0s autopkgtest [15:19:43]: starting date and time: 2025-10-18 15:19:43+0000 0s autopkgtest [15:19:43]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:19:43]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qlqx87x0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-7.secgroup --name adt-resolute-amd64-apbs-20251018-151943-juju-7f2275-prod-proposed-migration-environment-15-ad55d98c-da9d-482f-a138-1f1c18b7d96f --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-apbs-20251018-151943-juju-7f2275-prod-proposed-migration-environment-15-ad55d98c-da9d-482f-a138-1f1c18b7d96f from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID dd697a48-b6cc-4a02-84bf-0f9f2fad5f89)... 32s autopkgtest [15:20:15]: testbed dpkg architecture: amd64 32s autopkgtest [15:20:15]: testbed apt version: 3.1.6ubuntu2 32s autopkgtest [15:20:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [15:20:16]: testbed release detected to be: None 33s autopkgtest [15:20:16]: updating testbed package index (apt update) 33s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 33s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 34s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 34s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 34s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 34s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 34s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 34s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 34s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [46.6 kB] 34s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [85.2 kB] 34s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 34s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 34s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [233 kB] 34s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [87.6 kB] 34s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [2772 B] 34s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [8376 B] 34s Fetched 972 kB in 1s (1525 kB/s) 35s Reading package lists... 35s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 35s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 35s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 35s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 36s Reading package lists... 36s Reading package lists... 36s Building dependency tree... 36s Reading state information... 36s Calculating upgrade... 36s The following packages will be upgraded: 36s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 36s libpython3-stdlib python3 python3-minimal 36s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 36s Need to get 2751 kB of archives. 36s After this operation, 2048 B of additional disk space will be used. 36s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 36s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 36s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 36s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 36s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 36s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 36s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 36s dpkg-preconfigure: unable to re-open stdin: No such file or directory 36s Fetched 2751 kB in 0s (7443 kB/s) 37s (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 ... 78439 files and directories currently installed.) 37s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 37s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 37s Setting up python3-minimal (3.13.7-2) ... 37s (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 ... 78439 files and directories currently installed.) 37s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 37s running python pre-rtupdate hooks for python3.13... 37s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 37s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 37s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 37s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 37s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 37s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 37s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 37s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 37s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 37s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 37s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 37s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 37s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 37s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 37s Setting up apt (3.1.8ubuntu1) ... 37s Setting up python3 (3.13.7-2) ... 37s running python rtupdate hooks for python3.13... 37s running python post-rtupdate hooks for python3.13... 38s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 38s Processing triggers for man-db (2.13.1-1) ... 39s Processing triggers for libc-bin (2.42-0ubuntu3) ... 39s autopkgtest [15:20:22]: upgrading testbed (apt dist-upgrade and autopurge) 39s Reading package lists... 39s Building dependency tree... 39s Reading state information... 40s Calculating upgrade... 40s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 40s Reading package lists... 40s Building dependency tree... 40s Reading state information... 40s Solving dependencies... 40s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 40s autopkgtest [15:20:23]: rebooting testbed after setup commands that affected boot 55s autopkgtest [15:20:38]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 57s autopkgtest [15:20:40]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 62s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 62s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 62s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 62s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 62s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 62s gpgv: Can't check signature: No public key 62s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 64s autopkgtest [15:20:47]: testing package apbs version 3.4.1-6build2 68s autopkgtest [15:20:51]: build not needed 78s autopkgtest [15:21:01]: test test-apbs: preparing testbed 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Solving dependencies... 79s The following NEW packages will be installed: 79s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax 79s libamd-comgr2 libamd3 libamdhip64-5 libapbs-dev libapbs3t64 libarpack2t64 79s libblas3 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdrm-amdgpu1 79s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfetk-dev 79s libfetk1.9t64 libgfortran5 libgomp1 libhsa-runtime64-1 libhsakmt1 79s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libjs-jquery libjs-mathjax 79s libjs-sphinxdoc libjs-underscore liblapack3 libllvm17t64 libmaloc-dev 79s libmaloc1 libopenmpi40 libpciaccess0 libpsm2-2 librdmacm1t64 libspqr4 79s libsuitesparseconfig7 libsuperlu7 libucx0 libumfpack6 libxnvctrl0 libze1 79s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 79s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 85.7 MB of archives. 79s After this operation, 351 MB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1 [2781 kB] 79s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 apbs-data all 3.4.1-6build2 [1769 kB] 79s Get:3 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmaloc1 amd64 1.5-2 [90.9 kB] 79s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 80s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsuperlu7 amd64 7.0.1+dfsg1-2 [186 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.10.1+dfsg-1 [21.6 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.10.1+dfsg-1 [35.5 kB] 80s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcamd3 amd64 1:7.10.1+dfsg-1 [32.0 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 libccolamd3 amd64 1:7.10.1+dfsg-1 [34.1 kB] 80s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.10.1+dfsg-1 [27.2 kB] 80s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 80s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 80s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcholmod5 amd64 1:7.10.1+dfsg-1 [691 kB] 80s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 libumfpack6 amd64 1:7.10.1+dfsg-1 [290 kB] 80s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfetk1.9t64 amd64 3.4.1-6build2 [608 kB] 80s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapbs3t64 amd64 3.4.1-6build2 [271 kB] 80s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 80s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 81s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 libarpack2t64 amd64 3.9.1-6 [108 kB] 81s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build1 [98.8 kB] 81s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10build1 [8360 B] 81s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 81s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 librdmacm1t64 amd64 56.1-1ubuntu1 [71.4 kB] 81s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfabric1 amd64 2.1.0-1.1 [697 kB] 81s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc15 amd64 2.12.2-1 [181 kB] 81s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libllvm17t64 amd64 1:17.0.6-22build1 [25.9 MB] 82s Get:28 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build3 [14.3 MB] 82s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.125-1 [21.6 kB] 82s Get:30 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsakmt1 amd64 6.2.4+ds-1 [66.8 kB] 82s Get:31 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsa-runtime64-1 amd64 6.1.2-3 [564 kB] 82s Get:32 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamdhip64-5 amd64 5.7.1-6 [9698 kB] 82s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libibumad3 amd64 56.1-1ubuntu1 [31.3 kB] 82s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libibmad5 amd64 56.1-1ubuntu1 [44.0 kB] 82s Get:35 http://ftpmaster.internal/ubuntu resolute/universe amd64 libucx0 amd64 1.19.0+ds-1 [1308 kB] 82s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB] 82s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 82s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 libze1 amd64 1.24.1-2 [599 kB] 83s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [41.0 kB] 83s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc-plugins amd64 2.12.2-1 [22.2 kB] 83s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmpi40 amd64 5.0.8-8ubuntu1 [3384 kB] 83s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 libspqr4 amd64 1:7.10.1+dfsg-1 [148 kB] 83s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 apbs amd64 3.4.1-6build2 [76.5 kB] 83s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 83s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 83s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 83s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 83s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 83s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 apbs-doc all 3.4.1-6build2 [5850 kB] 83s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapbs-dev amd64 3.4.1-6build2 [99.5 kB] 83s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmaloc-dev amd64 1.5-2 [904 kB] 83s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfetk-dev amd64 3.4.1-6build2 [144 kB] 83s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-apbslib amd64 3.4.1-6build2 [219 kB] 83s Fetched 85.7 MB in 4s (19.1 MB/s) 83s Selecting previously unselected package fonts-lato. 83s (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 ... 78439 files and directories currently installed.) 83s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 83s Unpacking fonts-lato (2.015-1) ... 83s Selecting previously unselected package apbs-data. 83s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 83s Unpacking apbs-data (3.4.1-6build2) ... 84s Selecting previously unselected package libmaloc1:amd64. 84s Preparing to unpack .../02-libmaloc1_1.5-2_amd64.deb ... 84s Unpacking libmaloc1:amd64 (1.5-2) ... 84s Selecting previously unselected package libblas3:amd64. 84s Preparing to unpack .../03-libblas3_3.12.1-6build1_amd64.deb ... 84s Unpacking libblas3:amd64 (3.12.1-6build1) ... 84s Selecting previously unselected package libsuperlu7:amd64. 84s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_amd64.deb ... 84s Unpacking libsuperlu7:amd64 (7.0.1+dfsg1-2) ... 84s Selecting previously unselected package libgomp1:amd64. 84s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_amd64.deb ... 84s Unpacking libgomp1:amd64 (15.2.0-5ubuntu1) ... 84s Selecting previously unselected package libsuitesparseconfig7:amd64. 84s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_amd64.deb ... 84s Unpacking libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... 84s Selecting previously unselected package libamd3:amd64. 84s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 84s Unpacking libamd3:amd64 (1:7.10.1+dfsg-1) ... 84s Selecting previously unselected package libcamd3:amd64. 84s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 84s Unpacking libcamd3:amd64 (1:7.10.1+dfsg-1) ... 84s Selecting previously unselected package libccolamd3:amd64. 84s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 84s Unpacking libccolamd3:amd64 (1:7.10.1+dfsg-1) ... 84s Selecting previously unselected package libcolamd3:amd64. 84s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 84s Unpacking libcolamd3:amd64 (1:7.10.1+dfsg-1) ... 84s Selecting previously unselected package libgfortran5:amd64. 84s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 84s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 84s Selecting previously unselected package liblapack3:amd64. 84s Preparing to unpack .../12-liblapack3_3.12.1-6build1_amd64.deb ... 84s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 84s Selecting previously unselected package libcholmod5:amd64. 84s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_amd64.deb ... 84s Unpacking libcholmod5:amd64 (1:7.10.1+dfsg-1) ... 84s Selecting previously unselected package libumfpack6:amd64. 84s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_amd64.deb ... 84s Unpacking libumfpack6:amd64 (1:7.10.1+dfsg-1) ... 84s Selecting previously unselected package libfetk1.9t64:amd64. 84s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_amd64.deb ... 84s Unpacking libfetk1.9t64:amd64 (3.4.1-6build2) ... 84s Selecting previously unselected package libapbs3t64:amd64. 84s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_amd64.deb ... 84s Unpacking libapbs3t64:amd64 (3.4.1-6build2) ... 84s Selecting previously unselected package fonts-mathjax. 84s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 84s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 84s Selecting previously unselected package libjs-mathjax. 84s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 84s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 84s Selecting previously unselected package libarpack2t64:amd64. 84s Preparing to unpack .../19-libarpack2t64_3.9.1-6_amd64.deb ... 84s Unpacking libarpack2t64:amd64 (3.9.1-6) ... 84s Selecting previously unselected package libevent-core-2.1-7t64:amd64. 84s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_amd64.deb ... 84s Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 84s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 84s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_amd64.deb ... 84s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 84s Selecting previously unselected package libpsm2-2. 84s Preparing to unpack .../22-libpsm2-2_11.2.185-2.1_amd64.deb ... 84s Unpacking libpsm2-2 (11.2.185-2.1) ... 84s Selecting previously unselected package librdmacm1t64:amd64. 84s Preparing to unpack .../23-librdmacm1t64_56.1-1ubuntu1_amd64.deb 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libucx0:amd64. 85s Preparing to unpack .../34-libucx0_1.19.0+ds-1_amd64.deb ... 85s Unpacking libucx0:amd64 (1.19.0+ds-1) ... 85s Selecting previously unselected package libpciaccess0:amd64. 85s Preparing to unpack .../35-libpciaccess0_0.18.1-1ubuntu2_amd64.deb ... 85s Unpacking libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 85s Selecting previously unselected package libxnvctrl0:amd64. 85s Preparing to unpack .../36-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 85s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 85s Selecting previously unselected package libze1:amd64. 85s Preparing to unpack .../37-libze1_1.24.1-2_amd64.deb ... 85s Unpacking libze1:amd64 (1.24.1-2) ... 85s Selecting previously unselected package ocl-icd-libopencl1:amd64. 85s Preparing to unpack .../38-ocl-icd-libopencl1_2.3.3-1_amd64.deb ... 85s Unpacking ocl-icd-libopencl1:amd64 (2.3.3-1) ... 85s Selecting previously unselected package libhwloc-plugins:amd64. 85s Preparing to unpack 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Selecting previously unselected package libmaloc-dev. 85s Preparing to unpack .../50-libmaloc-dev_1.5-2_amd64.deb ... 85s Unpacking libmaloc-dev (1.5-2) ... 85s Selecting previously unselected package libfetk-dev:amd64. 85s Preparing to unpack .../51-libfetk-dev_3.4.1-6build2_amd64.deb ... 85s Unpacking libfetk-dev:amd64 (3.4.1-6build2) ... 85s Selecting previously unselected package python3-apbslib. 85s Preparing to unpack .../52-python3-apbslib_3.4.1-6build2_amd64.deb ... 85s Unpacking python3-apbslib (3.4.1-6build2) ... 85s Setting up libmaloc1:amd64 (1.5-2) ... 85s Setting up libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 85s Setting up fonts-lato (2.015-1) ... 85s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 85s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 85s Setting up libibumad3:amd64 (56.1-1ubuntu1) ... 85s Setting up libibmad5:amd64 (56.1-1ubuntu1) ... 85s Setting up apbs-data (3.4.1-6build2) ... 85s Setting up libgomp1:amd64 (15.2.0-5ubuntu1) ... 85s Setting up libze1:amd64 (1.24.1-2) ... 85s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 85s Setting up libblas3:amd64 (3.12.1-6build1) ... 85s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 85s Setting up libllvm17t64:amd64 (1:17.0.6-22build1) ... 85s Setting up libhwloc15:amd64 (2.12.2-1) ... 85s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 85s Setting up ocl-icd-libopencl1:amd64 (2.3.3-1) ... 85s Setting up libpsm2-2 (11.2.185-2.1) ... 85s Setting up libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up librdmacm1t64:amd64 (56.1-1ubuntu1) ... 85s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 85s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build3) ... 85s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 85s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 85s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 85s Setting up libmaloc-dev (1.5-2) ... 85s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 85s Setting up libdrm-amdgpu1:amd64 (2.4.125-1) ... 85s Setting up libfabric1:amd64 (2.1.0-1.1) ... 85s Setting up liblapack3:amd64 (3.12.1-6build1) ... 85s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 85s Setting up libarpack2t64:amd64 (3.9.1-6) ... 85s Setting up libamd3:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up libcolamd3:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 85s Setting up libhwloc-plugins:amd64 (2.12.2-1) ... 85s Setting up libcamd3:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up libsuperlu7:amd64 (7.0.1+dfsg1-2) ... 85s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 85s Setting up libccolamd3:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... 85s Setting up libcholmod5:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up libspqr4:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up apbs-doc (3.4.1-6build2) ... 85s Setting up libumfpack6:amd64 (1:7.10.1+dfsg-1) ... 85s Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... 85s Setting up libfetk1.9t64:amd64 (3.4.1-6build2) ... 