10037-10041 2001. 474s 474s 474s This executable compiled on Jan 3 2025 at 11:01:42 474s 474s Parsing input file apbs-mol-vdw.in... 474s rank 0 size 1... 474s Parsed input file. 474s Got paths for 3 molecules 474s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 474s asc_getToken: Error occurred (bailing out). 474s Vio_scanf: Format problem with input. 474s 47 atoms 474s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 474s Net charge 1.11e-16 e 474s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 474s asc_getToken: Error occurred (bailing out). 474s Vio_scanf: Format problem with input. 474s 3423 atoms 474s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 474s Net charge 1.00e+00 e 474s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 474s 3470 atoms 474s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 474s Net charge 1.00e+00 e 474s Preparing to run 6 PBE calculations. 474s ---------------------------------------- 474s CALCULATION #1 (lig-coarse): MULTIGRID 474s Setting up problem... 474s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 474s Debye length: 0 A 474s Current memory usage: 204.292 MB total, 204.292 MB high water 474s Using linear spline charge discretization. 474s Grid dimensions: 97 x 97 x 97 474s Grid spacings: 0.729 x 0.729 x 0.729 474s Grid lengths: 70.000 x 70.000 x 70.000 474s Grid center: (28.969, -32.507, 27.022) 474s Multigrid levels: 4 474s Molecule ID: 1 474s Linearized traditional PBE 474s Single Debye-Huckel sphere boundary conditions 474s 2 ion species (0.000 M ionic strength): 474s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 474s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 474s Solute dielectric: 2.000 474s Solvent dielectric: 78.000 474s Using "molecular" surface definition; no smoothing 474s Solvent probe radius: 0.000 A 474s Temperature: 298.150 K 474s Electrostatic energies will be calculated 474s Total electrostatic energy = 2.224988750664E+03 kJ/mol 474s Calculating forces... 474s ---------------------------------------- 474s CALCULATION #2 (lig-fine): MULTIGRID 474s Setting up problem... 474s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 474s Debye length: 0 A 474s Current memory usage: 204.292 MB total, 406.001 MB high water 474s Using linear spline charge discretization. 474s Grid dimensions: 97 x 97 x 97 474s Grid spacings: 0.250 x 0.250 x 0.250 474s Grid lengths: 24.000 x 24.000 x 24.000 474s Grid center: (24.822, -33.153, 21.545) 474s Multigrid levels: 4 474s Molecule ID: 1 474s Linearized traditional PBE 474s Boundary conditions from focusing 474s 2 ion species (0.000 M ionic strength): 474s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 474s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 474s Solute dielectric: 2.000 474s Solvent dielectric: 78.000 474s Using "molecular" surface definition; no smoothing 474s Solvent probe radius: 0.000 A 474s Temperature: 298.150 K 474s Electrostatic energies will be calculated 474s Total electrostatic energy = 1.049695084686E+04 kJ/mol 474s Calculating forces... 474s ---------------------------------------- 474s CALCULATION #3 (pka-coarse): MULTIGRID 474s Setting up problem... 474s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 474s Debye length: 0 A 474s Current memory usage: 291.151 MB total, 406.001 MB high water 474s Using linear spline charge discretization. 474s Grid dimensions: 97 x 97 x 97 474s Grid spacings: 0.729 x 0.729 x 0.729 474s Grid lengths: 70.000 x 70.000 x 70.000 474s Grid center: (28.969, -32.507, 27.022) 474s Multigrid levels: 4 474s Molecule ID: 2 474s Linearized traditional PBE 474s Single Debye-Huckel sphere boundary conditions 474s 2 ion species (0.000 M ionic strength): 474s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 474s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 474s Solute dielectric: 2.000 474s Solvent dielectric: 78.000 474s Using "molecular" surface definition; no smoothing 474s Solvent probe radius: 0.000 A 474s Temperature: 298.150 K 474s Electrostatic energies will be calculated 474s Total electrostatic energy = 1.818450789522E+05 kJ/mol 474s Calculating forces... 474s [focusFillBound()]: WARNING: 474s Unusually large potential values 474s detected on the focusing boundary! 474s Convergence not guaranteed for NPBE/NRPBE calculations! 474s 474s ---------------------------------------- 474s CALCULATION #4 (pka-fine): MULTIGRID 474s Setting up problem... 474s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 474s Debye length: 0 A 474s Current memory usage: 291.151 MB total, 533.426 MB high water 474s Using linear spline charge discretization. 474s Grid dimensions: 97 x 97 x 97 474s Grid spacings: 0.250 x 0.250 x 0.250 474s Grid lengths: 24.000 x 24.000 x 24.000 474s Grid center: (24.822, -33.153, 21.545) 474s Multigrid levels: 4 474s Molecule ID: 2 474s Linearized traditional PBE 474s Boundary conditions from focusing 474s 2 ion species (0.000 M ionic strength): 474s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 474s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 474s Solute dielectric: 2.000 474s Solvent dielectric: 78.000 474s Using "molecular" surface definition; no smoothing 474s Solvent probe radius: 0.000 A 474s Temperature: 298.150 K 474s Electrostatic energies will be calculated 474s Total electrostatic energy = 3.008254338259E+05 kJ/mol 474s Calculating forces... 474s ---------------------------------------- 474s CALCULATION #5 (complex-coarse): MULTIGRID 474s Setting up problem... 474s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 474s Debye length: 0 A 474s Current memory usage: 292.063 MB total, 533.426 MB high water 474s Using linear spline charge discretization. 474s Grid dimensions: 97 x 97 x 97 474s Grid spacings: 0.729 x 0.729 x 0.729 474s Grid lengths: 70.000 x 70.000 x 70.000 474s Grid center: (28.969, -32.507, 27.022) 474s Multigrid levels: 4 474s Molecule ID: 3 474s Linearized traditional PBE 474s Single Debye-Huckel sphere boundary conditions 474s 2 ion species (0.000 M ionic strength): 474s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 474s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 474s Solute dielectric: 2.000 474s Solvent dielectric: 78.000 474s Using "molecular" surface definition; no smoothing 474s Solvent probe radius: 0.000 A 474s Temperature: 298.150 K 474s Electrostatic energies will be calculated 474s Total electrostatic energy = 1.840918409896E+05 kJ/mol 474s Calculating forces... 474s [focusFillBound()]: WARNING: 474s Unusually large potential values 474s detected on the focusing boundary! 474s Convergence not guaranteed for NPBE/NRPBE calculations! 474s 474s ---------------------------------------- 474s CALCULATION #6 (complex-fine): MULTIGRID 474s Setting up problem... 474s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 474s Debye length: 0 A 474s Current memory usage: 292.063 MB total, 534.806 MB high water 474s Using linear spline charge discretization. 474s Grid dimensions: 97 x 97 x 97 474s Grid spacings: 0.250 x 0.250 x 0.250 474s Grid lengths: 24.000 x 24.000 x 24.000 474s Grid center: (24.822, -33.153, 21.545) 474s Multigrid levels: 4 474s Molecule ID: 3 474s Linearized traditional PBE 474s Boundary conditions from focusing 474s 2 ion species (0.000 M ionic strength): 474s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 474s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 474s Solute dielectric: 2.000 474s Solvent dielectric: 78.000 474s Using "molecular" surface definition; no smoothing 474s Solvent probe radius: 0.000 A 474s Temperature: 298.150 K 474s Electrostatic energies will be calculated 474s Total electrostatic energy = 3.113304681884E+05 kJ/mol 474s Calculating forces... 474s ---------------------------------------- 474s PRINT STATEMENTS 474s 474s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 474s Local net energy (PE 0) = 8.083515648803E+00 kJ/mol 474s Global net ELEC energy = 8.083515648803E+00 kJ/mol 474s ---------------------------------------- 474s CLEANING UP AND SHUTTING DOWN... 474s Destroying force arrays. 474s No energy arrays to destroy. 474s Destroying multigrid structures. 474s Destroying finite element structures. 474s Destroying 3 molecules 474s Final memory usage: 0.001 MB total, 534.806 MB high water 474s 474s 474s Thanks for using APBS! 474s 474s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 474s *** PASSED *** 474s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 474s *** PASSED *** 474s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 474s *** PASSED *** 474s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 474s *** PASSED *** 474s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 474s *** PASSED *** 474s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 474s *** PASSED *** 474s Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) 474s *** PASSED *** 474s Elapsed time: 16.337012 seconds 474s -------------------------------------------------------------------------------- 474s -------------------------------------------------------------------------------- 474s Testing input file apbs-smol-vdw.in 474s 486s Checking for intermediate energies in input file apbs-mol-vdw.out 486s EXPECTED COMPUTED: 7 486s EXPECTED EXPECTED: 7 486s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] 486s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 486s COMPUTED RESULT 2224.988750664 486s COMPUTED RESULT 10496.95084686 486s COMPUTED RESULT 181845.0789522 486s COMPUTED RESULT 300825.4338259 486s COMPUTED RESULT 184091.8409896 486s COMPUTED RESULT 311330.4681884 486s COMPUTED RESULT 8.083515648803 486s BINARY: /usr/bin/apbs 486s INPUT: apbs-smol-vdw.in 486s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 486s asc_getToken: Error occurred (bailing out). 486s Vio_scanf: Format problem with input. 486s 486s 486s ---------------------------------------------------------------------- 486s APBS -- Adaptive Poisson-Boltzmann Solver 486s Version APBS 3.4.1 486s 486s Nathan A. Baker (nathan.baker@pnnl.gov) 486s Pacific Northwest National Laboratory 486s 486s Additional contributing authors listed in the code documentation. 486s 486s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 486s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 486s Northwest Division for the U.S. Department of Energy. 486s 486s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 486s Portions Copyright (c) 2002-2020, Nathan A. Baker. 486s Portions Copyright (c) 1999-2002, The Regents of the University of California. 486s Portions Copyright (c) 1995, Michael Holst. 486s All rights reserved. 486s 486s Redistribution and use in source and binary forms, with or without 486s modification, are permitted provided that the following conditions are met: 486s 486s * Redistributions of source code must retain the above copyright notice, this 486s list of conditions and the following disclaimer. 486s 486s * Redistributions in binary form must reproduce the above copyright notice, 486s this list of conditions and the following disclaimer in the documentation 486s and/or other materials provided with the distribution. 486s 486s * Neither the name of the developer nor the names of its contributors may be 486s used to endorse or promote products derived from this software without 486s specific prior written permission. 486s 486s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 486s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 486s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 486s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 486s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 486s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 486s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 486s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 486s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 486s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 486s ---------------------------------------------------------------------- 486s APBS uses FETK (the Finite Element ToolKit) to solve the 486s Poisson-Boltzmann equation numerically. FETK is a portable collection 486s of finite element modeling class libraries developed by the Michael Holst 486s research group and written in an object-oriented form of C. FEtk is 486s designed to solve general coupled systems of nonlinear partial differential 486s equations using adaptive finite element methods, inexact Newton methods, 486s and algebraic multilevel methods. More information about FEtk may be found 486s at . 486s ---------------------------------------------------------------------- 486s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 486s Aqua is a modified form of the Holst group PMG library 486s which has been modified by Patrice Koehl 486s for improved efficiency and 486s memory usage when solving the Poisson-Boltzmann equation. 486s ---------------------------------------------------------------------- 486s Please cite your use of APBS as: 486s 486s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 486s nanosystems: application to microtubules and the ribosome. Proc. 486s Natl. Acad. Sci. USA 98, 10037-10041 2001. 486s 486s 486s This executable compiled on Jan 3 2025 at 11:01:42 486s 486s Parsing input file apbs-smol-vdw.in... 486s rank 0 size 1... 486s Parsed input file. 486s Got paths for 3 molecules 486s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 486s asc_getToken: Error occurred (bailing out). 486s Vio_scanf: Format problem with input. 486s 47 atoms 486s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 486s Net charge 1.11e-16 e 486s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 486s asc_getToken: Error occurred (bailing out). 486s Vio_scanf: Format problem with input. 