85s Setting up libapbs3t64:amd64 (3.4.1-6build2) ... 85s Setting up libfetk-dev:amd64 (3.4.1-6build2) ... 85s Setting up libamdhip64-5:amd64 (5.7.1-6) ... 85s Setting up libapbs-dev:amd64 (3.4.1-6build2) ... 85s Setting up python3-apbslib (3.4.1-6build2) ... 85s Setting up libucx0:amd64 (1.19.0+ds-1) ... 85s Setting up libopenmpi40:amd64 (5.0.8-8ubuntu1) ... 85s Setting up apbs (3.4.1-6build2) ... 85s Processing triggers for man-db (2.13.1-1) ... 86s Processing triggers for libc-bin (2.42-0ubuntu3) ... 87s autopkgtest [15:21:10]: test test-apbs: [----------------------- 88s TESTING WITH BINARY_NAME:apbs 88s START_DIR:/tmp/autopkgtest.fXQP58/autopkgtest_tmp/build 88s -------------------------------------------------------------------------------- 88s Testing forces from apbs-forces.in 88s 88s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000526 seconds 88s -------------------------------------------------------------------------------- 88s -------------------------------------------------------------------------------- 88s Testing input file apbs-mol-auto.in 88s 88s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 88s *** PASSED *** 88s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 88s *** PASSED *** 88s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 88s *** PASSED *** 88s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 88s *** PASSED *** 88s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 88s *** PASSED *** 88s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 88s *** PASSED *** 88s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 88s *** PASSED *** 88s Elapsed time: 0.669273 seconds 88s -------------------------------------------------------------------------------- 88s -------------------------------------------------------------------------------- 88s Testing input file apbs-smol-auto.in 88s 88s CHECKING:/usr/local/sbin/apbs 88s CHECKING:/usr/local/bin/apbs 88s CHECKING:/usr/sbin/apbs 88s CHECKING:/usr/bin/apbs 88s NOTE: Using apbs binary:/usr/bin/apbs 88s Testing all sections 88s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 88s ================================================================================ 88s Running tests for born section 88s BINARY: /usr/bin/apbs 88s INPUT: apbs-mol-auto.in 88s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 88s asc_getToken: Error occurred (bailing out). 88s Vio_scanf: Format problem with input. 88s 88s 88s ---------------------------------------------------------------------- 88s APBS -- Adaptive Poisson-Boltzmann Solver 88s Version APBS 3.4.1 88s 88s Nathan A. Baker (nathan.baker@pnnl.gov) 88s Pacific Northwest National Laboratory 88s 88s Additional contributing authors listed in the code documentation. 88s 88s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 88s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 88s Northwest Division for the U.S. Department of Energy. 88s 88s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 88s Portions Copyright (c) 2002-2020, Nathan A. Baker. 88s Portions Copyright (c) 1999-2002, The Regents of the University of California. 88s Portions Copyright (c) 1995, Michael Holst. 88s All rights reserved. 88s 88s Redistribution and use in source and binary forms, with or without 88s modification, are permitted provided that the following conditions are met: 88s 88s * Redistributions of source code must retain the above copyright notice, this 88s list of conditions and the following disclaimer. 88s 88s * Redistributions in binary form must reproduce the above copyright notice, 88s this list of conditions and the following disclaimer in the documentation 88s and/or other materials provided with the distribution. 88s 88s * Neither the name of the developer nor the names of its contributors may be 88s used to endorse or promote products derived from this software without 88s specific prior written permission. 88s 88s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 88s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 88s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 88s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 88s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 88s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 88s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 88s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 88s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 88s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 88s ---------------------------------------------------------------------- 88s APBS uses FETK (the Finite Element ToolKit) to solve the 88s Poisson-Boltzmann equation numerically. FETK is a portable collection 88s of finite element modeling class libraries developed by the Michael Holst 88s research group and written in an object-oriented form of C. FEtk is 88s designed to solve general coupled systems of nonlinear partial differential 88s equations using adaptive finite element methods, inexact Newton methods, 88s and algebraic multilevel methods. More information about FEtk may be found 88s at . 88s ---------------------------------------------------------------------- 88s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 88s Aqua is a modified form of the Holst group PMG library 88s which has been modified by Patrice Koehl 88s for improved efficiency and 88s memory usage when solving the Poisson-Boltzmann equation. 88s ---------------------------------------------------------------------- 88s Please cite your use of APBS as: 88s 88s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 88s nanosystems: application to microtubules and the ribosome. Proc. 88s Natl. Acad. Sci. USA 98, 10037-10041 2001. 88s 88s 88s This executable compiled on Jan 3 2025 at 11:01:42 88s 88s Parsing input file apbs-mol-auto.in... 88s rank 0 size 1... 88s Parsed input file. 88s Got paths for 1 molecules 88s Reading PQR-format atom data from ion.pqr. 88s 1 atoms 88s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 88s Net charge 1.00e+00 e 88s Preparing to run 6 PBE calculations. 88s ---------------------------------------- 88s CALCULATION #1 (solvated): MULTIGRID 88s Setting up problem... 88s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 88s Debye length: 0 A 88s Current memory usage: 61.280 MB total, 61.280 MB high water 88s Using cubic spline charge discretization. 88s Grid dimensions: 65 x 65 x 65 88s Grid spacings: 0.781 x 0.781 x 0.781 88s Grid lengths: 50.000 x 50.000 x 50.000 88s Grid center: (0.000, 0.000, 0.000) 88s Multigrid levels: 5 88s Molecule ID: 1 88s Linearized traditional PBE 88s Multiple Debye-Huckel sphere boundary conditions 88s 0 ion species (0.000 M ionic strength): 88s Solute dielectric: 1.000 88s Solvent dielectric: 78.540 88s Using "molecular" surface definition; no smoothing 88s Solvent probe radius: 1.400 A 88s Temperature: 298.150 K 88s Electrostatic energies will be calculated 88s Total electrostatic energy = 9.607073836227E+02 kJ/mol 88s Calculating forces... 88s ---------------------------------------- 88s CALCULATION #2 (solvated): MULTIGRID 88s Setting up problem... 88s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 88s Debye length: 0 A 88s Current memory usage: 61.280 MB total, 122.102 MB high water 88s Using cubic spline charge discretization. 88s Grid dimensions: 65 x 65 x 65 88s Grid spacings: 0.383 x 0.383 x 0.383 88s Grid lengths: 24.495 x 24.495 x 24.495 88s Grid center: (0.000, 0.000, 0.000) 88s Multigrid levels: 5 88s Molecule ID: 1 88s Linearized traditional PBE 88s Boundary conditions from focusing 88s 0 ion species (0.000 M ionic strength): 88s Solute dielectric: 1.000 88s Solvent dielectric: 78.540 88s Using "molecular" surface definition; no smoothing 88s Solvent probe radius: 1.400 A 88s Temperature: 298.150 K 88s Electrostatic energies will be calculated 88s Total electrostatic energy = 2.200266567971E+03 kJ/mol 88s Calculating forces... 88s ---------------------------------------- 88s CALCULATION #3 (solvated): MULTIGRID 88s Setting up problem... 88s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 88s Debye length: 0 A 88s Current memory usage: 61.280 MB total, 122.102 MB high water 88s Using cubic spline charge discretization. 88s Grid dimensions: 65 x 65 x 65 88s Grid spacings: 0.188 x 0.188 x 0.188 88s Grid lengths: 12.000 x 12.000 x 12.000 88s Grid center: (0.000, 0.000, 0.000) 88s Multigrid levels: 5 88s Molecule ID: 1 88s Linearized traditional PBE 88s Boundary conditions from focusing 88s 0 ion species (0.000 M ionic strength): 88s Solute dielectric: 1.000 88s Solvent dielectric: 78.540 88s Using "molecular" surface definition; no smoothing 88s Solvent probe radius: 1.400 A 88s Temperature: 298.150 K 88s Electrostatic energies will be calculated 88s Potential to be written to potential.dx.gz 88s Total electrostatic energy = 4.732245131587E+03 kJ/mol 88s Calculating forces... 88s Writing potential to potential-PE0.dx.gz 88s ---------------------------------------- 88s CALCULATION #4 (reference): MULTIGRID 88s Setting up problem... 88s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 88s Debye length: 0 A 88s Current memory usage: 61.207 MB total, 122.102 MB high water 88s Using cubic spline charge discretization. 88s Grid dimensions: 65 x 65 x 65 88s Grid spacings: 0.781 x 0.781 x 0.781 88s Grid lengths: 50.000 x 50.000 x 50.000 88s Grid center: (0.000, 0.000, 0.000) 88s Multigrid levels: 5 88s Molecule ID: 1 88s Linearized traditional PBE 88s Multiple Debye-Huckel sphere boundary conditions 88s 0 ion species (0.000 M ionic strength): 88s Solute dielectric: 1.000 88s Solvent dielectric: 1.000 88s Using "molecular" surface definition; no smoothing 88s Solvent probe radius: 1.400 A 88s Temperature: 298.150 K 88s Electrostatic energies will be calculated 88s Total electrostatic energy = 1.190871482831E+03 kJ/mol 88s Calculating forces... 88s ---------------------------------------- 88s CALCULATION #5 (reference): MULTIGRID 88s Setting up problem... 88s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 88s Debye length: 0 A 88s Current memory usage: 61.207 MB total, 122.102 MB high water 88s Using cubic spline charge discretization. 88s Grid dimensions: 65 x 65 x 65 88s Grid spacings: 0.383 x 0.383 x 0.383 88s Grid lengths: 24.495 x 24.495 x 24.495 88s Grid center: (0.000, 0.000, 0.000) 88s Multigrid levels: 5 88s Molecule ID: 1 88s Linearized traditional PBE 88s Boundary conditions from focusing 88s 0 ion species (0.000 M ionic strength): 88s Solute dielectric: 1.000 88s Solvent dielectric: 1.000 88s Using "molecular" surface definition; no smoothing 88s Solvent probe radius: 1.400 A 88s Temperature: 298.150 K 88s Electrostatic energies will be calculated 88s Total electrostatic energy = 2.430874049735E+03 kJ/mol 88s Calculating forces... 88s [focusFillBound()]: WARNING: 88s Unusually large potential values 88s detected on the focusing boundary! 88s Convergence not guaranteed for NPBE/NRPBE calculations! 88s 88s ---------------------------------------- 88s CALCULATION #6 (reference): MULTIGRID 88s Setting up problem... 88s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 88s Debye length: 0 A 88s Current memory usage: 61.207 MB total, 122.102 MB high water 88s Using cubic spline charge discretization. 88s Grid dimensions: 65 x 65 x 65 88s Grid spacings: 0.188 x 0.188 x 0.188 88s Grid lengths: 12.000 x 12.000 x 12.000 88s Grid center: (0.000, 0.000, 0.000) 88s Multigrid levels: 5 88s Molecule ID: 1 88s Linearized traditional PBE 88s Boundary conditions from focusing 88s 0 ion species (0.000 M ionic strength): 88s Solute dielectric: 1.000 88s Solvent dielectric: 1.000 88s Using "molecular" surface definition; no smoothing 88s Solvent probe radius: 1.400 A 88s Temperature: 298.150 K 88s Electrostatic energies will be calculated 88s Total electrostatic energy = 4.962018684215E+03 kJ/mol 88s Calculating forces... 88s ---------------------------------------- 88s PRINT STATEMENTS 88s 88s print energy 1 (solvated) - 2 (reference) end 88s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 88s Global net ELEC energy = -2.297735526282E+02 kJ/mol 88s ---------------------------------------- 88s CLEANING UP AND SHUTTING DOWN... 88s Destroying force arrays. 88s No energy arrays to destroy. 88s Destroying multigrid structures. 88s Destroying finite element structures. 88s Destroying 1 molecules 88s Final memory usage: 0.001 MB total, 122.102 MB high water 88s 88s 88s Thanks for using APBS! 88s 89s Checking for intermediate energies in input file apbs-mol-auto.out 89s EXPECTED COMPUTED: 7 89s EXPECTED EXPECTED: 7 89s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 89s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 89s COMPUTED RESULT 960.7073836227 89s COMPUTED RESULT 2200.266567971 89s COMPUTED RESULT 4732.245131587 89s COMPUTED RESULT 1190.871482831 89s COMPUTED RESULT 2430.874049735 89s COMPUTED RESULT 4962.018684215 89s COMPUTED RESULT -229.7735526282 89s BINARY: /usr/bin/apbs 89s INPUT: apbs-smol-auto.in 89s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 89s asc_getToken: Error occurred (bailing out). 89s Vio_scanf: Format problem with input. 89s 89s 89s ---------------------------------------------------------------------- 89s APBS -- Adaptive Poisson-Boltzmann Solver 89s Version APBS 3.4.1 89s 89s Nathan A. Baker (nathan.baker@pnnl.gov) 89s Pacific Northwest National Laboratory 89s 89s Additional contributing authors listed in the code documentation. 89s 89s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 89s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 89s Northwest Division for the U.S. Department of Energy. 89s 89s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 89s Portions Copyright (c) 2002-2020, Nathan A. Baker. 89s Portions Copyright (c) 1999-2002, The Regents of the University of California. 89s Portions Copyright (c) 1995, Michael Holst. 89s All rights reserved. 89s 89s Redistribution and use in source and binary forms, with or without 89s modification, are permitted provided that the following conditions are met: 89s 89s * Redistributions of source code must retain the above copyright notice, this 89s list of conditions and the following disclaimer. 89s 89s * Redistributions in binary form must reproduce the above copyright notice, 89s this list of conditions and the following disclaimer in the documentation 89s and/or other materials provided with the distribution. 89s 89s * Neither the name of the developer nor the names of its contributors may be 89s used to endorse or promote products derived from this software without 89s specific prior written permission. 89s 89s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 89s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 89s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 89s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 89s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 89s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 89s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 89s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 89s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 89s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 89s ---------------------------------------------------------------------- 89s APBS uses FETK (the Finite Element ToolKit) to solve the 89s Poisson-Boltzmann equation numerically. FETK is a portable collection 89s of finite element modeling class libraries developed by the Michael Holst 89s research group and written in an object-oriented form of C. FEtk is 89s designed to solve general coupled systems of nonlinear partial differential 89s equations using adaptive finite element methods, inexact Newton methods, 89s and algebraic multilevel methods. More information about FEtk may be found 89s at . 89s ---------------------------------------------------------------------- 89s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 89s Aqua is a modified form of the Holst group PMG library 89s which has been modified by Patrice Koehl 89s for improved efficiency and 89s memory usage when solving the Poisson-Boltzmann equation. 89s ---------------------------------------------------------------------- 89s Please cite your use of APBS as: 89s 89s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 89s nanosystems: application to microtubules and the ribosome. Proc. 89s Natl. Acad. Sci. USA 98, 10037-10041 2001. 89s 89s 89s This executable compiled on Jan 3 2025 at 11:01:42 89s 89s Parsing input file apbs-smol-auto.in... 89s rank 0 size 1... 89s Parsed input file. 89s Got paths for 1 molecules 89s Reading PQR-format atom data from ion.pqr. 89s 1 atoms 89s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 89s Net charge 1.00e+00 e 89s Preparing to run 6 PBE calculations. 89s ---------------------------------------- 89s CALCULATION #1 (solvated): MULTIGRID 89s Setting up problem... 89s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 89s Debye length: 0 A 89s Current memory usage: 61.280 MB total, 61.280 MB high water 89s Using cubic spline charge discretization. 89s Grid dimensions: 65 x 65 x 65 89s Grid spacings: 0.781 x 0.781 x 0.781 89s Grid lengths: 50.000 x 50.000 x 50.000 89s Grid center: (0.000, 0.000, 0.000) 89s Multigrid levels: 5 89s Molecule ID: 1 89s Linearized traditional PBE 89s Multiple Debye-Huckel sphere boundary conditions 89s 0 ion species (0.000 M ionic strength): 89s Solute dielectric: 1.000 89s Solvent dielectric: 78.540 89s Using "molecular" surface definition;harmonic average smoothing 89s Solvent probe radius: 1.400 A 89s Temperature: 298.150 K 89s Electrostatic energies will be calculated 89s Total electrostatic energy = 9.532928767450E+02 kJ/mol 89s Calculating forces... 89s ---------------------------------------- 89s CALCULATION #2 (solvated): MULTIGRID 89s Setting up problem... 89s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 89s Debye length: 0 A 89s Current memory usage: 61.280 MB total, 122.102 MB high water 89s Using cubic spline charge discretization. 89s Grid dimensions: 65 x 65 x 65 89s Grid spacings: 0.383 x 0.383 x 0.383 89s Grid lengths: 24.495 x 24.495 x 24.495 89s Grid center: (0.000, 0.000, 0.000) 89s Multigrid levels: 5 89s Molecule ID: 1 89s Linearized traditional PBE 89s Boundary conditions from focusing 89s 0 ion species (0.000 M ionic strength): 89s Solute dielectric: 1.000 89s Solvent dielectric: 78.540 89s Using "molecular" surface definition;harmonic average smoothing 89s Solvent probe radius: 1.400 A 89s Temperature: 298.150 K 89s Electrostatic energies will be calculated 89s Total electrostatic energy = 2.201243880085E+03 kJ/mol 89s Calculating forces... 89s ---------------------------------------- 89s CALCULATION #3 (solvated): MULTIGRID 89s Setting up problem... 89s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 89s Debye length: 0 A 89s Current memory usage: 61.280 MB total, 122.102 MB high water 89s Using cubic spline charge discretization. 89s Grid dimensions: 65 x 65 x 65 89s Grid spacings: 0.188 x 0.188 x 0.188 89s Grid lengths: 12.000 x 12.000 x 12.000 89s Grid center: (0.000, 0.000, 0.000) 89s Multigrid levels: 5 89s Molecule ID: 1 89s Linearized traditional PBE 89s Boundary conditions from focusing 89s 0 ion species (0.000 M ionic strength): 89s Solute dielectric: 1.000 89s Solvent dielectric: 78.540 89s Using "molecular" surface definition;harmonic average smoothing 89s Solvent probe radius: 1.400 A 89s Temperature: 298.150 K 89s Electrostatic energies will be calculated 89s Total electrostatic energy = 4.733006258977E+03 kJ/mol 89s Calculating forces... 89s ---------------------------------------- 89s CALCULATION #4 (reference): MULTIGRID 89s Setting up problem... 