486s 3423 atoms 486s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 486s Net charge 1.00e+00 e 486s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 486s 3470 atoms 486s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 486s Net charge 1.00e+00 e 486s Preparing to run 6 PBE calculations. 486s ---------------------------------------- 486s CALCULATION #1 (lig-coarse): MULTIGRID 486s Setting up problem... 486s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 486s Debye length: 0 A 486s Current memory usage: 204.292 MB total, 204.292 MB high water 486s Using linear spline charge discretization. 486s Grid dimensions: 97 x 97 x 97 486s Grid spacings: 0.729 x 0.729 x 0.729 486s Grid lengths: 70.000 x 70.000 x 70.000 486s Grid center: (28.969, -32.507, 27.022) 486s Multigrid levels: 4 486s Molecule ID: 1 486s Linearized traditional PBE 486s Single Debye-Huckel sphere boundary conditions 486s 2 ion species (0.000 M ionic strength): 486s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 486s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 486s Solute dielectric: 2.000 486s Solvent dielectric: 78.000 486s Using "molecular" surface definition;harmonic average smoothing 486s Solvent probe radius: 0.000 A 486s Temperature: 298.150 K 486s Electrostatic energies will be calculated 486s Total electrostatic energy = 2.226793167046E+03 kJ/mol 486s Calculating forces... 486s ---------------------------------------- 486s CALCULATION #2 (lig-fine): MULTIGRID 486s Setting up problem... 486s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 486s Debye length: 0 A 486s Current memory usage: 204.292 MB total, 406.001 MB high water 486s Using linear spline charge discretization. 486s Grid dimensions: 97 x 97 x 97 486s Grid spacings: 0.250 x 0.250 x 0.250 486s Grid lengths: 24.000 x 24.000 x 24.000 486s Grid center: (24.822, -33.153, 21.545) 486s Multigrid levels: 4 486s Molecule ID: 1 486s Linearized traditional PBE 486s Boundary conditions from focusing 486s 2 ion species (0.000 M ionic strength): 486s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 486s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 486s Solute dielectric: 2.000 486s Solvent dielectric: 78.000 486s Using "molecular" surface definition;harmonic average smoothing 486s Solvent probe radius: 0.000 A 486s Temperature: 298.150 K 486s Electrostatic energies will be calculated 486s Total electrostatic energy = 1.050504485887E+04 kJ/mol 486s Calculating forces... 486s ---------------------------------------- 486s CALCULATION #3 (pka-coarse): MULTIGRID 486s Setting up problem... 486s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 486s Debye length: 0 A 486s Current memory usage: 291.151 MB total, 406.001 MB high water 486s Using linear spline charge discretization. 486s Grid dimensions: 97 x 97 x 97 486s Grid spacings: 0.729 x 0.729 x 0.729 486s Grid lengths: 70.000 x 70.000 x 70.000 486s Grid center: (28.969, -32.507, 27.022) 486s Multigrid levels: 4 486s Molecule ID: 2 486s Linearized traditional PBE 486s Single Debye-Huckel sphere boundary conditions 486s 2 ion species (0.000 M ionic strength): 486s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 486s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 486s Solute dielectric: 2.000 486s Solvent dielectric: 78.000 486s Using "molecular" surface definition;harmonic average smoothing 486s Solvent probe radius: 0.000 A 486s Temperature: 298.150 K 486s Electrostatic energies will be calculated 486s Total electrostatic energy = 1.827976621645E+05 kJ/mol 486s Calculating forces... 486s [focusFillBound()]: WARNING: 486s Unusually large potential values 486s detected on the focusing boundary! 486s Convergence not guaranteed for NPBE/NRPBE calculations! 486s 486s ---------------------------------------- 486s CALCULATION #4 (pka-fine): MULTIGRID 486s Setting up problem... 486s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 486s Debye length: 0 A 486s Current memory usage: 291.151 MB total, 533.426 MB high water 486s Using linear spline charge discretization. 486s Grid dimensions: 97 x 97 x 97 486s Grid spacings: 0.250 x 0.250 x 0.250 486s Grid lengths: 24.000 x 24.000 x 24.000 486s Grid center: (24.822, -33.153, 21.545) 486s Multigrid levels: 4 486s Molecule ID: 2 486s Linearized traditional PBE 486s Boundary conditions from focusing 486s 2 ion species (0.000 M ionic strength): 486s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 486s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 486s Solute dielectric: 2.000 486s Solvent dielectric: 78.000 486s Using "molecular" surface definition;harmonic average smoothing 486s Solvent probe radius: 0.000 A 486s Temperature: 298.150 K 486s Electrostatic energies will be calculated 486s Total electrostatic energy = 3.017228546773E+05 kJ/mol 486s Calculating forces... 486s ---------------------------------------- 486s CALCULATION #5 (complex-coarse): MULTIGRID 486s Setting up problem... 486s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 486s Debye length: 0 A 486s Current memory usage: 292.063 MB total, 533.426 MB high water 486s Using linear spline charge discretization. 486s Grid dimensions: 97 x 97 x 97 486s Grid spacings: 0.729 x 0.729 x 0.729 486s Grid lengths: 70.000 x 70.000 x 70.000 486s Grid center: (28.969, -32.507, 27.022) 486s Multigrid levels: 4 486s Molecule ID: 3 486s Linearized traditional PBE 486s Single Debye-Huckel sphere boundary conditions 486s 2 ion species (0.000 M ionic strength): 486s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 486s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 486s Solute dielectric: 2.000 486s Solvent dielectric: 78.000 486s Using "molecular" surface definition;harmonic average smoothing 486s Solvent probe radius: 0.000 A 486s Temperature: 298.150 K 486s Electrostatic energies will be calculated 486s Total electrostatic energy = 1.850819075387E+05 kJ/mol 486s Calculating forces... 486s [focusFillBound()]: WARNING: 486s Unusually large potential values 486s detected on the focusing boundary! 486s Convergence not guaranteed for NPBE/NRPBE calculations! 486s 486s ---------------------------------------- 486s CALCULATION #6 (complex-fine): MULTIGRID 486s Setting up problem... 486s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 486s Debye length: 0 A 486s Current memory usage: 292.063 MB total, 534.806 MB high water 486s Using linear spline charge discretization. 486s Grid dimensions: 97 x 97 x 97 486s Grid spacings: 0.250 x 0.250 x 0.250 486s Grid lengths: 24.000 x 24.000 x 24.000 486s Grid center: (24.822, -33.153, 21.545) 486s Multigrid levels: 4 486s Molecule ID: 3 486s Linearized traditional PBE 486s Boundary conditions from focusing 486s 2 ion species (0.000 M ionic strength): 486s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 486s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 486s Solute dielectric: 2.000 486s Solvent dielectric: 78.000 486s Using "molecular" surface definition;harmonic average smoothing 486s Solvent probe radius: 0.000 A 486s Temperature: 298.150 K 486s Electrostatic energies will be calculated 486s Total electrostatic energy = 3.122488625388E+05 kJ/mol 486s Calculating forces... 486s ---------------------------------------- 486s PRINT STATEMENTS 486s 486s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 486s Local net energy (PE 0) = 2.096300255720E+01 kJ/mol 486s Global net ELEC energy = 2.096300255720E+01 kJ/mol 486s ---------------------------------------- 486s CLEANING UP AND SHUTTING DOWN... 486s Destroying force arrays. 486s No energy arrays to destroy. 486s Destroying multigrid structures. 486s Destroying finite element structures. 486s Destroying 3 molecules 486s Final memory usage: 0.001 MB total, 534.806 MB high water 486s 486s 486s Thanks for using APBS! 486s 487s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 487s *** PASSED *** 487s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 487s *** PASSED *** 487s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 487s *** PASSED *** 487s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 487s *** PASSED *** 487s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 487s *** PASSED *** 487s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 487s *** PASSED *** 487s Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) 487s *** PASSED *** 487s Elapsed time: 12.608553 seconds 487s -------------------------------------------------------------------------------- 487s -------------------------------------------------------------------------------- 487s Testing input file apbs-mol-surf.in 487s 500s Checking for intermediate energies in input file apbs-smol-vdw.out 500s EXPECTED COMPUTED: 7 500s EXPECTED EXPECTED: 7 500s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] 500s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 500s COMPUTED RESULT 2226.793167046 500s COMPUTED RESULT 10505.04485887 500s COMPUTED RESULT 182797.6621645 500s COMPUTED RESULT 301722.8546773 500s COMPUTED RESULT 185081.9075387 500s COMPUTED RESULT 312248.8625388 500s COMPUTED RESULT 20.9630025572 500s BINARY: /usr/bin/apbs 500s INPUT: apbs-mol-surf.in 500s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 500s asc_getToken: Error occurred (bailing out). 500s Vio_scanf: Format problem with input. 500s 500s 500s ---------------------------------------------------------------------- 500s APBS -- Adaptive Poisson-Boltzmann Solver 500s Version APBS 3.4.1 500s 500s Nathan A. Baker (nathan.baker@pnnl.gov) 500s Pacific Northwest National Laboratory 500s 500s Additional contributing authors listed in the code documentation. 500s 500s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 500s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 500s Northwest Division for the U.S. Department of Energy. 500s 500s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 500s Portions Copyright (c) 2002-2020, Nathan A. Baker. 500s Portions Copyright (c) 1999-2002, The Regents of the University of California. 500s Portions Copyright (c) 1995, Michael Holst. 500s All rights reserved. 500s 500s Redistribution and use in source and binary forms, with or without 500s modification, are permitted provided that the following conditions are met: 500s 500s * Redistributions of source code must retain the above copyright notice, this 500s list of conditions and the following disclaimer. 500s 500s * Redistributions in binary form must reproduce the above copyright notice, 500s this list of conditions and the following disclaimer in the documentation 500s and/or other materials provided with the distribution. 500s 500s * Neither the name of the developer nor the names of its contributors may be 500s used to endorse or promote products derived from this software without 500s specific prior written permission. 500s 500s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 500s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 500s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 500s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 500s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 500s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 500s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 500s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 500s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 500s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 500s ---------------------------------------------------------------------- 500s APBS uses FETK (the Finite Element ToolKit) to solve the 500s Poisson-Boltzmann equation numerically. FETK is a portable collection 500s of finite element modeling class libraries developed by the Michael Holst 500s research group and written in an object-oriented form of C. FEtk is 500s designed to solve general coupled systems of nonlinear partial differential 500s equations using adaptive finite element methods, inexact Newton methods, 500s and algebraic multilevel methods. More information about FEtk may be found 500s at . 500s ---------------------------------------------------------------------- 500s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 500s Aqua is a modified form of the Holst group PMG library 500s which has been modified by Patrice Koehl 500s for improved efficiency and 500s memory usage when solving the Poisson-Boltzmann equation. 500s ---------------------------------------------------------------------- 500s Please cite your use of APBS as: 500s 500s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 500s nanosystems: application to microtubules and the ribosome. Proc. 500s Natl. Acad. Sci. USA 98, 10037-10041 2001. 500s 500s 500s This executable compiled on Jan 3 2025 at 11:01:42 500s 500s Parsing input file apbs-mol-surf.in... 500s rank 0 size 1... 500s Parsed input file. 500s Got paths for 3 molecules 500s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 500s asc_getToken: Error occurred (bailing out). 500s Vio_scanf: Format problem with input. 500s 47 atoms 500s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 500s Net charge 1.11e-16 e 500s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 500s asc_getToken: Error occurred (bailing out). 500s Vio_scanf: Format problem with input. 500s 3423 atoms 500s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 500s Net charge 1.00e+00 e 500s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 500s 3470 atoms 500s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 500s Net charge 1.00e+00 e 500s Preparing to run 6 PBE calculations. 500s ---------------------------------------- 500s CALCULATION #1 (lig-coarse): MULTIGRID 500s Setting up problem... 500s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 500s Debye length: 0 A 500s Current memory usage: 203.877 MB total, 203.877 MB high water 500s Using linear spline charge discretization. 500s Grid dimensions: 97 x 97 x 97 500s Grid spacings: 0.729 x 0.729 x 0.729 500s Grid lengths: 70.000 x 70.000 x 70.000 500s Grid center: (28.969, -32.507, 27.022) 500s Multigrid levels: 4 500s Molecule ID: 1 500s Linearized traditional PBE 500s Single Debye-Huckel sphere boundary conditions 500s 2 ion species (0.000 M ionic strength): 500s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 500s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 500s Solute dielectric: 2.000 500s Solvent dielectric: 78.000 500s Using "molecular" surface definition; no smoothing 500s Solvent probe radius: 1.400 A 500s Temperature: 298.150 K 500s Electrostatic energies will be calculated 500s Total electrostatic energy = 2.244350164274E+03 kJ/mol 500s Calculating forces... 500s ---------------------------------------- 500s CALCULATION #2 (lig-fine): MULTIGRID 500s Setting up problem... 500s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 500s Debye length: 0 A 500s Current memory usage: 203.877 MB total, 405.586 MB high water 500s Using linear spline charge discretization. 500s Grid dimensions: 97 x 97 x 97 500s Grid spacings: 0.250 x 0.250 x 0.250 500s Grid lengths: 24.000 x 24.000 x 24.000 500s Grid center: (24.822, -33.153, 21.545) 500s Multigrid levels: 4 500s Molecule ID: 1 500s Linearized traditional PBE 500s Boundary conditions from focusing 500s 2 ion species (0.000 M ionic strength): 500s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 500s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 500s Solute dielectric: 2.000 500s Solvent dielectric: 78.000 500s Using "molecular" surface definition; no smoothing 500s Solvent probe radius: 1.400 A 500s Temperature: 298.150 K 500s Electrostatic energies will be calculated 500s Total electrostatic energy = 1.052149475373E+04 kJ/mol 500s Calculating forces... 500s ---------------------------------------- 500s CALCULATION #3 (pka-coarse): MULTIGRID 500s Setting up problem... 500s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 500s Debye length: 0 A 500s Current memory usage: 251.521 MB total, 405.586 MB high water 500s Using linear spline charge discretization. 500s Grid dimensions: 97 x 97 x 97 500s Grid spacings: 0.729 x 0.729 x 0.729 500s Grid lengths: 70.000 x 70.000 x 70.000 500s Grid center: (28.969, -32.507, 27.022) 500s Multigrid levels: 4 500s Molecule ID: 2 500s Linearized traditional PBE 500s Single Debye-Huckel sphere boundary conditions 500s 2 ion species (0.000 M ionic strength): 500s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 500s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 500s Solute dielectric: 2.000 500s Solvent dielectric: 78.000 500s Using "molecular" surface definition; no smoothing 500s Solvent probe radius: 1.400 A 500s Temperature: 298.150 K 500s Electrostatic energies will be calculated 500s Total electrostatic energy = 1.862615690066E+05 kJ/mol 500s Calculating forces... 500s [focusFillBound()]: WARNING: 500s Unusually large potential values 500s detected on the focusing boundary! 500s Convergence not guaranteed for NPBE/NRPBE calculations! 500s 500s ---------------------------------------- 500s CALCULATION #4 (pka-fine): MULTIGRID 500s Setting up problem... 500s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 500s Debye length: 0 A 500s Current memory usage: 251.521 MB total, 493.795 MB high water 500s Using linear spline charge discretization. 500s Grid dimensions: 97 x 97 x 97 500s Grid spacings: 0.250 x 0.250 x 0.250 500s Grid lengths: 24.000 x 24.000 x 24.000 500s Grid center: (24.822, -33.153, 21.545) 500s Multigrid levels: 4 500s Molecule ID: 2 500s Linearized traditional PBE 500s Boundary conditions from focusing 500s 2 ion species (0.000 M ionic strength): 500s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 500s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 500s Solute dielectric: 2.000 500s Solvent dielectric: 78.000 500s Using "molecular" surface definition; no smoothing 500s Solvent probe radius: 1.400 A 500s Temperature: 298.150 K 500s Electrostatic energies will be calculated 500s Total electrostatic energy = 3.051810884053E+05 kJ/mol 500s Calculating forces... 500s ---------------------------------------- 500s CALCULATION #5 (complex-coarse): MULTIGRID 500s Setting up problem... 500s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 500s Debye length: 0 A 500s Current memory usage: 251.858 MB total, 493.795 MB high water 500s Using linear spline charge discretization. 500s Grid dimensions: 97 x 97 x 97 500s Grid spacings: 0.729 x 0.729 x 0.729 500s Grid lengths: 70.000 x 70.000 x 70.000 500s Grid center: (28.969, -32.507, 27.022) 500s Multigrid levels: 4 500s Molecule ID: 3 500s Linearized traditional PBE 500s Single Debye-Huckel sphere boundary conditions 500s 2 ion species (0.000 M ionic strength): 500s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 500s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 500s Solute dielectric: 2.000 500s Solvent dielectric: 78.000 500s Using "molecular" surface definition; no smoothing 500s Solvent probe radius: 1.400 A 500s Temperature: 298.150 K 500s Electrostatic energies will be calculated 500s Total electrostatic energy = 1.886625455219E+05 kJ/mol 500s Calculating forces... 500s [focusFillBound()]: WARNING: 500s Unusually large potential values 500s detected on the focusing boundary! 500s Convergence not guaranteed for NPBE/NRPBE calculations! 500s 500s ---------------------------------------- 500s CALCULATION #6 (complex-fine): MULTIGRID 500s Setting up problem... 500s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 500s Debye length: 0 A 500s Current memory usage: 251.858 MB total, 494.601 MB high water 500s Using linear spline charge discretization. 500s Grid dimensions: 97 x 97 x 97 500s Grid spacings: 0.250 x 0.250 x 0.250 500s Grid lengths: 24.000 x 24.000 x 24.000 500s Grid center: (24.822, -33.153, 21.545) 500s Multigrid levels: 4 500s Molecule ID: 3 500s Linearized traditional PBE 500s Boundary conditions from focusing 500s 2 ion species (0.000 M ionic strength): 500s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 500s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 500s Solute dielectric: 2.000 500s Solvent dielectric: 78.000 500s Using "molecular" surface definition; no smoothing 500s Solvent probe radius: 1.400 A 500s Temperature: 298.150 K 500s Electrostatic energies will be calculated 500s Total electrostatic energy = 3.158218439277E+05 kJ/mol 500s Calculating forces... 500s ---------------------------------------- 500s PRINT STATEMENTS 500s 500s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 500s Local net energy (PE 0) = 1.192607686582E+02 kJ/mol 500s Global net ELEC energy = 1.192607686582E+02 kJ/mol 500s ---------------------------------------- 500s CLEANING UP AND SHUTTING DOWN... 500s Destroying force arrays. 500s No energy arrays to destroy. 500s Destroying multigrid structures. 500s Destroying finite element structures. 500s Destroying 3 molecules 500s Final memory usage: 0.001 MB total, 494.601 MB high water 500s 500s 500s Thanks for using APBS! 500s 500s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 501s *** PASSED *** 501s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 501s *** PASSED *** 501s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 501s *** PASSED *** 501s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 501s *** PASSED *** 501s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 501s *** PASSED *** 501s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 501s *** PASSED *** 501s Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) 501s *** PASSED *** 501s Elapsed time: 13.972157 seconds 501s -------------------------------------------------------------------------------- 501s -------------------------------------------------------------------------------- 501s Testing input file apbs-smol-surf.in 501s 512s Checking for intermediate energies in input file apbs-mol-surf.out 512s EXPECTED COMPUTED: 7 512s EXPECTED EXPECTED: 7 512s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] 512s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 512s COMPUTED RESULT 2244.350164274 512s COMPUTED RESULT 10521.49475373 512s COMPUTED RESULT 186261.5690066 512s COMPUTED RESULT 305181.0884053 512s COMPUTED RESULT 188662.5455219 512s COMPUTED RESULT 315821.8439277 512s COMPUTED RESULT 119.2607686582 512s BINARY: /usr/bin/apbs 512s INPUT: apbs-smol-surf.in 512s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 512s asc_getToken: Error occurred (bailing out). 512s Vio_scanf: Format problem with input. 512s 512s 512s ---------------------------------------------------------------------- 512s APBS -- Adaptive Poisson-Boltzmann Solver 512s Version APBS 3.4.1 512s 512s Nathan A. Baker (nathan.baker@pnnl.gov) 512s Pacific Northwest National Laboratory 512s 512s Additional contributing authors listed in the code documentation. 512s 512s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 512s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 512s Northwest Division for the U.S. Department of Energy. 512s 512s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 512s Portions Copyright (c) 2002-2020, Nathan A. Baker. 512s Portions Copyright (c) 1999-2002, The Regents of the University of California. 512s Portions Copyright (c) 1995, Michael Holst. 512s All rights reserved. 512s 512s Redistribution and use in source and binary forms, with or without 512s modification, are permitted provided that the following conditions are met: 512s 512s * Redistributions of source code must retain the above copyright notice, this 512s list of conditions and the following disclaimer. 512s 512s * Redistributions in binary form must reproduce the above copyright notice, 512s this list of conditions and the following disclaimer in the documentation 512s and/or other materials provided with the distribution. 512s 512s * Neither the name of the developer nor the names of its contributors may be 512s used to endorse or promote products derived from this software without 512s specific prior written permission. 512s 512s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 512s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 512s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 512s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 512s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 512s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 512s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 512s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 512s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 512s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 512s ---------------------------------------------------------------------- 512s APBS uses FETK (the Finite Element ToolKit) to solve the 512s Poisson-Boltzmann equation numerically. FETK is a portable collection 512s of finite element modeling class libraries developed by the Michael Holst 512s research group and written in an object-oriented form of C. FEtk is 512s designed to solve general coupled systems of nonlinear partial differential 512s equations using adaptive finite element methods, inexact Newton methods, 512s and algebraic multilevel methods. More information about FEtk may be found 512s at . 512s ---------------------------------------------------------------------- 512s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 512s Aqua is a modified form of the Holst group PMG library 512s which has been modified by Patrice Koehl 512s for improved efficiency and 512s memory usage when solving the Poisson-Boltzmann equation. 512s ---------------------------------------------------------------------- 512s Please cite your use of APBS as: 512s 512s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 512s nanosystems: application to microtubules and the ribosome. Proc. 512s Natl. Acad. Sci. USA 98, 10037-10041 2001. 512s 512s 512s This executable compiled on Jan 3 2025 at 11:01:42 512s 512s Parsing input file apbs-smol-surf.in... 512s rank 0 size 1... 512s Parsed input file. 512s Got paths for 3 molecules 512s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 512s asc_getToken: Error occurred (bailing out). 512s Vio_scanf: Format problem with input. 512s 47 atoms 512s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 512s Net charge 1.11e-16 e 512s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 512s asc_getToken: Error occurred (bailing out). 512s Vio_scanf: Format problem with input. 512s 3423 atoms 512s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 512s Net charge 1.00e+00 e 512s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 512s 3470 atoms 512s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 512s Net charge 1.00e+00 e 512s Preparing to run 6 PBE calculations. 512s ---------------------------------------- 512s CALCULATION #1 (lig-coarse): MULTIGRID 512s Setting up problem... 512s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 512s Debye length: 0 A 512s Current memory usage: 203.877 MB total, 203.877 MB high water 512s Using linear spline charge discretization. 512s Grid dimensions: 97 x 97 x 97 512s Grid spacings: 0.729 x 0.729 x 0.729 512s Grid lengths: 70.000 x 70.000 x 70.000 512s Grid center: (28.969, -32.507, 27.022) 512s Multigrid levels: 4 512s Molecule ID: 1 512s Linearized traditional PBE 512s Single Debye-Huckel sphere boundary conditions 512s 2 ion species (0.000 M ionic strength): 512s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 512s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 512s Solute dielectric: 2.000 512s Solvent dielectric: 78.000 512s Using "molecular" surface definition;harmonic average smoothing 512s Solvent probe radius: 1.400 A 512s Temperature: 298.150 K 512s Electrostatic energies will be calculated 512s Total electrostatic energy = 2.251466789420E+03 kJ/mol 512s Calculating forces... 512s ---------------------------------------- 512s CALCULATION #2 (lig-fine): MULTIGRID 512s Setting up problem... 