89s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 89s Debye length: 0 A 89s Current memory usage: 61.207 MB total, 122.102 MB high water 89s Using cubic spline charge discretization. 89s Grid dimensions: 65 x 65 x 65 89s Grid spacings: 0.781 x 0.781 x 0.781 89s Grid lengths: 50.000 x 50.000 x 50.000 89s Grid center: (0.000, 0.000, 0.000) 89s Multigrid levels: 5 89s Molecule ID: 1 89s Linearized traditional PBE 89s Multiple Debye-Huckel sphere boundary conditions 89s 0 ion species (0.000 M ionic strength): 89s Solute dielectric: 1.000 89s Solvent dielectric: 1.000 89s Using "molecularTesting computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 89s *** PASSED *** 89s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 89s *** PASSED *** 89s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 89s *** PASSED *** 89s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 89s *** PASSED *** 89s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 89s *** PASSED *** 89s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 89s *** PASSED *** 89s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 89s *** PASSED *** 89s Elapsed time: 0.648921 seconds 89s -------------------------------------------------------------------------------- 89s -------------------------------------------------------------------------------- 89s Testing input file apbs-mol-parallel.in 89s 89s Splitting the input file into 4 separate files using the inputgen utility 89s 89s " surface definition;harmonic average smoothing 89s Solvent probe radius: 1.400 A 89s Temperature: 298.150 K 89s Electrostatic energies will be calculated 89s Total electrostatic energy = 1.190871482831E+03 kJ/mol 89s Calculating forces... 89s ---------------------------------------- 89s CALCULATION #5 (reference): MULTIGRID 89s Setting up problem... 89s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 89s Debye length: 0 A 89s Current memory usage: 61.207 MB total, 122.102 MB high water 89s Using cubic spline charge discretization. 89s Grid dimensions: 65 x 65 x 65 89s Grid spacings: 0.383 x 0.383 x 0.383 89s Grid lengths: 24.495 x 24.495 x 24.495 89s Grid center: (0.000, 0.000, 0.000) 89s Multigrid levels: 5 89s Molecule ID: 1 89s Linearized traditional PBE 89s Boundary conditions from focusing 89s 0 ion species (0.000 M ionic strength): 89s Solute dielectric: 1.000 89s Solvent dielectric: 1.000 89s Using "molecular" surface definition;harmonic average smoothing 89s Solvent probe radius: 1.400 A 89s Temperature: 298.150 K 89s Electrostatic energies will be calculated 89s Total electrostatic energy = 2.430874049735E+03 kJ/mol 89s Calculating forces... 89s [focusFillBound()]: WARNING: 89s Unusually large potential values 89s detected on the focusing boundary! 89s Convergence not guaranteed for NPBE/NRPBE calculations! 89s 89s ---------------------------------------- 89s CALCULATION #6 (reference): MULTIGRID 89s Setting up problem... 89s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 89s Debye length: 0 A 89s Current memory usage: 61.207 MB total, 122.102 MB high water 89s Using cubic spline charge discretization. 89s Grid dimensions: 65 x 65 x 65 89s Grid spacings: 0.188 x 0.188 x 0.188 89s Grid lengths: 12.000 x 12.000 x 12.000 89s Grid center: (0.000, 0.000, 0.000) 89s Multigrid levels: 5 89s Molecule ID: 1 89s Linearized traditional PBE 89s Boundary conditions from focusing 89s 0 ion species (0.000 M ionic strength): 89s Solute dielectric: 1.000 89s Solvent dielectric: 1.000 89s Using "molecular" surface definition;harmonic average smoothing 89s Solvent probe radius: 1.400 A 89s Temperature: 298.150 K 89s Electrostatic energies will be calculated 89s Total electrostatic energy = 4.962018684215E+03 kJ/mol 89s Calculating forces... 89s ---------------------------------------- 89s PRINT STATEMENTS 89s 89s print energy 1 (solvated) - 2 (reference) end 89s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 89s Global net ELEC energy = -2.290124252387E+02 kJ/mol 89s ---------------------------------------- 89s CLEANING UP AND SHUTTING DOWN... 89s Destroying force arrays. 89s No energy arrays to destroy. 89s Destroying multigrid structures. 89s Destroying finite element structures. 89s Destroying 1 molecules 89s Final memory usage: 0.001 MB total, 122.102 MB high water 89s 89s 89s Thanks for using APBS! 89s 90s Checking for intermediate energies in input file apbs-smol-auto.out 90s EXPECTED COMPUTED: 7 90s EXPECTED EXPECTED: 7 90s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 90s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 90s COMPUTED RESULT 953.292876745 90s COMPUTED RESULT 2201.243880085 90s COMPUTED RESULT 4733.006258977 90s COMPUTED RESULT 1190.871482831 90s COMPUTED RESULT 2430.874049735 90s COMPUTED RESULT 4962.018684215 90s COMPUTED RESULT -229.0124252387 90s BINARY: /usr/bin/apbs 90s INPUT: apbs-mol-parallel-PE0.in 90s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 90s asc_getToken: Error occurred (bailing out). 90s Vio_scanf: Format problem with input. 90s 90s 90s ---------------------------------------------------------------------- 90s APBS -- Adaptive Poisson-Boltzmann Solver 90s Version APBS 3.4.1 90s 90s Nathan A. Baker (nathan.baker@pnnl.gov) 90s Pacific Northwest National Laboratory 90s 90s Additional contributing authors listed in the code documentation. 90s 90s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 90s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 90s Northwest Division for the U.S. Department of Energy. 90s 90s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 90s Portions Copyright (c) 2002-2020, Nathan A. Baker. 90s Portions Copyright (c) 1999-2002, The Regents of the University of California. 90s Portions Copyright (c) 1995, Michael Holst. 90s All rights reserved. 90s 90s Redistribution and use in source and binary forms, with or without 90s modification, are permitted provided that the following conditions are met: 90s 90s * Redistributions of source code must retain the above copyright notice, this 90s list of conditions and the following disclaimer. 90s 90s * Redistributions in binary form must reproduce the above copyright notice, 90s this list of conditions and the following disclaimer in the documentation 90s and/or other materials provided with the distribution. 90s 90s * Neither the name of the developer nor the names of its contributors may be 90s used to endorse or promote products derived from this software without 90s specific prior written permission. 90s 90s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 90s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 90s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 90s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 90s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 90s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 90s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 90s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 90s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 90s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 90s ---------------------------------------------------------------------- 90s APBS uses FETK (the Finite Element ToolKit) to solve the 90s Poisson-Boltzmann equation numerically. FETK is a portable collection 90s of finite element modeling class libraries developed by the Michael Holst 90s research group and written in an object-oriented form of C. FEtk is 90s designed to solve general coupled systems of nonlinear partial differential 90s equations using adaptive finite element methods, inexact Newton methods, 90s and algebraic multilevel methods. More information about FEtk may be found 90s at . 90s ---------------------------------------------------------------------- 90s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 90s Aqua is a modified form of the Holst group PMG library 90s which has been modified by Patrice Koehl 90s for improved efficiency and 90s memory usage when solving the Poisson-Boltzmann equation. 90s ---------------------------------------------------------------------- 90s Please cite your use of APBS as: 90s 90s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 90s nanosystems: application to microtubules and the ribosome. Proc. 90s Natl. Acad. Sci. USA 98, 10037-10041 2001. 90s 90s 90s This executable compiled on Jan 3 2025 at 11:01:42 90s 90s Parsing input file apbs-mol-parallel-PE0.in... 90s rank 0 size 1... 90s Parsed input file. 90s Got paths for 1 molecules 90s Reading PQR-format atom data from ion.pqr. 90s 1 atoms 90s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 90s Net charge 1.00e+00 e 90s Preparing to run 6 PBE calculations. 90s ---------------------------------------- 90s CALCULATION #1 (solvated): MULTIGRID 90s Setting up problem... 90s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 90s Debye length: 0 A 90s Current memory usage: 61.280 MB total, 61.280 MB high water 90s Using cubic spline charge discretization. 90s Partition overlap fraction = 0.1 90s Processor array = 2 x 2 x 1 90s Grid dimensions: 65 x 65 x 65 90s Grid spacings: 0.781 x 0.781 x 0.781 90s Grid lengths: 50.000 x 50.000 x 50.000 90s Grid center: (0.000, 0.000, 0.000) 90s Multigrid levels: 5 90s Molecule ID: 1 90s Linearized traditional PBE 90s Multiple Debye-Huckel sphere boundary conditions 90s 0 ion species (0.000 M ionic strength): 90s Solute dielectric: 1.000 90s Solvent dielectric: 78.540 90s Using "molecular" surface definition; no smoothing 90s Solvent probe radius: 1.400 A 90s Temperature: 298.150 K 90s Electrostatic energies will be calculated 90s Total electrostatic energy = 2.401768459022E+02 kJ/mol 90s Calculating forces... 90s ---------------------------------------- 90s CALCULATION #2 (solvated): MULTIGRID 90s Setting up problem... 90s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 90s Debye length: 0 A 90s Current memory usage: 61.280 MB total, 122.102 MB high water 90s Using cubic spline charge discretization. 90s Partition overlap fraction = 0.1 90s Processor array = 2 x 2 x 1 90s Grid dimensions: 65 x 65 x 65 90s Grid spacings: 0.296 x 0.296 x 0.383 90s Grid lengths: 18.944 x 18.944 x 24.495 90s Grid center: (-2.411, -2.411, 0.000) 90s Multigrid levels: 5 90s Molecule ID: 1 90s Linearized traditional PBE 90s Boundary conditions from focusing 90s 0 ion species (0.000 M ionic strength): 90s Solute dielectric: 1.000 90s Solvent dielectric: 78.540 90s Using "molecular" surface definition; no smoothing 90s Solvent probe radius: 1.400 A 90s Temperature: 298.150 K 90s Electrostatic energies will be calculated 90s Total electrostatic energy = 8.142935592471E+02 kJ/mol 90s Calculating forces... 90s [focusFillBound()]: WARNING: 90s Unusually large potential values 90s detected on the focusing boundary! 90s Convergence not guaranteed for NPBE/NRPBE calculations! 90s 90s ---------------------------------------- 90s CALCULATION #3 (solvated): MULTIGRID 90s Setting up problem... 90s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 90s Debye length: 0 A 90s Current memory usage: 61.280 MB total, 122.102 MB high water 90s Using cubic spline charge discretization. 90s Partition overlap fraction = 0.1 90s Processor array = 2 x 2 x 1 90s Grid dimensions: 65 x 65 x 65 90s Grid spacings: 0.112 x 0.112 x 0.188 90s Grid lengths: 7.178 x 7.178 x 12.000 90s Grid center: (-2.411, -2.411, 0.000) 90s Multigrid levels: 5 90s Molecule ID: 1 90s Linearized traditional PBE 90s Boundary conditions from focusing 90s 0 ion species (0.000 M ionic strength): 90s Solute dielectric: 1.000 90s Solvent dielectric: 78.540 90s Using "molecular" surface definition; no smoothing 90s Solvent probe radius: 1.400 A 90s Temperature: 298.150 K 90s Electrostatic energies will be calculated 90s Total electrostatic energy = 1.485255308186E+03 kJ/mol 90s Calculating forces... 90s ---------------------------------------- 90s CALCULATION #4 (reference): MULTIGRID 90s Setting up problem... 90s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 90s Debye length: 0 A 90s Current memory usage: 61.207 MB total, 122.102 MB high water 90s Using cubic spline charge discretization. 90s Partition overlap fraction = 0.1 90s Processor array = 2 x 2 x 1 90s Grid dimensions: 65 x 65 x 65 90s Grid spacings: 0.781 x 0.781 x 0.781 90s Grid lengths: 50.000 x 50.000 x 50.000 90s Grid center: (0.000, 0.000, 0.000) 90s Multigrid levels: 5 90s Molecule ID: 1 90s Linearized traditional PBE 90s Multiple Debye-Huckel sphere boundary conditions 90s 0 ion species (0.000 M ionic strength): 90s Solute dielectric: 1.000 90s Solvent dielectric: 1.000 90s Using "molecular" surface definition; no smoothing 90s Solvent probe radius: 1.400 A 90s Temperature: 298.150 K 90s Electrostatic energies will be calculated 90s Total electrostatic energy = 2.977178707009E+02 kJ/mol 90s Calculating forces... 90s ---------------------------------------- 90s CALCULATION #5 (reference): MULTIGRID 90s Setting up problem... 90s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 90s Debye length: 0 A 90s Current memory usage: 61.207 MB total, 122.102 MB high water 90s Using cubic spline charge discretization. 90s Partition overlap fraction = 0.1 90s Processor array = 2 x 2 x 1 90s Grid dimensions: 65 x 65 x 65 90s Grid spacings: 0.296 x 0.296 x 0.383 90s Grid lengths: 18.944 x 18.944 x 24.495 90s Grid center: (-2.411, -2.411, 0.000) 90s Multigrid levels: 5 90s Molecule ID: 1 90s Linearized traditional PBE 90s Boundary conditions from focusing 90s 0 ion species (0.000 M ionic strength): 90s Solute dielectric: 1.000 90s Solvent dielectric: 1.000 90s Using "molecular" surface definition; no smoothing 90s Solvent probe radius: 1.400 A 90s Temperature: 298.150 K 90s Electrostatic energies will be calculated 90s Total electrostatic energy = 8.799304557588E+02 kJ/mol 90s Calculating forces... 90s [focusFillBound()]: WARNING: 90s Unusually large potential values 90s detected on the focusing boundary! 90s Convergence not guaranteed for NPBE/NRPBE calculations! 90s 90s ---------------------------------------- 90s CALCULATION #6 (reference): MULTIGRID 90s Setting up problem... 90s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 90s Debye length: 0 A 90s Current memory usage: 61.207 MB total, 122.102 MB high water 90s Using cubic spline charge discretization. 90s Partition overlap fraction = 0.1 90s Processor array = 2 x 2 x 1 90s Grid dimensions: 65 x 65 x 65 90s Grid spacings: 0.112 x 0.112 x 0.188 90s Grid lengths: 7.178 x 7.178 x 12.000 90s Grid center: (-2.411, -2.411, 0.000) 90s Multigrid levels: 5 90s Molecule ID: 1 90s Linearized traditional PBE 90s Boundary conditions from focusing 90s 0 ion species (0.000 M ionic strength): 90s Solute dielectric: 1.000 90s Solvent dielectric: 1.000 90s Using "molecular" surface definition; no smoothing 90s Solvent probe radius: 1.400 A 90s Temperature: 298.150 K 90s Electrostatic energies will be calculated 90s Total electrostatic energy = 1.542873949131E+03 kJ/mol 90s Calculating forces... 90s ---------------------------------------- 90s PRINT STATEMENTS 90s 90s print energy 1 (solvated) - 2 (reference) end 90s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 90s Global net ELEC energy = -5.761864094552E+01 kJ/mol 90s ---------------------------------------- 90s CLEANING UP AND SHUTTING DOWN... 90s Destroying force arrays. 90s No energy arrays to destroy. 90s Destroying multigrid structures. 90s Destroying finite element structures. 90s Destroying 1 molecules 90s Final memory usage: 0.001 MB total, 122.102 MB high water 90s 90s 90s Thanks for using APBS! 90s 90s Processor 0 results: 90s 2.401768459022e+02 90s 8.142935592471e+02 90s 1.485255308186e+03 90s 2.977178707009e+02 90s 8.799304557588e+02 90s 1.542873949131e+03 90s -5.761864094552e+01 90s 91s Processor 1 results: 91s 2.401768459022e+02 91s 8.142778312125e+02 91s 1.485246667424e+03 91s 2.977178707009e+02 91s 8.799304557588e+02 91s 1.542873949131e+03 91s -5.762728170718e+01 91s 91s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 91s BINARY: /usr/bin/apbs 91s INPUT: apbs-mol-parallel-PE1.in 91s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 91s asc_getToken: Error occurred (bailing out). 91s Vio_scanf: Format problem with input. 91s 91s 91s ---------------------------------------------------------------------- 91s APBS -- Adaptive Poisson-Boltzmann Solver 91s Version APBS 3.4.1 91s 91s Nathan A. Baker (nathan.baker@pnnl.gov) 91s Pacific Northwest National Laboratory 91s 91s Additional contributing authors listed in the code documentation. 91s 91s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 91s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 91s Northwest Division for the U.S. Department of Energy. 91s 91s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 91s Portions Copyright (c) 2002-2020, Nathan A. Baker. 91s Portions Copyright (c) 1999-2002, The Regents of the University of California. 91s Portions Copyright (c) 1995, Michael Holst. 91s All rights reserved. 91s 91s Redistribution and use in source and binary forms, with or without 91s modification, are permitted provided that the following conditions are met: 91s 91s * Redistributions of source code must retain the above copyright notice, this 91s list of conditions and the following disclaimer. 91s 91s * Redistributions in binary form must reproduce the above copyright notice, 91s this list of conditions and the following disclaimer in the documentation 91s and/or other materials provided with the distribution. 91s 91s * Neither the name of the developer nor the names of its contributors may be 91s used to endorse or promote products derived from this software without 91s specific prior written permission. 91s 91s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 91s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 91s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 91s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 91s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 91s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 91s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 91s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 91s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 91s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 91s ---------------------------------------------------------------------- 91s APBS uses FETK (the Finite Element ToolKit) to solve the 91s Poisson-Boltzmann equation numerically. FETK is a portable collection 91s of finite element modeling class libraries developed by the Michael Holst 91s research group and written in an object-oriented form of C. FEtk is 91s designed to solve general coupled systems of nonlinear partial differential 91s equations using adaptive finite element methods, inexact Newton methods, 91s and algebraic multilevel methods. More information about FEtk may be found 91s at . 91s ---------------------------------------------------------------------- 91s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 91s Aqua is a modified form of the Holst group PMG library 91s which has been modified by Patrice Koehl 91s for improved efficiency and 91s memory usage when solving the Poisson-Boltzmann equation. 91s ---------------------------------------------------------------------- 91s Please cite your use of APBS as: 91s 91s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 91s nanosystems: application to microtubules and the ribosome. Proc. 91s Natl. Acad. Sci. USA 98, 10037-10041 2001. 91s 91s 91s This executable compiled on Jan 3 2025 at 11:01:42 91s 91s Parsing input file apbs-mol-parallel-PE1.in... 91s rank 0 size 1... 91s Parsed input file. 91s Got paths for 1 molecules 91s Reading PQR-format atom data from ion.pqr. 91s 1 atoms 91s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 91s Net charge 1.00e+00 e 91s Preparing to run 6 PBE calculations. 