512s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 512s Debye length: 0 A 512s Current memory usage: 203.877 MB total, 405.586 MB high water 512s Using linear spline charge discretization. 512s Grid dimensions: 97 x 97 x 97 512s Grid spacings: 0.250 x 0.250 x 0.250 512s Grid lengths: 24.000 x 24.000 x 24.000 512s Grid center: (24.822, -33.153, 21.545) 512s Multigrid levels: 4 512s Molecule ID: 1 512s Linearized traditional PBE 512s Boundary conditions from focusing 512s 2 ion species (0.000 M ionic strength): 512s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 512s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 512s Solute dielectric: 2.000 512s Solvent dielectric: 78.000 512s Using "molecular" surface definition;harmonic average smoothing 512s Solvent probe radius: 1.400 A 512s Temperature: 298.150 K 512s Electrostatic energies will be calculated 512s Total electrostatic energy = 1.052814502873E+04 kJ/mol 512s Calculating forces... 512s ---------------------------------------- 512s CALCULATION #3 (pka-coarse): MULTIGRID 512s Setting up problem... 512s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 512s Debye length: 0 A 512s Current memory usage: 251.521 MB total, 405.586 MB high water 512s Using linear spline charge discretization. 512s Grid dimensions: 97 x 97 x 97 512s Grid spacings: 0.729 x 0.729 x 0.729 512s Grid lengths: 70.000 x 70.000 x 70.000 512s Grid center: (28.969, -32.507, 27.022) 512s Multigrid levels: 4 512s Molecule ID: 2 512s Linearized traditional PBE 512s Single Debye-Huckel sphere boundary conditions 512s 2 ion species (0.000 M ionic strength): 512s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 512s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 512s Solute dielectric: 2.000 512s Solvent dielectric: 78.000 512s Using "molecular" surface definition;harmonic average smoothing 512s Solvent probe radius: 1.400 A 512s Temperature: 298.150 K 512s Electrostatic energies will be calculated 512s Total electrostatic energy = 1.864071689626E+05 kJ/mol 512s Calculating forces... 512s [focusFillBound()]: WARNING: 512s Unusually large potential values 512s detected on the focusing boundary! 512s Convergence not guaranteed for NPBE/NRPBE calculations! 512s 512s ---------------------------------------- 512s CALCULATION #4 (pka-fine): MULTIGRID 512s Setting up problem... 512s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 512s Debye length: 0 A 512s Current memory usage: 251.521 MB total, 493.795 MB high water 512s Using linear spline charge discretization. 512s Grid dimensions: 97 x 97 x 97 512s Grid spacings: 0.250 x 0.250 x 0.250 512s Grid lengths: 24.000 x 24.000 x 24.000 512s Grid center: (24.822, -33.153, 21.545) 512s Multigrid levels: 4 512s Molecule ID: 2 512s Linearized traditional PBE 512s Boundary conditions from focusing 512s 2 ion species (0.000 M ionic strength): 512s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 512s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 512s Solute dielectric: 2.000 512s Solvent dielectric: 78.000 512s Using "molecular" surface definition;harmonic average smoothing 512s Solvent probe radius: 1.400 A 512s Temperature: 298.150 K 512s Electrostatic energies will be calculated 512s Total electrostatic energy = 3.053319953673E+05 kJ/mol 512s Calculating forces... 512s ---------------------------------------- 512s CALCULATION #5 (complex-coarse): MULTIGRID 512s Setting up problem... 512s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 512s Debye length: 0 A 512s Current memory usage: 251.858 MB total, 493.795 MB high water 512s Using linear spline charge discretization. 512s Grid dimensions: 97 x 97 x 97 512s Grid spacings: 0.729 x 0.729 x 0.729 512s Grid lengths: 70.000 x 70.000 x 70.000 512s Grid center: (28.969, -32.507, 27.022) 512s Multigrid levels: 4 512s Molecule ID: 3 512s Linearized traditional PBE 512s Single Debye-Huckel sphere boundary conditions 512s 2 ion species (0.000 M ionic strength): 512s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 512s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 512s Solute dielectric: 2.000 512s Solvent dielectric: 78.000 512s Using "molecular" surface definition;harmonic average smoothing 512s Solvent probe radius: 1.400 A 512s Temperature: 298.150 K 512s Electrostatic energies will be calculated 512s Total electrostatic energy = 1.888027142979E+05 kJ/mol 512s Calculating forces... 512s [focusFillBound()]: WARNING: 512s Unusually large potential values 512s detected on the focusing boundary! 512s Convergence not guaranteed for NPBE/NRPBE calculations! 512s 512s ---------------------------------------- 512s CALCULATION #6 (complex-fine): MULTIGRID 512s Setting up problem... 512s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 512s Debye length: 0 A 512s Current memory usage: 251.858 MB total, 494.601 MB high water 512s Using linear spline charge discretization. 512s Grid dimensions: 97 x 97 x 97 512s Grid spacings: 0.250 x 0.250 x 0.250 512s Grid lengths: 24.000 x 24.000 x 24.000 512s Grid center: (24.822, -33.153, 21.545) 512s Multigrid levels: 4 512s Molecule ID: 3 512s Linearized traditional PBE 512s Boundary conditions from focusing 512s 2 ion species (0.000 M ionic strength): 512s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 512s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 512s Solute dielectric: 2.000 512s Solvent dielectric: 78.000 512s Using "molecular" surface definition;harmonic average smoothing 512s Solvent probe radius: 1.400 A 512s Temperature: 298.150 K 512s Electrostatic energies will be calculated 512s Total electrostatic energy = 3.159690177241E+05 kJ/mol 512s Calculating forces... 512s ---------------------------------------- 512s PRINT STATEMENTS 512s 512s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 512s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 512s Global net ELEC energy = 1.088773280806E+02 kJ/mol 512s ---------------------------------------- 512s CLEANING UP AND SHUTTING DOWN... 512s Destroying force arrays. 512s No energy arrays to destroy. 512s Destroying multigrid structures. 512s Destroying finite element structures. 512s Destroying 3 molecules 512s Final memory usage: 0.001 MB total, 494.601 MB high water 512s 512s 512s Thanks for using APBS! 512s 512s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 512s *** PASSED *** 512s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 512s *** PASSED *** 512s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 512s *** PASSED *** 512s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 512s *** PASSED *** 512s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 512s *** PASSED *** 512s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 512s *** PASSED *** 512s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 512s *** PASSED *** 512s Elapsed time: 11.881851 seconds 512s -------------------------------------------------------------------------------- 512s Total elapsed time: 54.799573 seconds 512s Test results have been logged 512s -------------------------------------------------------------------------------- 512s -------------------------------------------------------------------------------- 512s Testing input file complex-0_1.in 512s 513s Checking for intermediate energies in input file apbs-smol-surf.out 513s EXPECTED COMPUTED: 7 513s EXPECTED EXPECTED: 7 513s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 513s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 513s COMPUTED RESULT 2251.46678942 513s COMPUTED RESULT 10528.14502873 513s COMPUTED RESULT 186407.1689626 513s COMPUTED RESULT 305331.9953673 513s COMPUTED RESULT 188802.7142979 513s COMPUTED RESULT 315969.0177241 513s COMPUTED RESULT 108.8773280806 513s Running tests for point-pmf section 513s BINARY: /usr/bin/apbs 513s INPUT: complex-0_1.in 513s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 513s asc_getToken: Error occurred (bailing out). 513s Vio_scanf: Format problem with input. 513s 513s 513s ---------------------------------------------------------------------- 513s APBS -- Adaptive Poisson-Boltzmann Solver 513s Version APBS 3.4.1 513s 513s Nathan A. Baker (nathan.baker@pnnl.gov) 513s Pacific Northwest National Laboratory 513s 513s Additional contributing authors listed in the code documentation. 513s 513s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 513s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 513s Northwest Division for the U.S. Department of Energy. 513s 513s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 513s Portions Copyright (c) 2002-2020, Nathan A. Baker. 513s Portions Copyright (c) 1999-2002, The Regents of the University of California. 513s Portions Copyright (c) 1995, Michael Holst. 513s All rights reserved. 513s 513s Redistribution and use in source and binary forms, with or without 513s modification, are permitted provided that the following conditions are met: 513s 513s * Redistributions of source code must retain the above copyright notice, this 513s list of conditions and the following disclaimer. 513s 513s * Redistributions in binary form must reproduce the above copyright notice, 513s this list of conditions and the following disclaimer in the documentation 513s and/or other materials provided with the distribution. 513s 513s * Neither the name of the developer nor the names of its contributors may be 513s used to endorse or promote products derived from this software without 513s specific prior written permission. 513s 513s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 513s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 513s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 513s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 513s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 513s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 513s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 513s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 513s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 513s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 513s ---------------------------------------------------------------------- 513s APBS uses FETK (the Finite Element ToolKit) to solve the 513s Poisson-Boltzmann equation numerically. FETK is a portable collection 513s of finite element modeling class libraries developed by the Michael Holst 513s research group and written in an object-oriented form of C. FEtk is 513s designed to solve general coupled systems of nonlinear partial differential 513s equations using adaptive finite element methods, inexact Newton methods, 513s and algebraic multilevel methods. More information about FEtk may be found 513s at . 513s ---------------------------------------------------------------------- 513s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 513s Aqua is a modified form of the Holst group PMG library 513s which has been modified by Patrice Koehl 513s for improved efficiency and 513s memory usage when solving the Poisson-Boltzmann equation. 513s ---------------------------------------------------------------------- 513s Please cite your use of APBS as: 513s 513s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 513s nanosystems: application to microtubules and the ribosome. Proc. 513s Natl. Acad. Sci. USA 98, 10037-10041 2001. 513s 513s 513s This executable compiled on Jan 3 2025 at 11:01:42 513s 513s Parsing input file complex-0_1.in... 513s rank 0 size 1... 513s Parsed input file. 513s Got paths for 3 molecules 513s Reading PQR-format atom data from mol0.pqr. 513s asc_getToken: Error occurred (bailing out). 513s Vio_scanf: Format problem with input. 513s 1 atoms 513s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 513s Net charge 1.00e+00 e 513s Reading PQR-format atom data from mol1.pqr. 513s asc_getToken: Error occurred (bailing out). 513s Vio_scanf: Format problem with input. 513s 1 atoms 513s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 513s Net charge 1.00e+00 e 513s Reading PQR-format atom data from complex-0_1.pqr. 513s 2 atoms 513s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 513s Net charge 2.00e+00 e 513s Preparing to run 3 PBE calculations. 513s ---------------------------------------- 513s CALCULATION #1 (point1): MULTIGRID 513s Setting up problem... 513s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 513s Debye length: 0 A 513s Current memory usage: 61.060 MB total, 61.060 MB high water 513s Using linear spline charge discretization. 513s Grid dimensions: 65 x 65 x 65 513s Grid spacings: 0.210 x 0.210 x 0.210 513s Grid lengths: 13.440 x 13.440 x 13.440 513s Grid center: (0.000, 0.000, 0.000) 513s Multigrid levels: 5 513s Molecule ID: 1 513s Linearized traditional PBE 513s Multiple Debye-Huckel sphere boundary conditions 513s 0 ion species (0.000 M ionic strength): 513s Solute dielectric: 78.540 513s Solvent dielectric: 78.540 513s Using spline-based surface definition;window = 0.300 513s Temperature: 298.150 K 513s Electrostatic energies will be calculated 513s Total electrostatic energy = 9.776035707281E+01 kJ/mol 513s Fixed charge energy = 97.7604 kJ/mol 513s Mobile charge energy = 0 kJ/mol 513s Dielectric energy = 96.5336 kJ/mol 513s Per-atom energies: 513s Atom 0: 9.776035707281E+01 kJ/mol 513s Calculating forces... 513s ---------------------------------------- 513s CALCULATION #2 (point2): MULTIGRID 513s Setting up problem... 513s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 513s Debye length: 0 A 513s Current memory usage: 61.060 MB total, 61.067 MB high water 513s Using linear spline charge discretization. 