91s ---------------------------------------- 91s CALCULATION #1 (solvated): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.280 MB total, 61.280 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.781 x 0.781 x 0.781 91s Grid lengths: 50.000 x 50.000 x 50.000 91s Grid center: (0.000, 0.000, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Multiple Debye-Huckel sphere boundary conditions 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 78.540 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 2.401768459022E+02 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s CALCULATION #2 (solvated): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.280 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.296 x 0.296 x 0.383 91s Grid lengths: 18.944 x 18.944 x 24.495 91s Grid center: (2.411, -2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 78.540 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 8.142778312125E+02 kJ/mol 91s Calculating forces... 91s [focusFillBound()]: WARNING: 91s Unusually large potential values 91s detected on the focusing boundary! 91s Convergence not guaranteed for NPBE/NRPBE calculations! 91s 91s ---------------------------------------- 91s CALCULATION #3 (solvated): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.280 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.112 x 0.112 x 0.188 91s Grid lengths: 7.178 x 7.178 x 12.000 91s Grid center: (2.411, -2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 78.540 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 1.485246667424E+03 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s CALCULATION #4 (reference): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.207 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.781 x 0.781 x 0.781 91s Grid lengths: 50.000 x 50.000 x 50.000 91s Grid center: (0.000, 0.000, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Multiple Debye-Huckel sphere boundary conditions 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 1.000 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 2.977178707009E+02 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s CALCULATION #5 (reference): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.207 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.296 x 0.296 x 0.383 91s Grid lengths: 18.944 x 18.944 x 24.495 91s Grid center: (2.411, -2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 1.000 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 8.799304557588E+02 kJ/mol 91s Calculating forces... 91s [focusFillBound()]: WARNING: 91s Unusually large potential values 91s detected on the focusing boundary! 91s Convergence not guaranteed for NPBE/NRPBE calculations! 91s 91s ---------------------------------------- 91s CALCULATION #6 (reference): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.207 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.112 x 0.112 x 0.188 91s Grid lengths: 7.178 x 7.178 x 12.000 91s Grid center: (2.411, -2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 1.000 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 1.542873949131E+03 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s PRINT STATEMENTS 91s 91s print energy 1 (solvated) - 2 (reference) end 91s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 91s Global net ELEC energy = -5.762728170718E+01 kJ/mol 91s ---------------------------------------- 91s CLEANING UP AND SHUTTING DOWN... 91s Destroying force arrays. 91s No energy arrays to destroy. 91s Destroying multigrid structures. 91s Destroying finite element structures. 91s Destroying 1 molecules 91s Final memory usage: 0.001 MB total, 122.102 MB high water 91s 91s 91s Thanks for using APBS! 91s 91s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 91s BINARY: /usr/bin/apbs 91s INPUT: apbs-mol-parallel-PE2.in 91s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 91s asc_getToken: Error occurred (bailing out). 91s Vio_scanf: Format problem with input. 91s 91s 91s ---------------------------------------------------------------------- 91s APBS -- Adaptive Poisson-Boltzmann Solver 91s Version APBS 3.4.1 91s 91s Nathan A. Baker (nathan.baker@pnnl.gov) 91s Pacific Northwest National Laboratory 91s 91s Additional contributing authors listed in the code documentation. 91s 91s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 91s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 91s Northwest Division for the U.S. Department of Energy. 91s 91s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 91s Portions Copyright (c) 2002-2020, Nathan A. Baker. 91s Portions Copyright (c) 1999-2002, The Regents of the University of California. 91s Portions Copyright (c) 1995, Michael Holst. 91s All rights reserved. 91s 91s Redistribution and use in source and binary forms, with or without 91s modification, are permitted provided that the following conditions are met: 91s 91s * Redistributions of source code must retain the above copyright notice, this 91s list of conditions and the following disclaimer. 91s 91s * Redistributions in binary form must reproduce the above copyright notice, 91s this list of conditions and the following disclaimer in the documentation 91s and/or other materials provided with the distribution. 91s 91s * Neither the name of the developer nor the names of its contributors may be 91s used to endorse or promote products derived from this software without 91s specific prior written permission. 91s 91s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 91s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 91s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 91s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 91s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 91s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 91s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 91s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 91s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 91s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 91s ---------------------------------------------------------------------- 91s APBS uses FETK (the Finite Element ToolKit) to solve the 91s Poisson-Boltzmann equation numerically. FETK is a portable collection 91s of finite element modeling class libraries developed by the Michael Holst 91s research group and written in an object-oriented form of C. FEtk is 91s designed to solve general coupled systems of nonlinear partial differential 91s equations using adaptive finite element methods, inexact Newton methods, 91s and algebraic multilevel methods. More information about FEtk may be found 91s at . 91s ---------------------------------------------------------------------- 91s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 91s Aqua is a modified form of the Holst group PMG library 91s which has been modified by Patrice Koehl 91s for improved efficiency and 91s memory usage when solving the Poisson-Boltzmann equation. 91s ---------------------------------------------------------------------- 91s Please cite your use of APBS as: 91s 91s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 91s nanosystems: application to microtubules and the ribosome. Proc. 91s Natl. Acad. Sci. USA 98, 10037-10041 2001. 91s 91s 91s This executable compiled on Jan 3 2025 at 11:01:42 91s 91s Parsing input file apbs-mol-parallel-PE2.in... 91s rank 0 size 1... 91s Parsed input file. 91s Got paths for 1 molecules 91s Reading PQR-format atom data from ion.pqr. 91s 1 atoms 91s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 91s Net charge 1.00e+00 e 91s Preparing to run 6 PBE calculations. 91s ---------------------------------------- 91s CALCULATION #1 (solvated): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.280 MB total, 61.280 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.781 x 0.781 x 0.781 91s Grid lengths: 50.000 x 50.000 x 50.000 91s Grid center: (0.000, 0.000, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Multiple Debye-Huckel sphere boundary conditions 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 78.540 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 2.401768459091E+02 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s CALCULATION #2 (solvated): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.280 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.296 x 0.296 x 0.383 91s Grid lengths: 18.944 x 18.944 x 24.495 91s Grid center: (-2.411, 2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 78.540 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 8.142935605696E+02 kJ/mol 91s Calculating forces... 91s [focusFillBound()]: WARNING: 91s Unusually large potential values 91s detected on the focusing boundary! 91s Convergence not guaranteed for NPBE/NRPBE calculations! 91s 91s ---------------------------------------- 91s CALCULATION #3 (solvated): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.280 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.112 x 0.112 x 0.188 91s Grid lengths: 7.178 x 7.178 x 12.000 91s Grid center: (-2.411, 2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 78.540 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 1.485255306569E+03 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s CALCULATION #4 (reference): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.207 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.781 x 0.781 x 0.781 91s Grid lengths: 50.000 x 50.000 x 50.000 91s Grid center: (0.000, 0.000, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Multiple Debye-Huckel sphere boundary conditions 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 1.000 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 2.977178707146E+02 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s CALCULATION #5 (reference): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.207 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.296 x 0.296 x 0.383 91s Grid lengths: 18.944 x 18.944 x 24.495 91s Grid center: (-2.411, 2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 1.000 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 8.799304557596E+02 kJ/mol 91s Calculating forces... 91s [focusFillBound()]: WARNING: 91s Unusually large potential values 91s detected on the focusing boundary! 91s Convergence not guaranteed for NPBE/NRPBE calculations! 91s 91s ---------------------------------------- 91s CALCULATION #6 (reference): MULTIGRID 91s Setting up problem... 91s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 91s Debye length: 0 A 91s Current memory usage: 61.207 MB total, 122.102 MB high water 91s Using cubic spline charge discretization. 91s Partition overlap fraction = 0.1 91s Processor array = 2 x 2 x 1 91s Grid dimensions: 65 x 65 x 65 91s Grid spacings: 0.112 x 0.112 x 0.188 91s Grid lengths: 7.178 x 7.178 x 12.000 91s Grid center: (-2.411, 2.411, 0.000) 91s Multigrid levels: 5 91s Molecule ID: 1 91s Linearized traditional PBE 91s Boundary conditions from focusing 91s 0 ion species (0.000 M ionic strength): 91s Solute dielectric: 1.000 91s Solvent dielectric: 1.000 91s Using "molecular" surface definition; no smoothing 91s Solvent probe radius: 1.400 A 91s Temperature: 298.150 K 91s Electrostatic energies will be calculated 91s Total electrostatic energy = 1.542873949141E+03 kJ/mol 91s Calculating forces... 91s ---------------------------------------- 91s PRINT STATEMENTS 91s 91s print energy 1 (solvated) - 2 (reference) end 91s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 91s Global net ELEC energy = -5.761864257239E+01 kJ/mol 91s ---------------------------------------- 91s CLEANING UP AND SHUTTING DOWN... 91s Destroying force arrays. 91s No energy arrays to destroy. 91s Destroying multigrid structures. 91s Destroying finite element structures. 91s Destroying 1 molecules 91s Final memory usage: 0.001 MB total, 122.102 MB high water 91s 91s 91s Thanks for using APBS! 91s 91s Processor 2 results: 91s 2.401768459091e+02 91s 8.142935605696e+02 91s 1.485255306569e+03 91s 2.977178707146e+02 91s 8.799304557596e+02 91s 1.542873949141e+03 91s -5.761864257239e+01 91s 92s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 92s BINARY: /usr/bin/apbs 92s INPUT: apbs-mol-parallel-PE3.in 92s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 92s asc_getToken: Error occurred (bailing out). 92s Vio_scanf: Format problem with input. 92s 92s 92s ---------------------------------------------------------------------- 92s APBS -- Adaptive Poisson-Boltzmann Solver 92s Version APBS 3.4.1 92s 92s Nathan A. Baker (nathan.baker@pnnl.gov) 92s Pacific Northwest National Laboratory 92s 92s Additional contributing authors listed in the code documentation. 92s 92s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 92s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 92s Northwest Division for the U.S. Department of Energy. 92s 92s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 92s Portions Copyright (c) 2002-2020, Nathan A. Baker. 92s Portions Copyright (c) 1999-2002, The Regents of the University of California. 92s Portions Copyright (c) 1995, Michael Holst. 92s All rights reserved. 92s 92s Redistribution and use in source and binary forms, with or without 92s modification, are permitted provided that the following conditions are met: 92s 92s * Redistributions of source code must retain the above copyright notice, this 92s list of conditions and the following disclaimer. 92s 92s * Redistributions in binary form must reproduce the above copyright notice, 92s this list of conditions and the following disclaimer in the documentation 92s and/or other materials provided with the distribution. 92s 92s * Neither the name of the developer nor the names of its contributors may be 92s used to endorse or promote products derived from this software without 92s specific prior written permission. 92s 92s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 92s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 92s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 92s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 92s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 92s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 92s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 92s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 92s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 92s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 92s ---------------------------------------------------------------------- 92s APBS uses FETK (the Finite Element ToolKit) to solve the 92s Poisson-Boltzmann equation numerically. FETK is a portable collection 92s of finite element modeling class libraries developed by the Michael Holst 92s research group and written in an object-oriented form of C. FEtk is 92s designed to solve general coupled systems of nonlinear partial differential 92s equations using adaptive finite element methods, inexact Newton methods, 92s and algebraic multilevel methods. More information about FEtk may be found 92s at . 92s ---------------------------------------------------------------------- 92s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 92s Aqua is a modified form of the Holst group PMG library 92s which has been modified by Patrice Koehl 92s for improved efficiency and 92s memory usage when solving the Poisson-Boltzmann equation. 92s ---------------------------------------------------------------------- 92s Please cite your use of APBS as: 92s 92s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 92s nanosystems: application to microtubules and the ribosome. Proc. 92s Natl. Acad. Sci. USA 98, 10037-10041 2001. 92s 92s 92s This executable compiled on Jan 3 2025 at 11:01:42 92s 92s Parsing input file apbs-mol-parallel-PE3.in... 92s rank 0 size 1... 92s Parsed input file. 92s Got paths for 1 molecules 92s Reading PQR-format atom data from ion.pqr. 92s 1 atoms 92s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 92s Net charge 1.00e+00 e 92s Preparing to run 6 PBE calculations. 92s ---------------------------------------- 92s CALCULATION #1 (solvated): MULTIGRID 92s Setting up problem... 92s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 92s Debye length: 0 A 92s Current memory usage: 61.280 MB total, 61.280 MB high water 92s Using cubic spline charge discretization. 92s Partition overlap fraction = 0.1 92s Processor array = 2 x 2 x 1 92s Grid dimensions: 65 x 65 x 65 92s Grid spacings: 0.781 x 0.781 x 0.781 92s Grid lengths: 50.000 x 50.000 x 50.000 92s Grid center: (0.000, 0.000, 0.000) 92s Multigrid levels: 5 92s Molecule ID: 1 92s Linearized traditional PBE 92s Multiple Debye-Huckel sphere boundary conditions 92s 0 ion species (0.000 M ionic strength): 92s Solute dielectric: 1.000 92s Solvent dielectric: 78.540 92s Using "molecular" surface definition; no smoothing 92s Solvent probe radius: 1.400 A 92s Temperature: 298.150 K 92s Electrostatic energies will be calculated 92s Total electrostatic energy = 2.401768459091E+02 kJ/mol 92s Calculating forces... 92s ---------------------------------------- 92s CALCULATION #2 (solvated): MULTIGRID 92s Setting up problem... 92s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 92s Debye length: 0 A 92s Current memory usage: 61.280 MB total, 122.102 MB high water 92s Using cubic spline charge discretization. 92s Partition overlap fraction = 0.1 92s Processor array = 2 x 2 x 1 92s Grid dimensions: 65 x 65 x 65 92s Grid spacings: 0.296 x 0.296 x 0.383 92s Grid lengths: 18.944 x 18.944 x 24.495 92s Grid center: (2.411, 2.411, 0.000) 92s Multigrid levels: 5 92s Molecule ID: 1 92s Linearized traditional PBE 92s Boundary conditions from focusing 92s 0 ion species (0.000 M ionic strength): 92s Solute dielectric: 1.000 92s Solvent dielectric: 78.540 92s Using "molecular" surface definition; no smoothing 92s Solvent probe radius: 1.400 A 92s Temperature: 298.150 K 92s Electrostatic energies will be calculated 92s Total electrostatic energy = 8.142778325440E+02 kJ/mol 92s Calculating forces... 92s [focusFillBound()]: WARNING: 92s Unusually large potential values 92s detected on the focusing boundary! 92s Convergence not guaranteed for NPBE/NRPBE calculations! 92s 92s ---------------------------------------- 92s CALCULATION #3 (solvated): MULTIGRID 92s Setting up problem... 92s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 92s Debye length: 0 A 92s Current memory usage: 61.280 MB total, 122.102 MB high water 92s Using cubic spline charge discretization. 92s Partition overlap fraction = 0.1 92s Processor array = 2 x 2 x 1 92s Grid dimensions: 65 x 65 x 65 92s Grid spacings: 0.112 x 0.112 x 0.188 92s Grid lengths: 7.178 x 7.178 x 12.000 92s Grid center: (2.411, 2.411, 0.000) 92s Multigrid levels: 5 92s Molecule ID: 1 92s Linearized traditional PBE 92s Boundary conditions from focusing 92s 0 ion species (0.000 M ionic strength): 92s Solute dielectric: 1.000 92s Solvent dielectric: 78.540 92s Using "molecular" surface definition; no smoothing 92s Solvent probe radius: 1.400 A 92s Temperature: 298.150 K 92s Electrostatic energies will be calculated 92s Total electrostatic energy = 1.485246665692E+03 kJ/mol 92s Calculating forces... 92s ---------------------------------------- 92s CALCULATION #4 (reference): MULTIGRID 92s Setting up problem... 92s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 92s Debye length: 0 A 92s Current memory usage: 61.207 MB total, 122.102 MB high water 92s Using cubic spline charge discretization. 92s Partition overlap fraction = 0.1 92s Processor array = 2 x 2 x 1 92s Grid dimensions: 65 x 65 x 65 92s Grid spacings: 0.781 x 0.781 x 0.781 92s Grid lengths: 50.000 x 50.000 x 50.000 92s Grid center: (0.000, 0.000, 0.000) 92s Multigrid levels: 5 92s Molecule ID: 1 92s Linearized traditional PBE 92s Multiple Debye-Huckel sphere boundary conditions 92s 0 ion species (0.000 M ionic strength): 92s Solute dielectric: 1.000 92s Solvent dielectric: 1.000 92s Using "molecular" surface definition; no smoothing 92s Solvent probe radius: 1.400 A 92s Temperature: 298.150 K 92s Electrostatic energies will be calculated 92s Total electrostatic energy = 2.977178707146E+02 kJ/mol 92s Calculating forces... 