513s Grid dimensions: 65 x 65 x 65 513s Grid spacings: 0.210 x 0.210 x 0.210 513s Grid lengths: 13.440 x 13.440 x 13.440 513s Grid center: (0.000, 0.000, 0.000) 513s Multigrid levels: 5 513s Molecule ID: 2 513s Linearized traditional PBE 513s Multiple Debye-Huckel sphere boundary conditions 513s 0 ion species (0.000 M ionic strength): 513s Solute dielectric: 78.540 513s Solvent dielectric: 78.540 513s Using spline-based surface definition;window = 0.300 513s Temperature: 298.150 K 513s Electrostatic energies will be calculated 513s Total electrostatic energy = 8.975920687031E+01 kJ/mol 513s Fixed charge energy = 89.7592 kJ/mol 513s Mobile charge energy = 0 kJ/mol 513s Dielectric energy = 88.6151 kJ/mol 513s Per-atom energies: 513s Atom 0: 8.975920687031E+01 kJ/mol 513s Calculating forces... 513s ---------------------------------------- 513s CALCULATION #3 (complex): MULTIGRID 513s Setting up problem... 513s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 513s Debye length: 0 A 513s Current memory usage: 61.060 MB total, 61.067 MB high water 513s Using linear spline charge discretization. 513s Grid dimensions: 65 x 65 x 65 513s Grid spacings: 0.210 x 0.210 x 0.210 513s Grid lengths: 13.440 x 13.440 x 13.440 513s Grid center: (0.000, 0.000, 0.000) 513s Multigrid levels: 5 513s Molecule ID: 3 513s Linearized traditional PBE 513s Multiple Debye-Huckel sphere boundary conditions 513s 0 ion species (0.000 M ionic strength): 513s Solute dielectric: 78.540 513s Solvent dielectric: 78.540 513s Using spline-based surface definition;window = 0.300 513s Temperature: 298.150 K 513s Electrostatic energies will be calculated 513s Total electrostatic energy = 2.058277719334E+02 kJ/mol 513s Fixed charge energy = 205.828 kJ/mol 513s Mobile charge energy = 0 kJ/mol 513s Dielectric energy = 201.106 kJ/mol 513s Per-atom energies: 513s Atom 0: 1.069144350786E+02 kJ/mol 513s Atom 1: 9.891333685475E+01 kJ/mol 513s Calculating forces... 513s ---------------------------------------- 513s PRINT STATEMENTS 513s 513s print energy 3 (complex) - 1 (point1) - 2 (point2) end 513s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 513s Global net ELEC energy = 1.830820799027E+01 kJ/mol 513s ---------------------------------------- 513s CLEANING UP AND SHUTTING DOWN... 513s Destroying force arrays. 513s No energy arrays to destroy. 513s Destroying multigrid structures. 513s Destroying finite element structures. 513s Destroying 3 molecules 513s Final memory usage: 0.001 MB total, 61.067 MB high water 513s 513s 513s Thanks for using APBS! 513s 513s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 513s *** PASSED *** 513s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 513s *** PASSED *** 513s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 513s *** PASSED *** 513s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 513s *** PASSED *** 513s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 513s *** PASSED *** 513s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 513s *** PASSED *** 513s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 513s *** PASSED *** 513s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 513s *** PASSED *** 513s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 513s *** PASSED *** 513s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 513s *** PASSED *** 513s Elapsed time: 0.987394 seconds 513s -------------------------------------------------------------------------------- 513s -------------------------------------------------------------------------------- 513s Testing input file complex-0_2.in 513s 514s Checking for intermediate energies in input file complex-0_1.out 514s EXPECTED COMPUTED: 13 514s EXPECTED EXPECTED: 13 514s 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] 514s 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'] 514s COMPUTED RESULT 97.76035707281 514s COMPUTED RESULT 89.75920687031 514s COMPUTED RESULT 205.8277719334 514s COMPUTED RESULT 0.0 514s COMPUTED RESULT 0.0 514s COMPUTED RESULT 0.0 514s COMPUTED RESULT 97.7604 514s COMPUTED RESULT 89.7592 514s COMPUTED RESULT 205.828 514s COMPUTED RESULT 96.5336 514s COMPUTED RESULT 88.6151 514s COMPUTED RESULT 201.106 514s COMPUTED RESULT 18.30820799027 514s BINARY: /usr/bin/apbs 514s INPUT: complex-0_2.in 514s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 514s asc_getToken: Error occurred (bailing out). 514s Vio_scanf: Format problem with input. 514s 514s 514s ---------------------------------------------------------------------- 514s APBS -- Adaptive Poisson-Boltzmann Solver 514s Version APBS 3.4.1 514s 514s Nathan A. Baker (nathan.baker@pnnl.gov) 514s Pacific Northwest National Laboratory 514s 514s Additional contributing authors listed in the code documentation. 514s 514s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 514s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 514s Northwest Division for the U.S. Department of Energy. 514s 514s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 514s Portions Copyright (c) 2002-2020, Nathan A. Baker. 514s Portions Copyright (c) 1999-2002, The Regents of the University of California. 514s Portions Copyright (c) 1995, Michael Holst. 514s All rights reserved. 514s 514s Redistribution and use in source and binary forms, with or without 514s modification, are permitted provided that the following conditions are met: 514s 514s * Redistributions of source code must retain the above copyright notice, this 514s list of conditions and the following disclaimer. 514s 514s * Redistributions in binary form must reproduce the above copyright notice, 514s this list of conditions and the following disclaimer in the documentation 514s and/or other materials provided with the distribution. 514s 514s * Neither the name of the developer nor the names of its contributors may be 514s used to endorse or promote products derived from this software without 514s specific prior written permission. 514s 514s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 514s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 514s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 514s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 514s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 514s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 514s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 514s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 514s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 514s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 514s ---------------------------------------------------------------------- 514s APBS uses FETK (the Finite Element ToolKit) to solve the 514s Poisson-Boltzmann equation numerically. FETK is a portable collection 514s of finite element modeling class libraries developed by the Michael Holst 514s research group and written in an object-oriented form of C. FEtk is 514s designed to solve general coupled systems of nonlinear partial differential 514s equations using adaptive finite element methods, inexact Newton methods, 514s and algebraic multilevel methods. More information about FEtk may be found 514s at . 514s ---------------------------------------------------------------------- 514s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 514s Aqua is a modified form of the Holst group PMG library 514s which has been modified by Patrice Koehl 514s for improved efficiency and 514s memory usage when solving the Poisson-Boltzmann equation. 514s ---------------------------------------------------------------------- 514s Please cite your use of APBS as: 514s 514s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 514s nanosystems: application to microtubules and the ribosome. Proc. 514s Natl. Acad. Sci. USA 98, 10037-10041 2001. 514s 514s 514s This executable compiled on Jan 3 2025 at 11:01:42 514s 514s Parsing input file complex-0_2.in... 514s rank 0 size 1... 514s Parsed input file. 514s Got paths for 3 molecules 514s Reading PQR-format atom data from mol0.pqr. 514s asc_getToken: Error occurred (bailing out). 514s Vio_scanf: Format problem with input. 514s 1 atoms 514s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 514s Net charge 1.00e+00 e 514s Reading PQR-format atom data from mol2.pqr. 514s asc_getToken: Error occurred (bailing out). 514s Vio_scanf: Format problem with input. 514s 1 atoms 514s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 514s Net charge 1.00e+00 e 514s Reading PQR-format atom data from complex-0_2.pqr. 514s 2 atoms 514s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 514s Net charge 2.00e+00 e 514s Preparing to run 3 PBE calculations. 514s ---------------------------------------- 514s CALCULATION #1 (point1): MULTIGRID 514s Setting up problem... 514s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 514s Debye length: 0 A 514s Current memory usage: 61.060 MB total, 61.060 MB high water 514s Using linear spline charge discretization. 514s Grid dimensions: 65 x 65 x 65 514s Grid spacings: 0.210 x 0.210 x 0.210 514s Grid lengths: 13.440 x 13.440 x 13.440 514s Grid center: (0.000, 0.000, 0.000) 514s Multigrid levels: 5 514s Molecule ID: 1 514s Linearized traditional PBE 514s Multiple Debye-Huckel sphere boundary conditions 514s 0 ion species (0.000 M ionic strength): 514s Solute dielectric: 78.540 514s Solvent dielectric: 78.540 514s Using spline-based surface definition;window = 0.300 514s Temperature: 298.150 K 514s Electrostatic energies will be calculated 514s Total electrostatic energy = 9.776035707281E+01 kJ/mol 514s Fixed charge energy = 97.7604 kJ/mol 514s Mobile charge energy = 0 kJ/mol 514s Dielectric energy = 96.5336 kJ/mol 514s Per-atom energies: 514s Atom 0: 9.776035707281E+01 kJ/mol 514s Calculating forces... 514s ---------------------------------------- 514s CALCULATION #2 (point2): MULTIGRID 514s Setting up problem... 514s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 514s Debye length: 0 A 514s Current memory usage: 61.060 MB total, 61.067 MB high water 514s Using linear spline charge discretization. 514s Grid dimensions: 65 x 65 x 65 514s Grid spacings: 0.210 x 0.210 x 0.210 514s Grid lengths: 13.440 x 13.440 x 13.440 514s Grid center: (0.000, 0.000, 0.000) 514s Multigrid levels: 5 514s Molecule ID: 2 514s Linearized traditional PBE 514s Multiple Debye-Huckel sphere boundary conditions 514s 0 ion species (0.000 M ionic strength): 514s Solute dielectric: 78.540 514s Solvent dielectric: 78.540 514s Using spline-based surface definition;window = 0.300 514s Temperature: 298.150 K 514s Electrostatic energies will be calculated 514s Total electrostatic energy = 1.017611498797E+02 kJ/mol 514s Fixed charge energy = 101.761 kJ/mol 514s Mobile charge energy = 0 kJ/mol 514s Dielectric energy = 100.656 kJ/mol 514s Per-atom energies: 514s Atom 0: 1.017611498797E+02 kJ/mol 514s Calculating forces... 514s ---------------------------------------- 514s CALCULATION #3 (complex): MULTIGRID 514s Setting up problem... 514s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 514s Debye length: 0 A 514s Current memory usage: 61.060 MB total, 61.068 MB high water 514s Using linear spline charge discretization. 514s Grid dimensions: 65 x 65 x 65 514s Grid spacings: 0.210 x 0.210 x 0.210 514s Grid lengths: 13.440 x 13.440 x 13.440 514s Grid center: (0.000, 0.000, 0.000) 514s Multigrid levels: 5 514s Molecule ID: 3 514s Linearized traditional PBE 514s Multiple Debye-Huckel sphere boundary conditions 514s 0 ion species (0.000 M ionic strength): 514s Solute dielectric: 78.540 514s Solvent dielectric: 78.540 514s Using spline-based surface definition;window = 0.300 514s Temperature: 298.150 K 514s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 514s *** PASSED *** 514s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 514s *** PASSED *** 514s Electrostatic energies will be calculated 514s Total electrostatic energy = 2.084282010393E+02 kJ/mol 514s Fixed charge energy = 208.428 kJ/mol 514s Mobile charge energy = 0 kJ/mol 514s Dielectric energy = 203.83 kJ/mol 514s Per-atom energies: 514s Atom 0: 1.022136878480E+02 kJ/mol 514s Atom 1: 1.062145131913E+02 kJ/mol 514s Calculating forces... 514s ---------------------------------------- 514s PRINT STATEMENTS 514s 514s print energy 3 (complex) - 1 (point1) - 2 (point2) end 514s Local net energy (PE 0) = 8.906694086751E+00 kJ/mol 514s Global net ELEC energy = 8.906694086751E+00 kJ/mol 514s ---------------------------------------- 514s CLEANING UP AND SHUTTING DOWN... 514s Destroying force arrays. 514s No energy arrays to destroy. 514s Destroying multigrid structures. 514s Destroying finite element structures. 514s Destroying 3 molecules 514s Final memory usage: 0.001 MB total, 61.068 MB high water 514s 514s 514s Thanks for using APBS! 514s 514s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 514s *** PASSED *** 514s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 514s *** PASSED *** 514s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 514s *** PASSED *** 514s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 514s *** PASSED *** 514s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 514s *** PASSED *** 514s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 514s *** PASSED *** 514s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 514s *** PASSED *** 514s Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) 514s *** PASSED *** 514s Elapsed time: 0.977116 seconds 514s -------------------------------------------------------------------------------- 514s -------------------------------------------------------------------------------- 514s Testing input file complex-0_3.in 514s 515s Checking for intermediate energies in input file complex-0_2.out 515s EXPECTED COMPUTED: 13 515s EXPECTED EXPECTED: 13 515s 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] 515s 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'] 515s COMPUTED RESULT 97.76035707281 515s COMPUTED RESULT 101.7611498797 515s COMPUTED RESULT 208.4282010393 515s COMPUTED RESULT 0.0 515s COMPUTED RESULT 0.0 515s COMPUTED RESULT 0.0 515s COMPUTED RESULT 97.7604 515s COMPUTED RESULT 101.761 515s COMPUTED RESULT 208.428 515s COMPUTED RESULT 96.5336 515s COMPUTED RESULT 100.656 515s COMPUTED RESULT 203.83 515s COMPUTED RESULT 8.906694086751 515s BINARY: /usr/bin/apbs 515s INPUT: complex-0_3.in 515s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 515s asc_getToken: Error occurred (bailing out). 