92s ---------------------------------------- 92s CALCULATION #5 (reference): MULTIGRID 92s Setting up problem... 92s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 92s Debye length: 0 A 92s Current memory usage: 61.207 MB total, 122.102 MB high water 92s Using cubic spline charge discretization. 92s Partition overlap fraction = 0.1 92s Processor array = 2 x 2 x 1 92s Grid dimensions: 65 x 65 x 65 92s Grid spacings: 0.296 x 0.296 x 0.383 92s Grid lengths: 18.944 x 18.944 x 24.495 92s Grid center: (2.411, 2.411, 0.000) 92s Multigrid levels: 5 92s Molecule ID: 1 92s Linearized traditional PBE 92s Boundary conditions from focusing 92s 0 ion species (0.000 M ionic strength): 92s Solute dielectric: 1.000 92s Solvent dielectric: 1.000 92s Using "molecular" surface definition; no smoothing 92s Solvent probe radius: 1.400 A 92s Temperature: 298.150 K 92s Electrostatic energies will be calculated 92s Total electrostatic energy = 8.799304557596E+02 kJ/mol 92s Calculating forces... 92s [focusFillBound()]: WARNING: 92s Unusually large potential values 92s detected on the focusing boundary! 92s Convergence not guaranteed for NPBE/NRPBE calculations! 92s 92s ---------------------------------------- 92s CALCULATION #6 (reference): MULTIGRID 92s Setting up problem... 92s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 92s Debye length: 0 A 92s Current memory usage: 61.207 MB total, 122.102 MB high water 92s Using cubic spline charge discretization. 92s Partition overlap fraction = 0.1 92s Processor array = 2 x 2 x 1 92s Grid dimensions: 65 x 65 x 65 92s Grid spacings: 0.112 x 0.112 x 0.188 92s Grid lengths: 7.178 x 7.178 x 12.000 92s Grid center: (2.411, 2.411, 0.000) 92s Multigrid levels: 5 92s Molecule ID: 1 92s Linearized traditional PBE 92s Boundary conditions from focusing 92s 0 ion species (0.000 M ionic strength): 92s Solute dielectric: 1.000 92s Solvent dielectric: 1.000 92s Using "molecular" surface definition; no smoothing 92s Solvent probe radius: 1.400 A 92s Temperature: 298.150 K 92s Electrostatic energies will be calculated 92s Total electrostatic energy = 1.542873949141E+03 kJ/mol 92s Calculating forces... 92s ---------------------------------------- 92s PRINT STATEMENTS 92s 92s print energy 1 (solvated) - 2 (reference) end 92s Local net energy (PE 0) = -5.762728344954E+01 kJ/mol 92s Global net ELEC energy = -5.762728344954E+01 kJ/mol 92s ---------------------------------------- 92s CLEANING UP AND SHUTTING DOWN... 92s Destroying force arrays. 92s No energy arrays to destroy. 92s Destroying multigrid structures. 92s Destroying finite element structures. 92s Destroying 1 molecules 92s Final memory usage: 0.001 MB total, 122.102 MB high water 92s 92s 92s Thanks for using APBS! 92s 92s Processor 3 results: 92s 2.401768459091e+02 92s 8.142778325440e+02 92s 1.485246665692e+03 92s 2.977178707146e+02 92s 8.799304557596e+02 92s 1.542873949141e+03 92s -5.762728344954e+01 92s 92s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 92s *** PASSED *** 92s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 92s *** PASSED *** 92s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 92s *** PASSED *** 92s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 92s *** PASSED *** 92s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 92s *** PASSED *** 92s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 92s *** PASSED *** 92s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 92s *** PASSED *** 92s Elapsed time: 2.974355 seconds 92s -------------------------------------------------------------------------------- 92s -------------------------------------------------------------------------------- 92s Testing input file apbs-smol-parallel.in 92s 92s Splitting the input file into 4 separate files using the inputgen utility 92s 93s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 93s EXPECTED COMPUTED: 7 93s EXPECTED EXPECTED: 7 93s COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] 93s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 93s COMPUTED RESULT 960.7073836226 93s COMPUTED RESULT 3257.1427835731997 93s COMPUTED RESULT 5941.0039478710005 93s COMPUTED RESULT 1190.8714828309999 93s COMPUTED RESULT 3519.7218230368003 93s COMPUTED RESULT 6171.495796544 93s COMPUTED RESULT -230.49184867463003 93s BINARY: /usr/bin/apbs 93s INPUT: apbs-smol-parallel-PE0.in 93s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 93s asc_getToken: Error occurred (bailing out). 93s Vio_scanf: Format problem with input. 93s 93s 93s ---------------------------------------------------------------------- 93s APBS -- Adaptive Poisson-Boltzmann Solver 93s Version APBS 3.4.1 93s 93s Nathan A. Baker (nathan.baker@pnnl.gov) 93s Pacific Northwest National Laboratory 93s 93s Additional contributing authors listed in the code documentation. 93s 93s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 93s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 93s Northwest Division for the U.S. Department of Energy. 93s 93s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 93s Portions Copyright (c) 2002-2020, Nathan A. Baker. 93s Portions Copyright (c) 1999-2002, The Regents of the University of California. 93s Portions Copyright (c) 1995, Michael Holst. 93s All rights reserved. 93s 93s Redistribution and use in source and binary forms, with or without 93s modification, are permitted provided that the following conditions are met: 93s 93s * Redistributions of source code must retain the above copyright notice, this 93s list of conditions and the following disclaimer. 93s 93s * Redistributions in binary form must reproduce the above copyright notice, 93s this list of conditions and the following disclaimer in the documentation 93s and/or other materials provided with the distribution. 93s 93s * Neither the name of the developer nor the names of its contributors may be 93s used to endorse or promote products derived from this software without 93s specific prior written permission. 93s 93s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 93s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 93s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 93s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 93s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 93s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 93s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 93s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 93s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 93s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 93s ---------------------------------------------------------------------- 93s APBS uses FETK (the Finite Element ToolKit) to solve the 93s Poisson-Boltzmann equation numerically. FETK is a portable collection 93s of finite element modeling class libraries developed by the Michael Holst 93s research group and written in an object-oriented form of C. FEtk is 93s designed to solve general coupled systems of nonlinear partial differential 93s equations using adaptive finite element methods, inexact Newton methods, 93s and algebraic multilevel methods. More information about FEtk may be found 93s at . 93s ---------------------------------------------------------------------- 93s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 93s Aqua is a modified form of the Holst group PMG library 93s which has been modified by Patrice Koehl 93s for improved efficiency and 93s memory usage when solving the Poisson-Boltzmann equation. 93s ---------------------------------------------------------------------- 93s Please cite your use of APBS as: 93s 93s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 93s nanosystems: application to microtubules and the ribosome. Proc. 93s Natl. Acad. Sci. USA 98, 10037-10041 2001. 93s 93s 93s This executable compiled on Jan 3 2025 at 11:01:42 93s 93s Parsing input file apbs-smol-parallel-PE0.in... 93s rank 0 size 1... 93s Parsed input file. 93s Got paths for 1 molecules 93s Reading PQR-format atom data from ion.pqr. 93s 1 atoms 93s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 93s Net charge 1.00e+00 e 93s Preparing to run 6 PBE calculations. 93s ---------------------------------------- 93s CALCULATION #1 (solvated): MULTIGRID 93s Setting up problem... 93s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 93s Debye length: 0 A 93s Current memory usage: 61.280 MB total, 61.280 MB high water 93s Using cubic spline charge discretization. 93s Partition overlap fraction = 0.1 93s Processor array = 2 x 2 x 1 93s Grid dimensions: 65 x 65 x 65 93s Grid spacings: 0.781 x 0.781 x 0.781 93s Grid lengths: 50.000 x 50.000 x 50.000 93s Grid center: (0.000, 0.000, 0.000) 93s Multigrid levels: 5 93s Molecule ID: 1 93s Linearized traditional PBE 93s Multiple Debye-Huckel sphere boundary conditions 93s 0 ion species (0.000 M ionic strength): 93s Solute dielectric: 1.000 93s Solvent dielectric: 78.540 93s Using "molecular" surface definition;harmonic average smoothing 93s Solvent probe radius: 1.400 A 93s Temperature: 298.150 K 93s Electrostatic energies will be calculated 93s Total electrostatic energy = 2.383232191816E+02 kJ/mol 93s Calculating forces... 93s ---------------------------------------- 93s CALCULATION #2 (solvated): MULTIGRID 93s Setting up problem... 93s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 93s Debye length: 0 A 93s Current memory usage: 61.280 MB total, 122.102 MB high water 93s Using cubic spline charge discretization. 93s Partition overlap fraction = 0.1 93s Processor array = 2 x 2 x 1 93s Grid dimensions: 65 x 65 x 65 93s Grid spacings: 0.296 x 0.296 x 0.383 93s Grid lengths: 18.944 x 18.944 x 24.495 93s Grid center: (-2.411, -2.411, 0.000) 93s Multigrid levels: 5 93s Molecule ID: 1 93s Linearized traditional PBE 93s Boundary conditions from focusing 93s 0 ion species (0.000 M ionic strength): 93s Solute dielectric: 1.000 93s Solvent dielectric: 78.540 93s Using "molecular" surface definition;harmonic average smoothing 93s Solvent probe radius: 1.400 A 93s Temperature: 298.150 K 93s Electrostatic energies will be calculated 93s Total electrostatic energy = 8.145369591602E+02 kJ/mol 93s Calculating forces... 93s [focusFillBound()]: WARNING: 93s Unusually large potential values 93s detected on the focusing boundary! 93s Convergence not guaranteed for NPBE/NRPBE calculations! 93s 93s ---------------------------------------- 93s CALCULATION #3 (solvated): MULTIGRID 93s Setting up problem... 93s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 93s Debye length: 0 A 93s Current memory usage: 61.280 MB total, 122.102 MB high water 93s Using cubic spline charge discretization. 93s Partition overlap fraction = 0.1 93s Processor array = 2 x 2 x 1 93s Grid dimensions: 65 x 65 x 65 93s Grid spacings: 0.112 x 0.112 x 0.188 93s Grid lengths: 7.178 x 7.178 x 12.000 93s Grid center: (-2.411, -2.411, 0.000) 93s Multigrid levels: 5 93s Molecule ID: 1 93s Linearized traditional PBE 93s Boundary conditions from focusing 93s 0 ion species (0.000 M ionic strength): 93s Solute dielectric: 1.000 93s Solvent dielectric: 78.540 93s Using "molecular" surface definition;harmonic average smoothing 93s Solvent probe radius: 1.400 A 93s Temperature: 298.150 K 93s Electrostatic energies will be calculated 93s Total electrostatic energy = 1.485524998001E+03 kJ/mol 93s Calculating forces... 93s ---------------------------------------- 93s CALCULATION #4 (reference): MULTIGRID 93s Setting up problem... 93s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 93s Debye length: 0 A 93s Current memory usage: 61.207 MB total, 122.102 MB high water 93s Using cubic spline charge discretization. 93s Partition overlap fraction = 0.1 93s Processor array = 2 x 2 x 1 93s Grid dimensions: 65 x 65 x 65 93s Grid spacings: 0.781 x 0.781 x 0.781 93s Grid lengths: 50.000 x 50.000 x 50.000 93s Grid center: (0.000, 0.000, 0.000) 93s Multigrid levels: 5 93s Molecule ID: 1 93s Linearized traditional PBE 93s Multiple Debye-Huckel sphere boundary conditions 93s 0 ion species (0.000 M ionic strength): 93s Solute dielectric: 1.000 93s Solvent dielectric: 1.000 93s Using "molecular" surface definition;harmonic average smoothing 93s Solvent probe radius: 1.400 A 93s Temperature: 298.150 K 93s Electrostatic energies will be calculated 93s Total electrostatic energy = 2.977178707009E+02 kJ/mol 93s Calculating forces... 93s ---------------------------------------- 93s CALCULATION #5 (reference): MULTIGRID 93s Setting up problem... 93s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 93s Debye length: 0 A 93s Current memory usage: 61.207 MB total, 122.102 MB high water 93s Using cubic spline charge discretization. 93s Partition overlap fraction = 0.1 93s Processor array = 2 x 2 x 1 93s Grid dimensions: 65 x 65 x 65 93s Grid spacings: 0.296 x 0.296 x 0.383 93s Grid lengths: 18.944 x 18.944 x 24.495 93s Grid center: (-2.411, -2.411, 0.000) 93s Multigrid levels: 5 93s Molecule ID: 1 93s Linearized traditional PBE 93s Boundary conditions from focusing 93s 0 ion species (0.000 M ionic strength): 93s Solute dielectric: 1.000 93s Solvent dielectric: 1.000 93s Using "molecular" surface definition;harmonic average smoothing 93s Solvent probe radius: 1.400 A 93s Temperature: 298.150 K 93s Electrostatic energies will be calculated 93s Total electrostatic energy = 8.799304557588E+02 kJ/mol 93s Calculating forces... 93s [focusFillBound()]: WARNING: 93s Unusually large potential values 93s detected on the focusing boundary! 93s Convergence not guaranteed for NPBE/NRPBE calculations! 93s 93s ---------------------------------------- 93s CALCULATION #6 (reference): MULTIGRID 93s Setting up problem... 93s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 93s Debye length: 0 A 93s Current memory usage: 61.207 MB total, 122.102 MB high water 93s Using cubic spline charge discretization. 93s Partition overlap fraction = 0.1 93s Processor array = 2 x 2 x 1 93s Grid dimensions: 65 x 65 x 65 93s Grid spacings: 0.112 x 0.112 x 0.188 93s Grid lengths: 7.178 x 7.178 x 12.000 93s Grid center: (-2.411, -2.411, 0.000) 93s Multigrid levels: 5 93s Molecule ID: 1 93s Linearized traditional PBE 93s Boundary conditions from focusing 93s 0 ion species (0.000 M ionic strength): 93s Solute dielectric: 1.000 93s Solvent dielectric: 1.000 93s Using "molecular" surface definition;harmonic average smoothing 93s Solvent probe radius: 1.400 A 93s Temperature: 298.150 K 93s Electrostatic energies will be calculated 93s Total electrostatic energy = 1.542873949131E+03 kJ/mol 93s Calculating forces... 93s ---------------------------------------- 93s PRINT STATEMENTS 93s 93s print energy 1 (solvated) - 2 (reference) end 93s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 93s Global net ELEC energy = -5.734895113069E+01 kJ/mol 93s ---------------------------------------- 93s CLEANING UP AND SHUTTING DOWN... 93s Destroying force arrays. 93s No energy arrays to destroy. 93s Destroying multigrid structures. 93s Destroying finite element structures. 93s Destroying 1 molecules 93s Final memory usage: 0.001 MB total, 122.102 MB high water 93s 93s 93s Thanks for using APBS! 93s 93s Processor 0 results: 93s 2.383232191816e+02 93s 8.145369591602e+02 93s 1.485524998001e+03 93s 2.977178707009e+02 93s 8.799304557588e+02 93s 1.542873949131e+03 93s -5.734895113069e+01 93s 94s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 94s BINARY: /usr/bin/apbs 94s INPUT: apbs-smol-parallel-PE1.in 94s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 94s asc_getToken: Error occurred (bailing out). 94s Vio_scanf: Format problem with input. 94s 94s 94s ---------------------------------------------------------------------- 94s APBS -- Adaptive Poisson-Boltzmann Solver 94s Version APBS 3.4.1 94s 94s Nathan A. Baker (nathan.baker@pnnl.gov) 94s Pacific Northwest National Laboratory 94s 94s Additional contributing authors listed in the code documentation. 94s 94s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 94s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 94s Northwest Division for the U.S. Department of Energy. 94s 94s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 94s Portions Copyright (c) 2002-2020, Nathan A. Baker. 94s Portions Copyright (c) 1999-2002, The Regents of the University of California. 94s Portions Copyright (c) 1995, Michael Holst. 94s All rights reserved. 94s 94s Redistribution and use in source and binary forms, with or without 94s modification, are permitted provided that the following conditions are met: 94s 94s * Redistributions of source code must retain the above copyright notice, this 94s list of conditions and the following disclaimer. 94s 94s * Redistributions in binary form must reproduce the above copyright notice, 94s this list of conditions and the following disclaimer in the documentation 94s and/or other materials provided with the distribution. 94s 94s * Neither the name of the developer nor the names of its contributors may be 94s used to endorse or promote products derived from this software without 94s specific prior written permission. 94s 94s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 94s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 94s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 94s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 94s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 94s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 94s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 94s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 94s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 94s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 94s ---------------------------------------------------------------------- 94s APBS uses FETK (the Finite Element ToolKit) to solve the 94s Poisson-Boltzmann equation numerically. FETK is a portable collection 94s of finite element modeling class libraries developed by the Michael Holst 94s research group and written in an object-oriented form of C. FEtk is 94s designed to solve general coupled systems of nonlinear partial differential 94s equations using adaptive finite element methods, inexact Newton methods, 94s and algebraic multilevel methods. More information about FEtk may be found 94s at . 94s ---------------------------------------------------------------------- 94s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 94s Aqua is a modified form of the Holst group PMG library 94s which has been modified by Patrice Koehl 94s for improved efficiency and 94s memory usage when solving the Poisson-Boltzmann equation. 94s ---------------------------------------------------------------------- 94s Please cite your use of APBS as: 94s 94s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 94s nanosystems: application to microtubules and the ribosome. Proc. 94s Natl. Acad. Sci. USA 98, 10037-10041 2001. 94s 94s 94s This executable compiled on Jan 3 2025 at 11:01:42 94s 94s Parsing input file apbs-smol-parallel-PE1.in... 94s rank 0 size 1... 94s Parsed input file. 94s Got paths for 1 molecules 94s Reading PQR-format atom data from ion.pqr. 94s 1 atoms 94s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 94s Net charge 1.00e+00 e 94s Preparing to run 6 PBE calculations. 