515s Vio_scanf: Format problem with input. 515s 515s 515s ---------------------------------------------------------------------- 515s APBS -- Adaptive Poisson-Boltzmann Solver 515s Version APBS 3.4.1 515s 515s Nathan A. Baker (nathan.baker@pnnl.gov) 515s Pacific Northwest National Laboratory 515s 515s Additional contributing authors listed in the code documentation. 515s 515s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 515s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 515s Northwest Division for the U.S. Department of Energy. 515s 515s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 515s Portions Copyright (c) 2002-2020, Nathan A. Baker. 515s Portions Copyright (c) 1999-2002, The Regents of the University of California. 515s Portions Copyright (c) 1995, Michael Holst. 515s All rights reserved. 515s 515s Redistribution and use in source and binary forms, with or without 515s modification, are permitted provided that the following conditions are met: 515s 515s * Redistributions of source code must retain the above copyright notice, this 515s list of conditions and the following disclaimer. 515s 515s * Redistributions in binary form must reproduce the above copyright notice, 515s this list of conditions and the following disclaimer in the documentation 515s and/or other materials provided with the distribution. 515s 515s * Neither the name of the developer nor the names of its contributors may be 515s used to endorse or promote products derived from this software without 515s specific prior written permission. 515s 515s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 515s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 515s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 515s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 515s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 515s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 515s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 515s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 515s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 515s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 515s ---------------------------------------------------------------------- 515s APBS uses FETK (the Finite Element ToolKit) to solve the 515s Poisson-Boltzmann equation numerically. FETK is a portable collection 515s of finite element modeling class libraries developed by the Michael Holst 515s research group and written in an object-oriented form of C. FEtk is 515s designed to solve general coupled systems of nonlinear partial differential 515s equations using adaptive finite element methods, inexact Newton methods, 515s and algebraic multilevel methods. More information about FEtk may be found 515s at . 515s ---------------------------------------------------------------------- 515s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 515s Aqua is a modified form of the Holst group PMG library 515s which has been modified by Patrice Koehl 515s for improved efficiency and 515s memory usage when solving the Poisson-Boltzmann equation. 515s ---------------------------------------------------------------------- 515s Please cite your use of APBS as: 515s 515s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 515s nanosystems: application to microtubules and the ribosome. Proc. 515s Natl. Acad. Sci. USA 98, 10037-10041 2001. 515s 515s 515s This executable compiled on Jan 3 2025 at 11:01:42 515s 515s Parsing input file complex-0_3.in... 515s rank 0 size 1... 515s Parsed input file. 515s Got paths for 3 molecules 515s Reading PQR-format atom data from mol0.pqr. 515s asc_getToken: Error occurred (bailing out). 515s Vio_scanf: Format problem with input. 515s 1 atoms 515s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 515s Net charge 1.00e+00 e 515s Reading PQR-format atom data from mol3.pqr. 515s asc_getToken: Error occurred (bailing out). 515s Vio_scanf: Format problem with input. 515s 1 atoms 515s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 515s Net charge 1.00e+00 e 515s Reading PQR-format atom data from complex-0_3.pqr. 515s 2 atoms 515s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 515s Net charge 2.00e+00 e 515s Preparing to run 3 PBE calculations. 515s ---------------------------------------- 515s CALCULATION #1 (point1): MULTIGRID 515s Setting up problem... 515s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 515s Debye length: 0 A 515s Current memory usage: 61.060 MB total, 61.060 MB high water 515s Using linear spline charge discretization. 515s Grid dimensions: 65 x 65 x 65 515s Grid spacings: 0.210 x 0.210 x 0.210 515s Grid lengths: 13.440 x 13.440 x 13.440 515s Grid center: (0.000, 0.000, 0.000) 515s Multigrid levels: 5 515s Molecule ID: 1 515s Linearized traditional PBE 515s Multiple Debye-Huckel sphere boundary conditions 515s 0 ion species (0.000 M ionic strength): 515s Solute dielectric: 78.540 515s Solvent dielectric: 78.540 515s Using spline-based surface definition;window = 0.300 515s Temperature: 298.150 K 515s Electrostatic energies will be calculated 515s Total electrostatic energy = 9.776035707281E+01 kJ/mol 515s Fixed charge energy = 97.7604 kJ/mol 515s Mobile charge energy = 0 kJ/mol 515s Dielectric energy = 96.5336 kJ/mol 515s Per-atom energies: 515s Atom 0: 9.776035707281E+01 kJ/mol 515s Calculating forces... 515s ---------------------------------------- 515s CALCULATION #2 (point2): MULTIGRID 515s Setting up problem... 515s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 515s Debye length: 0 A 515s Current memory usage: 61.060 MB total, 61.067 MB high water 515s Using linear spline charge discretization. 515s Grid dimensions: 65 x 65 x 65 515s Grid spacings: 0.210 x 0.210 x 0.210 515s Grid lengths: 13.440 x 13.440 x 13.440 515s Grid center: (0.000, 0.000, 0.000) 515s Multigrid levels: 5 515s Molecule ID: 2 515s Linearized traditional PBE 515s Multiple Debye-Huckel sphere boundary conditions 515s 0 ion species (0.000 M ionic strength): 515s Solute dielectric: 78.540 515s Solvent dielectric: 78.540 515s Using spline-based surface definition;window = 0.300 515s Temperature: 298.150 K 515s Electrostatic energies will be calculated 515s Total electrostatic energy = 1.337661883222E+02 kJ/mol 515s Fixed charge energy = 133.766 kJ/mol 515s Mobile charge energy = 0 kJ/mol 515s Dielectric energy = 132.672 kJ/mol 515s Per-atom energies: 515s Atom 0: 1.337661883222E+02 kJ/mol 515s Calculating forces... 515s ---------------------------------------- 515s CALCULATION #3 (complex): MULTIGRID 515s Setting up problem... 515s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 515s Debye length: 0 A 515s Current memory usage: 61.060 MB total, 61.068 MB high water 515s Using linear spline charge discretization. 515s Grid dimensions: 65 x 65 x 65 515s Grid spacings: 0.210 x 0.210 x 0.210 515s Grid lengths: 13.440 x 13.440 x 13.440 515s Grid center: (0.000, 0.000, 0.000) 515s Multigrid levels: 5 515s Molecule ID: 3 515s Linearized traditional PBE 515s Multiple Debye-Huckel sphere boundary conditions 515s 0 ion species (0.000 M ionic strength): 515s Solute dielectric: 78.540 515s Solvent dielectric: 78.540 515s Using spline-based surface definition;window = 0.300 515s Temperature: 298.150 K 515s Electrostatic energies will be calculated 515s Total electrostatic energy = 2.374361452120E+02 kJ/mol 515s Fixed charge energy = 237.436 kJ/mol 515s Mobile charge energy = 0 kJ/mol 515s Dielectric energy = 232.924 kJ/mol 515s Per-atom energies: 515s Atom 0: 1.007151570480E+02 kJ/mol 515s Atom 1: 1.367209881640E+02 kJ/mol 515s Calculating forces... 515s ---------------------------------------- 515s PRINT STATEMENTS 515s 515s print energy 3 (complex) - 1 (point1) - 2 (point2) end 515s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 515s Global net ELEC energy = 5.909599816984E+00 kJ/mol 515s ---------------------------------------- 515s CLEANING UP AND SHUTTING DOWN... 515s Destroying force arrays. 515s No energy arrays to destroy. 515s Destroying multigrid structures. 515s Destroying finite element structures. 515s Destroying 3 molecules 515s Final memory usage: 0.001 MB total, 61.068 MB high water 515s 515s 515s Thanks for using APBS! 515s 515s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 515s *** PASSED *** 515s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 515s *** PASSED *** 515s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 515s *** PASSED *** 515s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 515s *** PASSED *** 515s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 515s *** PASSED *** 515s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 515s *** PASSED *** 515s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 515s *** PASSED *** 515s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 515s *** PASSED *** 515s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 515s *** PASSED *** 515s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 515s *** PASSED *** 515s Elapsed time: 0.958566 seconds 515s -------------------------------------------------------------------------------- 515s -------------------------------------------------------------------------------- 515s Testing input file complex-0_4.in 515s 516s Checking for intermediate energies in input file complex-0_3.out 516s EXPECTED COMPUTED: 13 516s EXPECTED EXPECTED: 13 516s 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] 516s 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'] 516s COMPUTED RESULT 97.76035707281 516s COMPUTED RESULT 133.7661883222 516s COMPUTED RESULT 237.436145212 516s COMPUTED RESULT 0.0 516s COMPUTED RESULT 0.0 516s COMPUTED RESULT 0.0 516s COMPUTED RESULT 97.7604 516s COMPUTED RESULT 133.766 516s COMPUTED RESULT 237.436 516s COMPUTED RESULT 96.5336 516s COMPUTED RESULT 132.672 516s COMPUTED RESULT 232.924 516s COMPUTED RESULT 5.909599816984 516s BINARY: /usr/bin/apbs 516s INPUT: complex-0_4.in 516s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 516s asc_getToken: Error occurred (bailing out). 516s Vio_scanf: Format problem with input. 516s 516s 516s ---------------------------------------------------------------------- 516s APBS -- Adaptive Poisson-Boltzmann Solver 516s Version APBS 3.4.1 516s 516s Nathan A. Baker (nathan.baker@pnnl.gov) 516s Pacific Northwest National Laboratory 516s 516s Additional contributing authors listed in the code documentation. 516s 516s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 516s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 516s Northwest Division for the U.S. Department of Energy. 516s 516s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 516s Portions Copyright (c) 2002-2020, Nathan A. Baker. 516s Portions Copyright (c) 1999-2002, The Regents of the University of California. 516s Portions Copyright (c) 1995, Michael Holst. 516s All rights reserved. 516s 516s Redistribution and use in source and binary forms, with or without 516s modification, are permitted provided that the following conditions are met: 516s 516s * Redistributions of source code must retain the above copyright notice, this 516s list of conditions and the following disclaimer. 516s 516s * Redistributions in binary form must reproduce the above copyright notice, 516s this list of conditions and the following disclaimer in the documentation 516s and/or other materials provided with the distribution. 516s 516s * Neither the name of the developer nor the names of its contributors may be 516s used to endorse or promote products derived from this software without 516s specific prior written permission. 516s 516s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 516s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 516s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 516s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 516s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 516s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 516s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 516s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 516s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 516s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 516s ---------------------------------------------------------------------- 516s APBS uses FETK (the Finite Element ToolKit) to solve the 516s Poisson-Boltzmann equation numerically. FETK is a portable collection 516s of finite element modeling class libraries developed by the Michael Holst 516s research group and written in an object-oriented form of C. FEtk is 516s designed to solve general coupled systems of nonlinear partial differential 516s equations using adaptive finite element methods, inexact Newton methods, 516s and algebraic multilevel methods. More information about FEtk may be found 516s at . 516s ---------------------------------------------------------------------- 516s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 516s Aqua is a modified form of the Holst group PMG library 516s which has been modified by Patrice Koehl 516s for improved efficiency and 516s memory usage when solving the Poisson-Boltzmann equation. 516s ---------------------------------------------------------------------- 516s Please cite your use of APBS as: 516s 516s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 516s nanosystems: application to microtubules and the ribosome. Proc. 516s Natl. Acad. Sci. USA 98, 10037-10041 2001. 516s 516s 516s This executable compiled on Jan 3 2025 at 11:01:42 516s 516s Parsing input file complex-0_4.in... 516s rank 0 size 1... 516s Parsed input file. 516s Got paths for 3 molecules 516s Reading PQR-format atom data from mol0.pqr. 516s asc_getToken: Error occurred (bailing out). 