94s ---------------------------------------- 94s CALCULATION #1 (solvated): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.280 MB total, 61.280 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.781 x 0.781 x 0.781 94s Grid lengths: 50.000 x 50.000 x 50.000 94s Grid center: (0.000, 0.000, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Multiple Debye-Huckel sphere boundary conditions 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 78.540 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 2.383232191816E+02 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s CALCULATION #2 (solvated): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.280 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.296 x 0.296 x 0.383 94s Grid lengths: 18.944 x 18.944 x 24.495 94s Grid center: (2.411, -2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 78.540 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 8.145419898332E+02 kJ/mol 94s Calculating forces... 94s [focusFillBound()]: WARNING: 94s Unusually large potential values 94s detected on the focusing boundary! 94s Convergence not guaranteed for NPBE/NRPBE calculations! 94s 94s ---------------------------------------- 94s CALCULATION #3 (solvated): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.280 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.112 x 0.112 x 0.188 94s Grid lengths: 7.178 x 7.178 x 12.000 94s Grid center: (2.411, -2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 78.540 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 1.485529328612E+03 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s CALCULATION #4 (reference): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.207 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.781 x 0.781 x 0.781 94s Grid lengths: 50.000 x 50.000 x 50.000 94s Grid center: (0.000, 0.000, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Multiple Debye-Huckel sphere boundary conditions 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 1.000 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 2.977178707009E+02 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s CALCULATION #5 (reference): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.207 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.296 x 0.296 x 0.383 94s Grid lengths: 18.944 x 18.944 x 24.495 94s Grid center: (2.411, -2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 1.000 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 8.799304557588E+02 kJ/mol 94s Calculating forces... 94s [focusFillBound()]: WARNING: 94s Unusually large potential values 94s detected on the focusing boundary! 94s Convergence not guaranteed for NPBE/NRPBE calculations! 94s 94s ---------------------------------------- 94s CALCULATION #6 (reference): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.207 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.112 x 0.112 x 0.188 94s Grid lengths: 7.178 x 7.178 x 12.000 94s Grid center: (2.411, -2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 1.000 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 1.542873949131E+03 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s PRINT STATEMENTS 94s 94s print energy 1 (solvated) - 2 (reference) end 94s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 94s Global net ELEC energy = -5.734462051928E+01 kJ/mol 94s ---------------------------------------- 94s CLEANING UP AND SHUTTING DOWN... 94s Destroying force arrays. 94s No energy arrays to destroy. 94s Destroying multigrid structures. 94s Destroying finite element structures. 94s Destroying 1 molecules 94s Final memory usage: 0.001 MB total, 122.102 MB high water 94s 94s 94s Thanks for using APBS! 94s 94s Processor 1 results: 94s 2.383232191816e+02 94s 8.145419898332e+02 94s 1.485529328612e+03 94s 2.977178707009e+02 94s 8.799304557588e+02 94s 1.542873949131e+03 94s -5.734462051928e+01 94s 94s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 94s BINARY: /usr/bin/apbs 94s INPUT: apbs-smol-parallel-PE2.in 94s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 94s asc_getToken: Error occurred (bailing out). 94s Vio_scanf: Format problem with input. 94s 94s 94s ---------------------------------------------------------------------- 94s APBS -- Adaptive Poisson-Boltzmann Solver 94s Version APBS 3.4.1 94s 94s Nathan A. Baker (nathan.baker@pnnl.gov) 94s Pacific Northwest National Laboratory 94s 94s Additional contributing authors listed in the code documentation. 94s 94s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 94s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 94s Northwest Division for the U.S. Department of Energy. 94s 94s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 94s Portions Copyright (c) 2002-2020, Nathan A. Baker. 94s Portions Copyright (c) 1999-2002, The Regents of the University of California. 94s Portions Copyright (c) 1995, Michael Holst. 94s All rights reserved. 94s 94s Redistribution and use in source and binary forms, with or without 94s modification, are permitted provided that the following conditions are met: 94s 94s * Redistributions of source code must retain the above copyright notice, this 94s list of conditions and the following disclaimer. 94s 94s * Redistributions in binary form must reproduce the above copyright notice, 94s this list of conditions and the following disclaimer in the documentation 94s and/or other materials provided with the distribution. 94s 94s * Neither the name of the developer nor the names of its contributors may be 94s used to endorse or promote products derived from this software without 94s specific prior written permission. 94s 94s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 94s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 94s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 94s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 94s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 94s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 94s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 94s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 94s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 94s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 94s ---------------------------------------------------------------------- 94s APBS uses FETK (the Finite Element ToolKit) to solve the 94s Poisson-Boltzmann equation numerically. FETK is a portable collection 94s of finite element modeling class libraries developed by the Michael Holst 94s research group and written in an object-oriented form of C. FEtk is 94s designed to solve general coupled systems of nonlinear partial differential 94s equations using adaptive finite element methods, inexact Newton methods, 94s and algebraic multilevel methods. More information about FEtk may be found 94s at . 94s ---------------------------------------------------------------------- 94s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 94s Aqua is a modified form of the Holst group PMG library 94s which has been modified by Patrice Koehl 94s for improved efficiency and 94s memory usage when solving the Poisson-Boltzmann equation. 94s ---------------------------------------------------------------------- 94s Please cite your use of APBS as: 94s 94s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 94s nanosystems: application to microtubules and the ribosome. Proc. 94s Natl. Acad. Sci. USA 98, 10037-10041 2001. 94s 94s 94s This executable compiled on Jan 3 2025 at 11:01:42 94s 94s Parsing input file apbs-smol-parallel-PE2.in... 94s rank 0 size 1... 94s Parsed input file. 94s Got paths for 1 molecules 94s Reading PQR-format atom data from ion.pqr. 94s 1 atoms 94s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 94s Net charge 1.00e+00 e 94s Preparing to run 6 PBE calculations. 94s ---------------------------------------- 94s CALCULATION #1 (solvated): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.280 MB total, 61.280 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.781 x 0.781 x 0.781 94s Grid lengths: 50.000 x 50.000 x 50.000 94s Grid center: (0.000, 0.000, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Multiple Debye-Huckel sphere boundary conditions 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 78.540 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 2.383232191909E+02 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s CALCULATION #2 (solvated): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.280 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.296 x 0.296 x 0.383 94s Grid lengths: 18.944 x 18.944 x 24.495 94s Grid center: (-2.411, 2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 78.540 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 8.145369593489E+02 kJ/mol 94s Calculating forces... 94s [focusFillBound()]: WARNING: 94s Unusually large potential values 94s detected on the focusing boundary! 94s Convergence not guaranteed for NPBE/NRPBE calculations! 94s 94s ---------------------------------------- 94s CALCULATION #3 (solvated): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.280 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.112 x 0.112 x 0.188 94s Grid lengths: 7.178 x 7.178 x 12.000 94s Grid center: (-2.411, 2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 78.540 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 1.485524997676E+03 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s CALCULATION #4 (reference): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.207 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.781 x 0.781 x 0.781 94s Grid lengths: 50.000 x 50.000 x 50.000 94s Grid center: (0.000, 0.000, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Multiple Debye-Huckel sphere boundary conditions 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 1.000 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 2.977178707146E+02 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s CALCULATION #5 (reference): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.207 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.296 x 0.296 x 0.383 94s Grid lengths: 18.944 x 18.944 x 24.495 94s Grid center: (-2.411, 2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 1.000 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 8.799304557596E+02 kJ/mol 94s Calculating forces... 94s [focusFillBound()]: WARNING: 94s Unusually large potential values 94s detected on the focusing boundary! 94s Convergence not guaranteed for NPBE/NRPBE calculations! 94s 94s ---------------------------------------- 94s CALCULATION #6 (reference): MULTIGRID 94s Setting up problem... 94s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 94s Debye length: 0 A 94s Current memory usage: 61.207 MB total, 122.102 MB high water 94s Using cubic spline charge discretization. 94s Partition overlap fraction = 0.1 94s Processor array = 2 x 2 x 1 94s Grid dimensions: 65 x 65 x 65 94s Grid spacings: 0.112 x 0.112 x 0.188 94s Grid lengths: 7.178 x 7.178 x 12.000 94s Grid center: (-2.411, 2.411, 0.000) 94s Multigrid levels: 5 94s Molecule ID: 1 94s Linearized traditional PBE 94s Boundary conditions from focusing 94s 0 ion species (0.000 M ionic strength): 94s Solute dielectric: 1.000 94s Solvent dielectric: 1.000 94s Using "molecular" surface definition;harmonic average smoothing 94s Solvent probe radius: 1.400 A 94s Temperature: 298.150 K 94s Electrostatic energies will be calculated 94s Total electrostatic energy = 1.542873949141E+03 kJ/mol 94s Calculating forces... 94s ---------------------------------------- 94s PRINT STATEMENTS 94s 94s print energy 1 (solvated) - 2 (reference) end 94s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 94s Global net ELEC energy = -5.734895146550E+01 kJ/mol 94s ---------------------------------------- 94s CLEANING UP AND SHUTTING DOWN... 94s Destroying force arrays. 94s No energy arrays to destroy. 94s Destroying multigrid structures. 94s Destroying finite element structures. 94s Destroying 1 molecules 94s Final memory usage: 0.001 MB total, 122.102 MB high water 94s 94s 94s Thanks for using APBS! 94s 94s Processor 2 results: 94s 2.383232191909e+02 94s 8.145369593489e+02 94s 1.485524997676e+03 94s 2.977178707146e+02 94s 8.799304557596e+02 94s 1.542873949141e+03 94s -5.734895146550e+01 94s 95s Processor 3 results: 95s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 95s BINARY: /usr/bin/apbs 95s INPUT: apbs-smol-parallel-PE3.in 95s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 95s asc_getToken: Error occurred (bailing out). 95s Vio_scanf: Format problem with input. 95s 95s 95s ---------------------------------------------------------------------- 95s APBS -- Adaptive Poisson-Boltzmann Solver 95s Version APBS 3.4.1 95s 95s Nathan A. Baker (nathan.baker@pnnl.gov) 95s Pacific Northwest National Laboratory 95s 95s Additional contributing authors listed in the code documentation. 95s 95s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 95s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 95s Northwest Division for the U.S. Department of Energy. 95s 95s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 95s Portions Copyright (c) 2002-2020, Nathan A. Baker. 95s Portions Copyright (c) 1999-2002, The Regents of the University of California. 95s Portions Copyright (c) 1995, Michael Holst. 95s All rights reserved. 95s 95s Redistribution and use in source and binary forms, with or without 95s modification, are permitted provided that the following conditions are met: 95s 95s * Redistributions of source code must retain the above copyright notice, this 95s list of conditions and the following disclaimer. 95s 95s * Redistributions in binary form must reproduce the above copyright notice, 95s this list of conditions and the following disclaimer in the documentation 95s and/or other materials provided with the distribution. 95s 95s * Neither the name of the developer nor the names of its contributors may be 95s used to endorse or promote products derived from this software without 95s specific prior written permission. 95s 95s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 95s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 95s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 95s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 95s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 95s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 95s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 95s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 95s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 95s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 95s ---------------------------------------------------------------------- 95s APBS uses FETK (the Finite Element ToolKit) to solve the 95s Poisson-Boltzmann equation numerically. FETK is a portable collection 95s of finite element modeling class libraries developed by the Michael Holst 95s research group and written in an object-oriented form of C. FEtk is 95s designed to solve general coupled systems of nonlinear partial differential 95s equations using adaptive finite element methods, inexact Newton methods, 95s and algebraic multilevel methods. More information about FEtk may be found 95s at . 95s ---------------------------------------------------------------------- 95s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 95s Aqua is a modified form of the Holst group PMG library 95s which has been modified by Patrice Koehl 95s for improved efficiency and 95s memory usage when solving the Poisson-Boltzmann equation. 95s ---------------------------------------------------------------------- 95s Please cite your use of APBS as: 95s 95s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 95s nanosystems: application to microtubules and the ribosome. Proc. 95s Natl. Acad. Sci. USA 98, 10037-10041 2001. 95s 95s 95s This executable compiled on Jan 3 2025 at 11:01:42 95s 95s Parsing input file apbs-smol-parallel-PE3.in... 95s rank 0 size 1... 95s Parsed input file. 95s Got paths for 1 molecules 95s Reading PQR-format atom data from ion.pqr. 95s 1 atoms 95s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 95s Net charge 1.00e+00 e 95s Preparing to run 6 PBE calculations. 95s ---------------------------------------- 95s CALCULATION #1 (solvated): MULTIGRID 95s Setting up problem... 95s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 95s Debye length: 0 A 95s Current memory usage: 61.280 MB total, 61.280 MB high water 95s Using cubic spline charge discretization. 95s Partition overlap fraction = 0.1 95s Processor array = 2 x 2 x 1 95s Grid dimensions: 65 x 65 x 65 95s Grid spacings: 0.781 x 0.781 x 0.781 95s Grid lengths: 50.000 x 50.000 x 50.000 95s Grid center: (0.000, 0.000, 0.000) 95s Multigrid levels: 5 95s Molecule ID: 1 95s Linearized traditional PBE 95s Multiple Debye-Huckel sphere boundary conditions 95s 0 ion species (0.000 M ionic strength): 95s Solute dielectric: 1.000 95s Solvent dielectric: 78.540 95s Using "molecular" surface definition;harmonic average smoothing 95s Solvent probe radius: 1.400 A 95s Temperature: 298.150 K 95s Electrostatic energies will be calculated 95s Total electrostatic energy = 2.383232191909E+02 kJ/mol 95s Calculating forces... 95s ---------------------------------------- 95s CALCULATION #2 (solvated): MULTIGRID 95s Setting up problem... 95s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 95s Debye length: 0 A 95s Current memory usage: 61.280 MB total, 122.102 MB high water 95s Using cubic spline charge discretization. 95s Partition overlap fraction = 0.1 95s Processor array = 2 x 2 x 1 95s Grid dimensions: 65 x 65 x 65 95s Grid spacings: 0.296 x 0.296 x 0.383 95s Grid lengths: 18.944 x 18.944 x 24.495 95s Grid center: (2.411, 2.411, 0.000) 95s Multigrid levels: 5 95s Molecule ID: 1 95s Linearized traditional PBE 95s Boundary conditions from focusing 95s 0 ion species (0.000 M ionic strength): 95s Solute dielectric: 1.000 95s Solvent dielectric: 78.540 95s Using "molecular" surface definition;harmonic average smoothing 95s Solvent probe radius: 1.400 A 95s Temperature: 298.150 K 95s Electrostatic energies will be calculated 95s Total electrostatic energy = 8.145419900310E+02 kJ/mol 95s Calculating forces... 95s [focusFillBound()]: WARNING: 95s Unusually large potential values 95s detected on the focusing boundary! 95s Convergence not guaranteed for NPBE/NRPBE calculations! 95s 95s ---------------------------------------- 95s CALCULATION #3 (solvated): MULTIGRID 95s Setting up problem... 95s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 95s Debye length: 0 A 95s Current memory usage: 61.280 MB total, 122.102 MB high water 95s Using cubic spline charge discretization. 95s Partition overlap fraction = 0.1 95s Processor array = 2 x 2 x 1 95s Grid dimensions: 65 x 65 x 65 95s Grid spacings: 0.112 x 0.112 x 0.188 95s Grid lengths: 7.178 x 7.178 x 12.000 95s Grid center: (2.411, 2.411, 0.000) 95s Multigrid levels: 5 95s Molecule ID: 1 95s Linearized traditional PBE 95s Boundary conditions from focusing 95s 0 ion species (0.000 M ionic strength): 95s Solute dielectric: 1.000 95s Solvent dielectric: 78.540 95s Using "molecular" surface definition;harmonic average smoothing 95s Solvent probe radius: 1.400 A 95s Temperature: 298.150 K 95s Electrostatic energies will be calculated 95s Total electrostatic energy = 1.485529328301E+03 kJ/mol 95s Calculating forces... 95s ---------------------------------------- 95s CALCULATION #4 (reference): MULTIGRID 95s Setting up problem... 95s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 95s Debye length: 0 A 95s Current memory usage: 61.207 MB total, 122.102 MB high water 95s Using cubic spline charge discretization. 