516s Vio_scanf: Format problem with input. 516s 1 atoms 516s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 516s Net charge 1.00e+00 e 516s Reading PQR-format atom data from mol4.pqr. 516s asc_getToken: Error occurred (bailing out). 516s Vio_scanf: Format problem with input. 516s 1 atoms 516s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 516s Net charge 1.00e+00 e 516s Reading PQR-format atom data from complex-0_4.pqr. 516s 2 atoms 516s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 516s Net charge 2.00e+00 e 516s Preparing to run 3 PBE calculations. 516s ---------------------------------------- 516s CALCULATION #1 (point1): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 61.060 MB total, 61.060 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 65 x 65 x 65 516s Grid spacings: 0.210 x 0.210 x 0.210 516s Grid lengths: 13.440 x 13.440 x 13.440 516s Grid center: (0.000, 0.000, 0.000) 516s Multigrid levels: 5 516s Molecule ID: 1 516s Linearized traditional PBE 516s Multiple Debye-Huckel sphere boundary conditions 516s 0 ion species (0.000 M ionic strength): 516s Solute dielectric: 78.540 516s Solvent dielectric: 78.540 516s Using spline-based surface definition;window = 0.300 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 9.776035707281E+01 kJ/mol 516s Fixed charge energy = 97.7604 kJ/mol 516s Mobile charge energy = 0 kJ/mol 516s Dielectric energy = 96.5336 kJ/mol 516s Per-atom energies: 516s Atom 0: 9.776035707281E+01 kJ/mol 516s Calculating forces... 516s ---------------------------------------- 516s CALCULATION #2 (point2): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 61.060 MB total, 61.067 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 65 x 65 x 65 516s Grid spacings: 0.210 x 0.210 x 0.210 516s Grid lengths: 13.440 x 13.440 x 13.440 516s Grid center: (0.000, 0.000, 0.000) 516s Multigrid levels: 5 516s Molecule ID: 2 516s Linearized traditional PBE 516s Multiple Debye-Huckel sphere boundary conditions 516s 0 ion species (0.000 M ionic strength): 516s Solute dielectric: 78.540 516s Solvent dielectric: 78.540 516s Using spline-based surface definition;window = 0.300 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 1.017611498797E+02 kJ/mol 516s Fixed charge energy = 101.761 kJ/mol 516s Mobile charge energy = 0 kJ/mol 516s Dielectric energy = 100.654 kJ/mol 516s Per-atom energies: 516s Atom 0: 1.017611498797E+02 kJ/mol 516s Calculating forces... 516s ---------------------------------------- 516s CALCULATION #3 (complex): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 61.061 MB total, 61.068 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 65 x 65 x 65 516s Grid spacings: 0.210 x 0.210 x 0.210 516s Grid lengths: 13.440 x 13.440 x 13.440 516s Grid center: (0.000, 0.000, 0.000) 516s Multigrid levels: 5 516s Molecule ID: 3 516s Linearized traditional PBE 516s Multiple Debye-Huckel sphere boundary conditions 516s 0 ion species (0.000 M ionic strength): 516s Solute dielectric: 78.540 516s Solvent dielectric: 78.540 516s Using spline-based surface definition;window = 0.300 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 2.039516519000E+02 kJ/mol 516s Fixed charge energy = 203.952 kJ/mol 516s Mobile charge energy = 0 kJ/mol 516s Dielectric energy = 199.493 kJ/mol 516s Per-atom energies: 516s Atom 0: 9.997541697022E+01 kJ/mol 516s Atom 1: 1.039762349297E+02 kJ/mol 516s Calculating forces... 516s ---------------------------------------- 516s PRINT STATEMENTS 516s 516s print energy 3 (complex) - 1 (point1) - 2 (point2) end 516s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 516s Global net ELEC energy = 4.430144947418E+00 kJ/mol 516s ---------------------------------------- 516s CLEANING UP AND SHUTTING DOWN... 516s Destroying force arrays. 516s No energy arrays to destroy. 516s Destroying multigrid structures. 516s Destroying finite element structures. 516s Destroying 3 molecules 516s Final memory usage: 0.001 MB total, 61.068 MB high water 516s 516s 516s Thanks for using APBS! 516s 516s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 516s *** PASSED *** 516s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 516s *** PASSED *** 516s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 516s *** PASSED *** 516s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 516s *** PASSED *** 516s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 516s *** PASSED *** 516s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 516s *** PASSED *** 516s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 516s *** PASSED *** 516s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 516s *** PASSED *** 516s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 516s *** PASSED *** 516s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 516s *** PASSED *** 516s Elapsed time: 0.943157 seconds 516s -------------------------------------------------------------------------------- 516s Total elapsed time: 3.8662330000000003 seconds 516s Test results have been logged 516s -------------------------------------------------------------------------------- 516s -------------------------------------------------------------------------------- 516s Testing input file apbs-mol.in 516s 518s Checking for intermediate energies in input file complex-0_4.out 518s EXPECTED COMPUTED: 13 518s EXPECTED EXPECTED: 13 518s 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] 518s 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'] 518s COMPUTED RESULT 97.76035707281 518s COMPUTED RESULT 101.7611498797 518s COMPUTED RESULT 203.9516519 518s COMPUTED RESULT 0.0 518s COMPUTED RESULT 0.0 518s COMPUTED RESULT 0.0 518s COMPUTED RESULT 97.7604 518s COMPUTED RESULT 101.761 518s COMPUTED RESULT 203.952 518s COMPUTED RESULT 96.5336 518s COMPUTED RESULT 100.654 518s COMPUTED RESULT 199.493 518s COMPUTED RESULT 4.430144947418 518s Running tests for solv section 518s BINARY: /usr/bin/apbs 518s INPUT: apbs-mol.in 518s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 518s asc_getToken: Error occurred (bailing out). 518s Vio_scanf: Format problem with input. 518s 518s 518s ---------------------------------------------------------------------- 518s APBS -- Adaptive Poisson-Boltzmann Solver 518s Version APBS 3.4.1 518s 518s Nathan A. Baker (nathan.baker@pnnl.gov) 518s Pacific Northwest National Laboratory 518s 518s Additional contributing authors listed in the code documentation. 518s 518s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 518s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 518s Northwest Division for the U.S. Department of Energy. 518s 518s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 518s Portions Copyright (c) 2002-2020, Nathan A. Baker. 518s Portions Copyright (c) 1999-2002, The Regents of the University of California. 518s Portions Copyright (c) 1995, Michael Holst. 518s All rights reserved. 518s 518s Redistribution and use in source and binary forms, with or without 518s modification, are permitted provided that the following conditions are met: 518s 518s * Redistributions of source code must retain the above copyright notice, this 518s list of conditions and the following disclaimer. 518s 518s * Redistributions in binary form must reproduce the above copyright notice, 518s this list of conditions and the following disclaimer in the documentation 518s and/or other materials provided with the distribution. 518s 518s * Neither the name of the developer nor the names of its contributors may be 518s used to endorse or promote products derived from this software without 518s specific prior written permission. 518s 518s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 518s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 518s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 518s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 518s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 518s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 518s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 518s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 518s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 518s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 518s ---------------------------------------------------------------------- 518s APBS uses FETK (the Finite Element ToolKit) to solve the 518s Poisson-Boltzmann equation numerically. FETK is a portable collection 518s of finite element modeling class libraries developed by the Michael Holst 518s research group and written in an object-oriented form of C. FEtk is 518s designed to solve general coupled systems of nonlinear partial differential 518s equations using adaptive finite element methods, inexact Newton methods, 518s and algebraic multilevel methods. More information about FEtk may be found 518s at . 518s ---------------------------------------------------------------------- 518s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 518s Aqua is a modified form of the Holst group PMG library 518s which has been modified by Patrice Koehl 518s for improved efficiency and 518s memory usage when solving the Poisson-Boltzmann equation. 518s ---------------------------------------------------------------------- 518s Please cite your use of APBS as: 518s 518s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 518s nanosystems: application to microtubules and the ribosome. Proc. 518s Natl. Acad. Sci. USA 98, 10037-10041 2001. 518s 518s 518s This executable compiled on Jan 3 2025 at 11:01:42 518s 518s Parsing input file apbs-mol.in... 518s rank 0 size 1... 518s Parsed input file. 518s Got paths for 2 molecules 518s Reading PQR-format atom data from methanol.pqr. 518s asc_getToken: Error occurred (bailing out). 518s Vio_scanf: Format problem with input. 518s 3 atoms 518s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 518s Net charge 5.55e-17 e 518s Reading PQR-format atom data from methoxide.pqr. 518s 2 atoms 518s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 518s Net charge -1.00e+00 e 518s Preparing to run 4 PBE calculations. 518s ---------------------------------------- 518s CALCULATION #1 (methanol-solv): MULTIGRID 518s Setting up problem... 518s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 518s Debye length: 0 A 518s Current memory usage: 61.253 MB total, 61.253 MB high water 518s Using linear spline charge discretization. 518s Grid dimensions: 65 x 65 x 65 518s Grid spacings: 0.250 x 0.250 x 0.250 518s Grid lengths: 16.000 x 16.000 x 16.000 518s Grid center: (0.309, 0.000, -0.242) 518s Multigrid levels: 5 518s Molecule ID: 1 518s Linearized traditional PBE 518s Multiple Debye-Huckel sphere boundary conditions 518s 2 ion species (0.000 M ionic strength): 518s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 518s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 518s Solute dielectric: 2.000 518s Solvent dielectric: 78.000 518s Using "molecular" surface definition; no smoothing 518s Solvent probe radius: 0.000 A 518s Temperature: 300.000 K 518s Electrostatic energies will be calculated 518s Total electrostatic energy = 1.847663548071E+03 kJ/mol 518s Calculating forces... 518s ---------------------------------------- 518s CALCULATION #2 (methanol-ref): MULTIGRID 518s Setting up problem... 518s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 518s Debye length: 0 A 518s Current memory usage: 61.253 MB total, 61.328 MB high water 518s Using linear spline charge discretization. 518s Grid dimensions: 65 x 65 x 65 518s Grid spacings: 0.250 x 0.250 x 0.250 518s Grid lengths: 16.000 x 16.000 x 16.000 518s Grid center: (0.309, 0.000, -0.242) 518s Multigrid levels: 5 518s Molecule ID: 1 518s Linearized traditional PBE 518s Multiple Debye-Huckel sphere boundary conditions 518s 2 ion species (0.000 M ionic strength): 518s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 518s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 518s Solute dielectric: 2.000 518s Solvent dielectric: 1.000 518s Using "molecular" surface definition; no smoothing 518s Solvent probe radius: 0.000 A 518s Temperature: 300.000 K 518s Electrostatic energies will be calculated 518s Total electrostatic energy = 1.883912182952E+03 kJ/mol 518s Calculating forces... 518s ---------------------------------------- 518s CALCULATION #3 (methoxide-solv): MULTIGRID 518s Setting up problem... 518s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 518s Debye length: 0 A 518s Current memory usage: 61.250 MB total, 61.328 MB high water 518s Using linear spline charge discretization. 518s Grid dimensions: 65 x 65 x 65 518s Grid spacings: 0.250 x 0.250 x 0.250 518s Grid lengths: 16.000 x 16.000 x 16.000 518s Grid center: (0.000, 0.000, -0.128) 518s Multigrid levels: 5 518s Molecule ID: 2 518s Linearized traditional PBE 518s Multiple Debye-Huckel sphere boundary conditions 518s 2 ion species (0.000 M ionic strength): 518s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 518s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 518s Solute dielectric: 2.000 518s Solvent dielectric: 78.000 518s Using "molecular" surface definition; no smoothing 518s Solvent probe radius: 0.000 A 518s Temperature: 300.000 K 518s Electrostatic energies will be calculated 518s Total electrostatic energy = 2.732623683321E+03 kJ/mol 518s Calculating forces... 518s ---------------------------------------- 518s CALCULATION #4 (methoxide-ref): MULTIGRID 518s Setting up problem... 518s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 518s Debye length: 0 A 518s Current memory usage: 61.250 MB total, 61.328 MB high water 518s Using linear spline charge discretization. 