95s Partition overlap fraction = 0.1 95s Processor array = 2 x 2 x 1 95s Grid dimensions: 65 x 65 x 65 95s Grid spacings: 0.781 x 0.781 x 0.781 95s Grid lengths: 50.000 x 50.000 x 50.000 95s Grid center: (0.000, 0.000, 0.000) 95s Multigrid levels: 5 95s Molecule ID: 1 95s Linearized traditional PBE 95s Multiple Debye-Huckel sphere boundary conditions 95s 0 ion species (0.000 M ionic strength): 95s Solute dielectric: 1.000 95s Solvent dielectric: 1.000 95s Using "molecular" surface definition;harmonic average smoothing 95s Solvent probe radius: 1.400 A 95s Temperature: 298.150 K 95s Electrostatic energies will be calculated 95s Total electrostatic energy = 2.977178707146E+02 kJ/mol 95s Calculating forces... 95s ---------------------------------------- 95s CALCULATION #5 (reference): MULTIGRID 95s Setting up problem... 95s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 95s Debye length: 0 A 95s Current memory usage: 61.207 MB total, 122.102 MB high water 95s Using cubic spline charge discretization. 95s Partition overlap fraction = 0.1 95s Processor array = 2 x 2 x 1 95s Grid dimensions: 65 x 65 x 65 95s Grid spacings: 0.296 x 0.296 x 0.383 95s Grid lengths: 18.944 x 18.944 x 24.495 95s Grid center: (2.411, 2.411, 0.000) 95s Multigrid levels: 5 95s Molecule ID: 1 95s Linearized traditional PBE 95s Boundary conditions from focusing 95s 0 ion species (0.000 M ionic strength): 95s Solute dielectric: 1.000 95s Solvent dielectric: 1.000 95s Using "molecular" surface definition;harmonic average smoothing 95s Solvent probe radius: 1.400 A 95s Temperature: 298.150 K 95s Electrostatic energies will be calculated 95s Total electrostatic energy = 8.799304557596E+02 kJ/mol 95s Calculating forces... 95s [focusFillBound()]: WARNING: 95s Unusually large potential values 95s detected on the focusing boundary! 95s Convergence not guaranteed for NPBE/NRPBE calculations! 95s 95s ---------------------------------------- 95s CALCULATION #6 (reference): MULTIGRID 95s Setting up problem... 95s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 95s Debye length: 0 A 95s Current memory usage: 61.207 MB total, 122.102 MB high water 95s Using cubic spline charge discretization. 95s Partition overlap fraction = 0.1 95s Processor array = 2 x 2 x 1 95s Grid dimensions: 65 x 65 x 65 95s Grid spacings: 0.112 x 0.112 x 0.188 95s Grid lengths: 7.178 x 7.178 x 12.000 95s Grid center: (2.411, 2.411, 0.000) 95s Multigrid levels: 5 95s Molecule ID: 1 95s Linearized traditional PBE 95s Boundary conditions from focusing 95s 0 ion species (0.000 M ionic strength): 95s Solute dielectric: 1.000 95s Solvent dielectric: 1.000 95s Using "molecular" surface definition;harmonic average smoothing 95s Solvent probe radius: 1.400 A 95s Temperature: 298.150 K 95s Electrostatic energies will be calculated 95s Total electrostatic energy = 1.542873949141E+03 kJ/mol 95s Calculating forces... 95s ---------------------------------------- 95s PRINT STATEMENTS 95s 95s print energy 1 (solvated) - 2 (reference) end 95s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 95s Global net ELEC energy = -5.734462084052E+01 kJ/mol 95s ---------------------------------------- 95s CLEANING UP AND SHUTTING DOWN... 95s Destroying force arrays. 95s No energy arrays to destroy. 95s Destroying multigrid structures. 95s Destroying finite element structures. 95s Destroying 1 molecules 95s Final memory usage: 0.001 MB total, 122.102 MB high water 95s 95s 95s Thanks for using APBS! 95s 95s 2.383232191909e+02 95s 8.145419900310e+02 95s 1.485529328301e+03 95s 2.977178707146e+02 95s 8.799304557596e+02 95s 1.542873949141e+03 95s -5.734462084052e+01 95s 95s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 95s *** PASSED *** 95s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 95s *** PASSED *** 95s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 95s *** PASSED *** 95s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 95s *** PASSED *** 95s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 95s *** PASSED *** 95s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 95s *** PASSED *** 95s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 95s *** PASSED *** 95s Elapsed time: 3.016837 seconds 95s -------------------------------------------------------------------------------- 95s Total elapsed time: 7.309912 seconds 95s Test results have been logged 95s -------------------------------------------------------------------------------- 95s -------------------------------------------------------------------------------- 95s Testing input file apbs-mol-auto.in 95s 133s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 133s EXPECTED COMPUTED: 7 133s EXPECTED EXPECTED: 7 133s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 133s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 133s COMPUTED RESULT 953.292876745 133s COMPUTED RESULT 3258.1578983732998 133s COMPUTED RESULT 5942.108652589999 133s COMPUTED RESULT 1190.8714828309999 133s COMPUTED RESULT 3519.7218230368003 133s COMPUTED RESULT 6171.495796544 133s COMPUTED RESULT -229.38714395599 133s Running tests for actin-dimer-auto section 133s BINARY: /usr/bin/apbs 133s INPUT: apbs-mol-auto.in 133s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 133s asc_getToken: Error occurred (bailing out). 133s Vio_scanf: Format problem with input. 133s 133s 133s ---------------------------------------------------------------------- 133s APBS -- Adaptive Poisson-Boltzmann Solver 133s Version APBS 3.4.1 133s 133s Nathan A. Baker (nathan.baker@pnnl.gov) 133s Pacific Northwest National Laboratory 133s 133s Additional contributing authors listed in the code documentation. 133s 133s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 133s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 133s Northwest Division for the U.S. Department of Energy. 133s 133s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 133s Portions Copyright (c) 2002-2020, Nathan A. Baker. 133s Portions Copyright (c) 1999-2002, The Regents of the University of California. 133s Portions Copyright (c) 1995, Michael Holst. 133s All rights reserved. 133s 133s Redistribution and use in source and binary forms, with or without 133s modification, are permitted provided that the following conditions are met: 133s 133s * Redistributions of source code must retain the above copyright notice, this 133s list of conditions and the following disclaimer. 133s 133s * Redistributions in binary form must reproduce the above copyright notice, 133s this list of conditions and the following disclaimer in the documentation 133s and/or other materials provided with the distribution. 133s 133s * Neither the name of the developer nor the names of its contributors may be 133s used to endorse or promote products derived from this software without 133s specific prior written permission. 133s 133s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 133s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 133s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 133s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 133s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 133s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 133s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 133s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 133s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 133s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 133s ---------------------------------------------------------------------- 133s APBS uses FETK (the Finite Element ToolKit) to solve the 133s Poisson-Boltzmann equation numerically. FETK is a portable collection 133s of finite element modeling class libraries developed by the Michael Holst 133s research group and written in an object-oriented form of C. FEtk is 133s designed to solve general coupled systems of nonlinear partial differential 133s equations using adaptive finite element methods, inexact Newton methods, 133s and algebraic multilevel methods. More information about FEtk may be found 133s at . 133s ---------------------------------------------------------------------- 133s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 133s Aqua is a modified form of the Holst group PMG library 133s which has been modified by Patrice Koehl 133s for improved efficiency and 133s memory usage when solving the Poisson-Boltzmann equation. 133s ---------------------------------------------------------------------- 133s Please cite your use of APBS as: 133s 133s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 133s nanosystems: application to microtubules and the ribosome. Proc. 133s Natl. Acad. Sci. USA 98, 10037-10041 2001. 133s 133s 133s This executable compiled on Jan 3 2025 at 11:01:42 133s 133s Parsing input file apbs-mol-auto.in... 133s rank 0 size 1... 133s Parsed input file. 133s Got paths for 3 molecules 133s Reading PQR-format atom data from mol1.pqr. 133s asc_getToken: Error occurred (bailing out). 133s Vio_scanf: Format problem with input. 133s 5877 atoms 133s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 133s Net charge -1.20e+01 e 133s Reading PQR-format atom data from mol2.pqr. 133s asc_getToken: Error occurred (bailing out). 133s Vio_scanf: Format problem with input. 133s 5877 atoms 133s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 133s Net charge -1.20e+01 e 133s Reading PQR-format atom data from complex.pqr. 133s 11754 atoms 133s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 133s Net charge -2.40e+01 e 133s Preparing to run 6 PBE calculations. 133s ---------------------------------------- 133s CALCULATION #1 (mol1): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 133s Debye length: 13.5959 A 133s Current memory usage: 1028.322 MB total, 1028.322 MB high water 133s Using linear spline charge discretization. 133s Grid dimensions: 161 x 161 x 161 133s Grid spacings: 0.975 x 0.756 x 1.012 133s Grid lengths: 156.000 x 121.000 x 162.000 133s Grid center: (2.518, -2.465, 16.742) 133s Multigrid levels: 4 133s Molecule ID: 1 133s Nonlinear traditional PBE 133s Single Debye-Huckel sphere boundary conditions 133s 2 ion species (0.050 M ionic strength): 133s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 133s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 133s Solute dielectric: 2.000 133s Solvent dielectric: 78.400 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 1.527617850342E+05 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #2 (mol1): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 133s Debye length: 13.5959 A 133s Current memory usage: 1028.322 MB total, 2042.113 MB high water 133s Using linear spline charge discretization. 133s Grid dimensions: 161 x 161 x 161 133s Grid spacings: 0.700 x 0.569 x 0.725 133s Grid lengths: 112.000 x 91.000 x 116.000 133s Grid center: (2.518, -2.465, 16.742) 133s Multigrid levels: 4 133s Molecule ID: 1 133s Nonlinear traditional PBE 133s Boundary conditions from focusing 133s 2 ion species (0.050 M ionic strength): 133s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 133s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 133s Solute dielectric: 2.000 133s Solvent dielectric: 78.400 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 2.919510754196E+05 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #3 (mol2): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 133s Debye length: 13.5959 A 133s Current memory usage: 1030.291 MB total, 2042.113 MB high water 133s Using linear spline charge discretization. 133s Grid dimensions: 161 x 161 x 161 133s Grid spacings: 0.975 x 0.756 x 1.012 133s Grid lengths: 156.000 x 121.000 x 162.000 133s Grid center: (2.518, -2.465, 16.742) 133s Multigrid levels: 4 133s Molecule ID: 2 133s Nonlinear traditional PBE 133s Single Debye-Huckel sphere boundary conditions 133s 2 ion species (0.050 M ionic strength): 133s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 133s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 133s Solute dielectric: 2.000 133s Solvent dielectric: 78.400 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 1.527671844880E+05 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #4 (mol2): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 133s Debye length: 13.5959 A 133s Current memory usage: 1030.291 MB total, 2046.048 MB high water 133s Using linear spline charge discretization. 133s Grid dimensions: 161 x 161 x 161 133s Grid spacings: 0.700 x 0.569 x 0.725 133s Grid lengths: 112.000 x 91.000 x 116.000 133s Grid center: (2.518, -2.465, 16.742) 133s Multigrid levels: 4 133s Molecule ID: 2 133s Nonlinear traditional PBE 133s Boundary conditions from focusing 133s 2 ion species (0.050 M ionic strength): 133s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 133s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 133s Solute dielectric: 2.000 133s Solvent dielectric: 78.400 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 2.915468859278E+05 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #5 (complex): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 133s Debye length: 13.5959 A 133s Current memory usage: 1046.446 MB total, 2046.048 MB high water 133s Using linear spline charge discretization. 133s Grid dimensions: 161 x 161 x 161 133s Grid spacings: 0.975 x 0.756 x 1.012 133s Grid lengths: 156.000 x 121.000 x 162.000 133s Grid center: (2.518, -2.465, 16.742) 133s Multigrid levels: 4 133s Molecule ID: 3 133s Nonlinear traditional PBE 133s Single Debye-Huckel sphere boundary conditions 133s 2 ion species (0.050 M ionic strength): 133s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 133s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 133s Solute dielectric: 2.000 133s Solvent dielectric: 78.400 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 3.056317807611E+05 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #6 (complex): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 133s Debye length: 13.5959 A 133s Current memory usage: 1046.446 MB total, 2069.492 MB high water 133s Using linear spline charge discretization. 133s Grid dimensions: 161 x 161 x 161 133s Grid spacings: 0.700 x 0.569 x 0.725 133s Grid lengths: 112.000 x 91.000 x 116.000 133s Grid center: (2.518, -2.465, 16.742) 133s Multigrid levels: 4 133s Molecule ID: 3 133s Nonlinear traditional PBE 133s Boundary conditions from focusing 133s 2 ion species (0.050 M ionic strength): 133s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 133s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 133s Solute dielectric: 2.000 133s Solvent dielectric: 78.400 133s Using "molecular" surface definition; no smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 5.836028296532E+05 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s PRINT STATEMENTS 133s 133s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 133s Local net energy (PE 0) = 1.048683058625E+02 kJ/mol 133s Global net ELEC energy = 1.048683058625E+02 kJ/mol 133s ---------------------------------------- 133s CLEANING UP AND SHUTTING DOWN... 133s Destroying force arrays. 133s No energy arrays to destroy. 133s Destroying multigrid structures. 133s Destroying finite element structures. 133s Destroying 3 molecules 133s Final memory usage: 0.001 MB total, 2069.492 MB high water 133s 133s 133s Thanks for using APBS! 133s 133s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 133s *** PASSED *** 133s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 133s *** PASSED *** 133s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 133s *** PASSED *** 133s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 133s *** PASSED *** 133s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 133s *** PASSED *** 133s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 133s *** PASSED *** 133s Testing computed result against expected result (1.048683058625e+02, 1.048683060915e+02) 133s *** PASSED *** 133s Elapsed time: 38.277198 seconds 133s -------------------------------------------------------------------------------- 133s -------------------------------------------------------------------------------- 133s Testing input file apbs-smol-auto.in 133s 163s Checking for intermediate energies in input file apbs-mol-auto.out 163s EXPECTED COMPUTED: 7 163s EXPECTED EXPECTED: 7 163s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058625] 163s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 163s COMPUTED RESULT 152761.7850342 163s COMPUTED RESULT 291951.0754196 163s COMPUTED RESULT 152767.184488 163s COMPUTED RESULT 291546.8859278 163s COMPUTED RESULT 305631.7807611 163s COMPUTED RESULT 583602.8296532 163s COMPUTED RESULT 104.8683058625 163s BINARY: /usr/bin/apbs 163s INPUT: apbs-smol-auto.in 163s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 163s asc_getToken: Error occurred (bailing out). 163s Vio_scanf: Format problem with input. 163s 163s 163s ---------------------------------------------------------------------- 163s APBS -- Adaptive Poisson-Boltzmann Solver 163s Version APBS 3.4.1 163s 163s Nathan A. Baker (nathan.baker@pnnl.gov) 163s Pacific Northwest National Laboratory 163s 163s Additional contributing authors listed in the code documentation. 163s 163s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 163s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 163s Northwest Division for the U.S. Department of Energy. 163s 163s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 163s Portions Copyright (c) 2002-2020, Nathan A. Baker. 163s Portions Copyright (c) 1999-2002, The Regents of the University of California. 163s Portions Copyright (c) 1995, Michael Holst. 163s All rights reserved. 163s 163s Redistribution and use in source and binary forms, with or without 163s modification, are permitted provided that the following conditions are met: 163s 163s * Redistributions of source code must retain the above copyright notice, this 163s list of conditions and the following disclaimer. 163s 163s * Redistributions in binary form must reproduce the above copyright notice, 163s this list of conditions and the following disclaimer in the documentation 163s and/or other materials provided with the distribution. 163s 163s * Neither the name of the developer nor the names of its contributors may be 163s used to endorse or promote products derived from this software without 163s specific prior written permission. 163s 163s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 163s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 163s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 163s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 163s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 163s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 163s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 163s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 163s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 163s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 163s ---------------------------------------------------------------------- 163s APBS uses FETK (the Finite Element ToolKit) to solve the 163s Poisson-Boltzmann equation numerically. FETK is a portable collection 163s of finite element modeling class libraries developed by the Michael Holst 163s research group and written in an object-oriented form of C. FEtk is 163s designed to solve general coupled systems of nonlinear partial differential 163s equations using adaptive finite element methods, inexact Newton methods, 163s and algebraic multilevel methods. More information about FEtk may be found 163s at . 163s ---------------------------------------------------------------------- 163s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 163s Aqua is a modified form of the Holst group PMG library 163s which has been modified by Patrice Koehl 163s for improved efficiency and 163s memory usage when solving the Poisson-Boltzmann equation. 163s ---------------------------------------------------------------------- 163s Please cite your use of APBS as: 163s 163s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 163s nanosystems: application to microtubules and the ribosome. Proc. 163s Natl. Acad. Sci. USA 98, 10037-10041 2001. 