518s Grid dimensions: 65 x 65 x 65 518s Grid spacings: 0.250 x 0.250 x 0.250 518s Grid lengths: 16.000 x 16.000 x 16.000 518s Grid center: (0.000, 0.000, -0.128) 518s Multigrid levels: 5 518s Molecule ID: 2 518s Linearized traditional PBE 518s Multiple Debye-Huckel sphere boundary conditions 518s 2 ion species (0.000 M ionic strength): 518s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 518s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 518s Solute dielectric: 2.000 518s Solvent dielectric: 1.000 518s Using "molecular" surface definition; no smoothing 518s Solvent probe radius: 0.000 A 518s Temperature: 300.000 K 518s Electrostatic energies will be calculated 518s Total electrostatic energy = 3.123035854133E+03 kJ/mol 518s Calculating forces... 518s ---------------------------------------- 518s PRINT STATEMENTS 518s 518s print energy 1 (methanol-solv) - 2 (methanol-ref) end 518s Local net energy (PE 0) = -3.624863488075E+01 kJ/mol 518s Global net ELEC energy = -3.624863488075E+01 kJ/mol 518s 518s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 518s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 518s Global net ELEC energy = -3.904121708125E+02 kJ/mol 518s 518s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 518s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 518s Global net ELEC energy = -3.541635359318E+02 kJ/mol 518s ---------------------------------------- 518s CLEANING UP AND SHUTTING DOWN... 518s Destroying force arrays. 518s No energy arrays to destroy. 518s Destroying multigrid structures. 518s Destroying finite element structures. 518s Destroying 2 molecules 518s Final memory usage: 0.001 MB total, 61.328 MB high water 518s 518s 518s Thanks for using APBS! 518s 518s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 518s *** PASSED *** 518s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 518s *** PASSED *** 518s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 518s *** PASSED *** 518s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 518s *** PASSED *** 518s Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) 518s *** PASSED *** 518s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 518s *** PASSED *** 518s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 518s *** PASSED *** 518s Elapsed time: 1.463027 seconds 518s -------------------------------------------------------------------------------- 518s -------------------------------------------------------------------------------- 518s Testing input file apbs-smol.in 518s 519s Checking for intermediate energies in input file apbs-mol.out 519s EXPECTED COMPUTED: 7 519s EXPECTED EXPECTED: 7 519s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] 519s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 519s COMPUTED RESULT 1847.663548071 519s COMPUTED RESULT 1883.912182952 519s COMPUTED RESULT 2732.623683321 519s COMPUTED RESULT 3123.035854133 519s COMPUTED RESULT -36.24863488075 519s COMPUTED RESULT -390.4121708125 519s COMPUTED RESULT -354.1635359318 519s BINARY: /usr/bin/apbs 519s INPUT: apbs-smol.in 519s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 519s asc_getToken: Error occurred (bailing out). 519s Vio_scanf: Format problem with input. 519s 519s 519s ---------------------------------------------------------------------- 519s APBS -- Adaptive Poisson-Boltzmann Solver 519s Version APBS 3.4.1 519s 519s Nathan A. Baker (nathan.baker@pnnl.gov) 519s Pacific Northwest National Laboratory 519s 519s Additional contributing authors listed in the code documentation. 519s 519s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 519s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 519s Northwest Division for the U.S. Department of Energy. 519s 519s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 519s Portions Copyright (c) 2002-2020, Nathan A. Baker. 519s Portions Copyright (c) 1999-2002, The Regents of the University of California. 519s Portions Copyright (c) 1995, Michael Holst. 519s All rights reserved. 519s 519s Redistribution and use in source and binary forms, with or without 519s modification, are permitted provided that the following conditions are met: 519s 519s * Redistributions of source code must retain the above copyright notice, this 519s list of conditions and the following disclaimer. 519s 519s * Redistributions in binary form must reproduce the above copyright notice, 519s this list of conditions and the following disclaimer in the documentation 519s and/or other materials provided with the distribution. 519s 519s * Neither the name of the developer nor the names of its contributors may be 519s used to endorse or promote products derived from this software without 519s specific prior written permission. 519s 519s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 519s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 519s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 519s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 519s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 519s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 519s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 519s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 519s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 519s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 519s ---------------------------------------------------------------------- 519s APBS uses FETK (the Finite Element ToolKit) to solve the 519s Poisson-Boltzmann equation numerically. FETK is a portable collection 519s of finite element modeling class libraries developed by the Michael Holst 519s research group and written in an object-oriented form of C. FEtk is 519s designed to solve general coupled systems of nonlinear partial differential 519s equations using adaptive finite element methods, inexact Newton methods, 519s and algebraic multilevel methods. More information about FEtk may be found 519s at . 519s ---------------------------------------------------------------------- 519s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 519s Aqua is a modified form of the Holst group PMG library 519s which has been modified by Patrice Koehl 519s for improved efficiency and 519s memory usage when solving the Poisson-Boltzmann equation. 519s ---------------------------------------------------------------------- 519s Please cite your use of APBS as: 519s 519s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 519s nanosystems: application to microtubules and the ribosome. Proc. 519s Natl. Acad. Sci. USA 98, 10037-10041 2001. 519s 519s 519s This executable compiled on Jan 3 2025 at 11:01:42 519s 519s Parsing input file apbs-smol.in... 519s rank 0 size 1... 519s Parsed input file. 519s Got paths for 2 molecules 519s Reading PQR-format atom data from methanol.pqr. 519s asc_getToken: Error occurred (bailing out). 519s Vio_scanf: Format problem with input. 519s 3 atoms 519s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 519s Net charge 5.55e-17 e 519s Reading PQR-format atom data from methoxide.pqr. 519s 2 atoms 519s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 519s Net charge -1.00e+00 e 519s Preparing to run 4 PBE calculations. 519s ---------------------------------------- 519s CALCULATION #1 (methanol-solv): MULTIGRID 519s Setting up problem... 519s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 519s Debye length: 0 A 519s Current memory usage: 61.253 MB total, 61.253 MB high water 519s Using linear spline charge discretization. 519s Grid dimensions: 65 x 65 x 65 519s Grid spacings: 0.250 x 0.250 x 0.250 519s Grid lengths: 16.000 x 16.000 x 16.000 519s Grid center: (0.309, 0.000, -0.242) 519s Multigrid levels: 5 519s Molecule ID: 1 519s Linearized traditional PBE 519s Multiple Debye-Huckel sphere boundary conditions 519s 2 ion species (0.000 M ionic strength): 519s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 519s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 519s Solute dielectric: 2.000 519s Solvent dielectric: 78.000 519s Using "molecular" surface definition;harmonic average smoothing 519s Solvent probe radius: 0.000 A 519s Temperature: 300.000 K 519s Electrostatic energies will be calculated 519s Total electrostatic energy = 1.847860440020E+03 kJ/mol 519s Calculating forces... 519s ---------------------------------------- 519s CALCULATION #2 (methanol-ref): MULTIGRID 519s Setting up problem... 519s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 519s Debye length: 0 A 519s Current memory usage: 61.253 MB total, 61.328 MB high water 519s Using linear spline charge discretization. 519s Grid dimensions: 65 x 65 x 65 519s Grid spacings: 0.250 x 0.250 x 0.250 519s Grid lengths: 16.000 x 16.000 x 16.000 519s Grid center: (0.309, 0.000, -0.242) 519s Multigrid levels: 5 519s Molecule ID: 1 519s Linearized traditional PBE 519s Multiple Debye-Huckel sphere boundary conditions 519s 2 ion species (0.000 M ionic strength): 519s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 519s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 519s Solute dielectric: 2.000 519s Solvent dielectric: 1.000 519s Using "molecular" surface definition;harmonic average smoothing 519s Solvent probe radius: 0.000 A 519s Temperature: 300.000 K 519s Electrostatic energies will be calculated 519s Total electrostatic energy = 1.885436377745E+03 kJ/mol 519s Calculating forces... 519s ---------------------------------------- 519s CALCULATION #3 (methoxide-solv): MULTIGRID 519s Setting up problem... 519s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 519s Debye length: 0 A 519s Current memory usage: 61.250 MB total, 61.328 MB high water 519s Using linear spline charge discretization. 519s Grid dimensions: 65 x 65 x 65 519s Grid spacings: 0.250 x 0.250 x 0.250 519s Grid lengths: 16.000 x 16.000 x 16.000 519s Grid center: (0.000, 0.000, -0.128) 519s Multigrid levels: 5 519s Molecule ID: 2 519s Linearized traditional PBE 519s Multiple Debye-Huckel sphere boundary conditions 519s 2 ion species (0.000 M ionic strength): 519s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 519s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 519s Solute dielectric: 2.000 519s Solvent dielectric: 78.000 519s Using "molecular" surface definition;harmonic average smoothing 519s Solvent probe radius: 0.000 A 519s Temperature: 300.000 K 519s Electrostatic energies will be calculated 519s Total electrostatic energy = 2.734040568569E+03 kJ/mol 519s Calculating forces... 519s ---------------------------------------- 519s CALCULATION #4 (methoxide-ref): MULTIGRID 519s Setting up problem... 519s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 519s Debye length: 0 A 519s Current memory usage: 61.250 MB total, 61.328 MB high water 519s Using linear spline charge discretization. 519s Grid dimensions: 65 x 65 x 65 519s Grid spacings: 0.250 x 0.250 x 0.250 519s Grid lengths: 16.000 x 16.000 x 16.000 519s Grid center: (0.000, 0.000, -0.128) 519s Multigrid levels: 5 519s Molecule ID: 2 519s Linearized traditional PBE 519s Multiple Debye-Huckel sphere boundary conditions 519s 2 ion species (0.000 M ionic strength): 519s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 519s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 519s Solute dielectric: 2.000 519s Solvent dielectric: 1.000 519s Using "molecular" surface definition;harmonic average smoothing 519s Solvent probe radius: 0.000 A 519s Temperature: 300.000 K 519s Electrostatic energies will be calculated 519s Total electrostatic energy = 3.125279428954E+03 kJ/mol 519s Calculating forces... 519s ---------------------------------------- 519s PRINT STATEMENTS 519s 519s print energy 1 (methanol-solv) - 2 (methanol-ref) end 519s Local net energy (PE 0) = -3.757593772492E+01 kJ/mol 519s Global net ELEC energy = -3.757593772492E+01 kJ/mol 519s 519s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 519s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 519s Global net ELEC energy = -3.912388603848E+02 kJ/mol 519s 519s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 519s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 519s Global net ELEC energy = -3.536629226599E+02 kJ/mol 519s ---------------------------------------- 519s CLEANING UP AND SHUTTING DOWN... 519s Destroying force arrays. 519s No energy arrays to destroy. 519s Destroying multigrid structures. 519s Destroying finite element structures. 519s Destroying 2 molecules 519s Final memory usage: 0.001 MB total, 61.328 MB high water 519s 519s 519s Thanks for using APBS! 519s 519s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 519s *** PASSED *** 519s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 519s *** PASSED *** 519s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 519s *** PASSED *** 519s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 519s *** PASSED *** 519s Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) 519s Checking for intermediate energies in input file apbs-smol.out 519s EXPECTED COMPUTED: 7 519s EXPECTED EXPECTED: 7 519s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] 519s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 519s COMPUTED RESULT 1847.86044002 519s COMPUTED RESULT 1885.436377745 519s COMPUTED RESULT 2734.040568569 519s COMPUTED RESULT 3125.279428954 519s COMPUTED RESULT -37.57593772492 519s COMPUTED RESULT -391.2388603848 519s COMPUTED RESULT -353.6629226599 519s *** PASSED *** 519s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 519s *** PASSED *** 519s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 519s *** PASSED *** 519s Elapsed time: 1.315912 seconds 519s -------------------------------------------------------------------------------- 519s Total elapsed time: 2.7789390000000003 seconds 519s Test results have been logged 519s -------------------------------------------------------------------------------- 519s autopkgtest [00:37:41]: test test-apbs: -----------------------] 520s test-apbs PASS 520s autopkgtest [00:37:42]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 520s autopkgtest [00:37:42]: @@@@@@@@@@@@@@@@@@@@ summary 520s test-apbs PASS