163s 163s 163s This executable compiled on Jan 3 2025 at 11:01:42 163s 163s Parsing input file apbs-smol-auto.in... 163s rank 0 size 1... 163s Parsed input file. 163s Got paths for 3 molecules 163s Reading PQR-format atom data from mol1.pqr. 163s asc_getToken: Error occurred (bailing out). 163s Vio_scanf: Format problem with input. 163s 5877 atoms 163s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 163s Net charge -1.20e+01 e 163s Reading PQR-format atom data from mol2.pqr. 163s asc_getToken: Error occurred (bailing out). 163s Vio_scanf: Format problem with input. 163s 5877 atoms 163s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 163s Net charge -1.20e+01 e 163s Reading PQR-format atom data from complex.pqr. 163s 11754 atoms 163s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 163s Net charge -2.40e+01 e 163s Preparing to run 6 PBE calculations. 163s ---------------------------------------- 163s CALCULATION #1 (mol1): MULTIGRID 163s Setting up problem... 163s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 163s Debye length: 13.5959 A 163s Current memory usage: 1028.322 MB total, 1028.322 MB high water 163s Using linear spline charge discretization. 163s Grid dimensions: 161 x 161 x 161 163s Grid spacings: 0.975 x 0.756 x 1.012 163s Grid lengths: 156.000 x 121.000 x 162.000 163s Grid center: (2.518, -2.465, 16.742) 163s Multigrid levels: 4 163s Molecule ID: 1 163s Nonlinear traditional PBE 163s Single Debye-Huckel sphere boundary conditions 163s 2 ion species (0.050 M ionic strength): 163s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 163s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 163s Solute dielectric: 2.000 163s Solvent dielectric: 78.400 163s Using "molecular" surface definition;harmonic average smoothing 163s Solvent probe radius: 1.400 A 163s Temperature: 298.150 K 163s Electrostatic energies will be calculated 163s Total electrostatic energy = 1.528632421825E+05 kJ/mol 163s Calculating forces... 163s ---------------------------------------- 163s CALCULATION #2 (mol1): MULTIGRID 163s Setting up problem... 163s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 163s Debye length: 13.5959 A 163s Current memory usage: 1028.322 MB total, 2042.113 MB high water 163s Using linear spline charge discretization. 163s Grid dimensions: 161 x 161 x 161 163s Grid spacings: 0.700 x 0.569 x 0.725 163s Grid lengths: 112.000 x 91.000 x 116.000 163s Grid center: (2.518, -2.465, 16.742) 163s Multigrid levels: 4 163s Molecule ID: 1 163s Nonlinear traditional PBE 163s Boundary conditions from focusing 163s 2 ion species (0.050 M ionic strength): 163s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 163s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 163s Solute dielectric: 2.000 163s Solvent dielectric: 78.400 163s Using "molecular" surface definition;harmonic average smoothing 163s Solvent probe radius: 1.400 A 163s Temperature: 298.150 K 163s Electrostatic energies will be calculated 163s Total electrostatic energy = 2.920618662320E+05 kJ/mol 163s Calculating forces... 163s ---------------------------------------- 163s CALCULATION #3 (mol2): MULTIGRID 163s Setting up problem... 163s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 163s Debye length: 13.5959 A 163s Current memory usage: 1030.291 MB total, 2042.113 MB high water 163s Using linear spline charge discretization. 163s Grid dimensions: 161 x 161 x 161 163s Grid spacings: 0.975 x 0.756 x 1.012 163s Grid lengths: 156.000 x 121.000 x 162.000 163s Grid center: (2.518, -2.465, 16.742) 163s Multigrid levels: 4 163s Molecule ID: 2 163s Nonlinear traditional PBE 163s Single Debye-Huckel sphere boundary conditions 163s 2 ion species (0.050 M ionic strength): 163s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 163s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 163s Solute dielectric: 2.000 163s Solvent dielectric: 78.400 163s Using "molecular" surface definition;harmonic average smoothing 163s Solvent probe radiuTesting computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 163s *** PASSED *** 163s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 163s *** PASSED *** 163s s: 1.400 A 163s Temperature: 298.150 K 163s Electrostatic energies will be calculated 163s Total electrostatic energy = 1.529297900572E+05 kJ/mol 163s Calculating forces... 163s ---------------------------------------- 163s CALCULATION #4 (mol2): MULTIGRID 163s Setting up problem... 163s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 163s Debye length: 13.5959 A 163s Current memory usage: 1030.291 MB total, 2046.048 MB high water 163s Using linear spline charge discretization. 163s Grid dimensions: 161 x 161 x 161 163s Grid spacings: 0.700 x 0.569 x 0.725 163s Grid lengths: 112.000 x 91.000 x 116.000 163s Grid center: (2.518, -2.465, 16.742) 163s Multigrid levels: 4 163s Molecule ID: 2 163s Nonlinear traditional PBE 163s Boundary conditions from focusing 163s 2 ion species (0.050 M ionic strength): 163s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 163s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 163s Solute dielectric: 2.000 163s Solvent dielectric: 78.400 163s Using "molecular" surface definition;harmonic average smoothing 163s Solvent probe radius: 1.400 A 163s Temperature: 298.150 K 163s Electrostatic energies will be calculated 163s Total electrostatic energy = 2.916592202835E+05 kJ/mol 163s Calculating forces... 163s ---------------------------------------- 163s CALCULATION #5 (complex): MULTIGRID 163s Setting up problem... 163s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 163s Debye length: 13.5959 A 163s Current memory usage: 1046.446 MB total, 2046.048 MB high water 163s Using linear spline charge discretization. 163s Grid dimensions: 161 x 161 x 161 163s Grid spacings: 0.975 x 0.756 x 1.012 163s Grid lengths: 156.000 x 121.000 x 162.000 163s Grid center: (2.518, -2.465, 16.742) 163s Multigrid levels: 4 163s Molecule ID: 3 163s Nonlinear traditional PBE 163s Single Debye-Huckel sphere boundary conditions 163s 2 ion species (0.050 M ionic strength): 163s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 163s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 163s Solute dielectric: 2.000 163s Solvent dielectric: 78.400 163s Using "molecular" surface definition;harmonic average smoothing 163s Solvent probe radius: 1.400 A 163s Temperature: 298.150 K 163s Electrostatic energies will be calculated 163s Total electrostatic energy = 3.059244262535E+05 kJ/mol 163s Calculating forces... 163s ---------------------------------------- 163s CALCULATION #6 (complex): MULTIGRID 163s Setting up problem... 163s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 163s Debye length: 13.5959 A 163s Current memory usage: 1046.446 MB total, 2069.492 MB high water 163s Using linear spline charge discretization. 163s Grid dimensions: 161 x 161 x 161 163s Grid spacings: 0.700 x 0.569 x 0.725 163s Grid lengths: 112.000 x 91.000 x 116.000 163s Grid center: (2.518, -2.465, 16.742) 163s Multigrid levels: 4 163s Molecule ID: 3 163s Nonlinear traditional PBE 163s Boundary conditions from focusing 163s 2 ion species (0.050 M ionic strength): 163s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 163s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 163s Solute dielectric: 2.000 163s Solvent dielectric: 78.400 163s Using "molecular" surface definition;harmonic average smoothing 163s Solvent probe radius: 1.400 A 163s Temperature: 298.150 K 163s Electrostatic energies will be calculated 163s Total electrostatic energy = 5.838306706232E+05 kJ/mol 163s Calculating forces... 163s ---------------------------------------- 163s PRINT STATEMENTS 163s 163s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 163s Local net energy (PE 0) = 1.095841077691E+02 kJ/mol 163s Global net ELEC energy = 1.095841077691E+02 kJ/mol 163s ---------------------------------------- 163s CLEANING UP AND SHUTTING DOWN... 163s Destroying force arrays. 163s No energy arrays to destroy. 163s Destroying multigrid structures. 163s Destroying finite element structures. 163s Destroying 3 molecules 163s Final memory usage: 0.001 MB total, 2069.492 MB high water 163s 163s 163s Thanks for using APBS! 163s 163s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 163s *** PASSED *** 163s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 163s *** PASSED *** 163s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 163s *** PASSED *** 163s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 163s *** PASSED *** 163s Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) 163s *** PASSED *** 163s Elapsed time: 29.774646 seconds 163s -------------------------------------------------------------------------------- 163s Total elapsed time: 68.051844 seconds 163s Test results have been logged 163s -------------------------------------------------------------------------------- 163s -------------------------------------------------------------------------------- 163s Testing input file alkanes.in 163s 169s Checking for intermediate energies in input file apbs-smol-auto.out 169s EXPECTED COMPUTED: 7 169s EXPECTED EXPECTED: 7 169s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] 169s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 169s COMPUTED RESULT 152863.2421825 169s COMPUTED RESULT 292061.866232 169s COMPUTED RESULT 152929.7900572 169s COMPUTED RESULT 291659.2202835 169s COMPUTED RESULT 305924.4262535 169s COMPUTED RESULT 583830.6706232 169s COMPUTED RESULT 109.5841077691 169s Running tests for alkanes section 169s BINARY: /usr/bin/apbs 169s INPUT: alkanes.in 169s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 169s 169s ---------------------------------------------------------------------- 169s APBS -- Adaptive Poisson-Boltzmann Solver 169s Version APBS 3.4.1 169s 169s Nathan A. Baker (nathan.baker@pnnl.gov) 169s Pacific Northwest National Laboratory 169s 169s Additional contributing authors listed in the code documentation. 169s 169s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 169s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 169s Northwest Division for the U.S. Department of Energy. 169s 169s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 169s Portions Copyright (c) 2002-2020, Nathan A. Baker. 169s Portions Copyright (c) 1999-2002, The Regents of the University of California. 169s Portions Copyright (c) 1995, Michael Holst. 169s All rights reserved. 169s 169s Redistribution and use in source and binary forms, with or without 169s modification, are permitted provided that the following conditions are met: 169s 169s * Redistributions of source code must retain the above copyright notice, this 169s list of conditions and the following disclaimer. 169s 169s * Redistributions in binary form must reproduce the above copyright notice, 169s this list of conditions and the following disclaimer in the documentation 169s and/or other materials provided with the distribution. 169s 169s * Neither the name of the developer nor the names of its contributors may be 169s used to endorse or promote products derived from this software without 169s specific prior written permission. 169s 169s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 169s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 169s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 169s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 169s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 169s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 169s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 169s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 169s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 169s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 169s ---------------------------------------------------------------------- 169s APBS uses FETK (the Finite Element ToolKit) to solve the 169s Poisson-Boltzmann equation numerically. FETK is a portable collection 169s of finite element modeling class libraries developed by the Michael Holst 169s research group and written in an object-oriented form of C. FEtk is 169s designed to solve general coupled systems of nonlinear partial differential 169s equations using adaptive finite element methods, inexact Newton methods, 169s and algebraic multilevel methods. More information about FEtk may be found 169s at . 169s ---------------------------------------------------------------------- 169s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 169s Aqua is a modified form of the Holst group PMG library 169s which has been modified by Patrice Koehl 169s for improved efficiency and 169s memory usage when solving the Poisson-Boltzmann equation. 169s ---------------------------------------------------------------------- 169s Please cite your use of APBS as: 169s 169s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 169s nanosystems: application to microtubules and the ribosome. Proc. 169s Natl. Acad. Sci. USA 98, 10037-10041 2001. 169s 169s 169s This executable compiled on Jan 3 2025 at 11:01:42 169s 169s Parsing input file alkanes.in... 169s rank 0 size 1... 169s Parsed input file. 169s Reading parameter data from parm.dat. 169s Got paths for 11 molecules 169s Reading PDB-format atom data from 2-methylbutane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 17 atoms 169s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 169s Net charge 4.33e+00 e 169s Reading PDB-format atom data from butane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 14 atoms 169s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 169s Net charge 3.51e+00 e 169s Reading PDB-format atom data from cyclohexane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 18 atoms 169s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 169s Net charge 4.93e+00 e 169s Reading PDB-format atom data from cyclopentane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 13 atoms 169s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 169s Net charge 3.88e+00 e 169s Reading PDB-format atom data from ethane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 8 atoms 169s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 169s Net charge 1.87e+00 e 169s Reading PDB-format atom data from hexane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 20 atoms 169s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 169s Net charge 5.16e+00 e 169s Reading PDB-format atom data from isobutane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 14 atoms 169s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 169s Net charge 3.51e+00 e 169s Reading PDB-format atom data from methane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 5 atoms 169s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 169s Net charge 1.05e+00 e 169s Reading PDB-format atom data from neopentane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 17 atoms 169s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 169s Net charge 4.33e+00 e 169s Reading PDB-format atom data from pentane.pdb. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 17 atoms 169s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 169s Net charge 4.33e+00 e 169s Reading PDB-format atom data from propane.pdb. 169s 11 atoms 169s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 169s Net charge 2.69e+00 e 169s Preparing to run 11 PBE calculations. 169s ---------------------------------------- 169s CALCULATION #1 (solvated-2-methylbutane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 3.815624614267E+00 169s SASA for atom 1: 0.000000000000E+00 169s SASA for atom 2: 6.122920124655E-01 169s SASA for atom 3: 3.957497153740E+00 169s SASA for atom 4: 4.308445014544E+00 169s SASA for atom 5: 1.843264951960E+01 169s SASA for atom 6: 1.837011296483E+01 169s SASA for atom 7: 1.666599184724E+01 169s SASA for atom 8: 1.480031796315E+01 169s SASA for atom 9: 1.603020354037E+01 169s SASA for atom 10: 1.473778140838E+01 169s SASA for atom 11: 1.611879699297E+01 169s SASA for atom 12: 1.810954398660E+01 169s SASA for atom 13: 1.420100931324E+01 169s SASA for atom 14: 1.437298483886E+01 169s SASA for atom 15: 1.814081226399E+01 169s SASA for atom 16: 2.152820898091E+01 169s 169s Total solvent accessible surface area: 214.202 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 3.243280922127E-02 169s Surface tension*area energy for atom 1: 0.000000000000E+00 169s Surface tension*area energy for atom 2: 5.204482105957E-03 169s Surface tension*area energy for atom 3: 3.363872580679E-02 169s Surface tension*area energy for atom 4: 3.662178262362E-02 169s Surface tension*area energy for atom 5: 1.566775209166E-01 169s Surface tension*area energy for atom 6: 1.561459602010E-01 169s Surface tension*area energy for atom 7: 1.416609307015E-01 169s Surface tension*area energy for atom 8: 1.258027026868E-01 169s Surface tension*area energy for atom 9: 1.362567300932E-01 169s Surface tension*area energy for atom 10: 1.252711419712E-01 169s Surface tension*area energy for atom 11: 1.370097744402E-01 169s Surface tension*area energy for atom 12: 1.539311238861E-01 169s Surface tension*area energy for atom 13: 1.207085791625E-01 169s Surface tension*area energy for atom 14: 1.221703711303E-01 169s Surface tension*area energy for atom 15: 1.541969042439E-01 169s Surface tension*area energy for atom 16: 1.829897763377E-01 169s 169s Total surface tension energy: 1.82072 kJ/mol 169s 169s Total solvent accessible volume: 253.665 A^3 169s 169s Total pressure*volume energy: 60.7274 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.271287875274E+00 169s WCA energy for atom 1: -5.600872869478E+00 169s WCA energy for atom 2: -5.773775123943E+00 169s WCA energy for atom 3: -6.072801488986E+00 169s WCA energy for atom 4: -6.378470721845E+00 169s WCA energy for atom 5: -1.573474558351E+00 169s WCA energy for atom 6: -1.582338715648E+00 169s WCA energy for atom 7: -1.504044838266E+00 169s WCA energy for atom 8: -1.351002262819E+00 169s WCA energy for atom 9: -1.437367175239E+00 169s WCA energy for atom 10: -1.384626257493E+00 169s WCA energy for atom 11: -1.468867560891E+00 169s WCA energy for atom 12: -1.557005662832E+00 169s WCA energy for atom 13: -1.473759654043E+00 169s WCA energy for atom 14: -1.502261431335E+00 169s WCA energy for atom 15: -1.550940901474E+00 169s WCA energy for atom 16: -1.667828659696E+00 169s 169s Total WCA energy: -48.1507 kJ/mol 169s 169s Total non-polar energy = 1.439739455792E+01 kJ/mol 169s ---------------------------------------- 169s CALCULATION #2 (solvated-butane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 4.405515699447E+00 169s SASA for atom 1: 8.213673337951E-01 169s SASA for atom 2: 8.064333822716E-01 169s SASA for atom 3: 4.375647796400E+00 169s SASA for atom 4: 1.855251124959E+01 169s SASA for atom 5: 2.147609518526E+01 169s SASA for atom 6: 1.852645435176E+01 169s SASA for atom 7: 1.660345529247E+01 169s SASA for atom 8: 1.658782115377E+01 169s SASA for atom 9: 1.658260977421E+01 169s SASA for atom 10: 1.658260977421E+01 169s SASA for atom 11: 2.145003828744E+01 169s SASA for atom 12: 1.852124297220E+01 169s SASA for atom 13: 1.856293400871E+01 169s 169s Total solvent accessible surface area: 193.855 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 3.744688344530E-02 169s Surface tension*area energy for atom 1: 6.981622337259E-03 169s Surface tension*area energy for atom 2: 6.854683749309E-03 169s Surface tension*area energy for atom 3: 3.719300626940E-02 169s Surface tension*area energy for atom 4: 1.576963456215E-01 169s Surface tension*area energy for atom 5: 1.825468090747E-01 169s Surface tension*area energy for atom 6: 1.574748619900E-01 169s Surface tension*area energy for atom 7: 1.411293699860E-01 169s Surface tension*area energy for atom 8: 1.409964798071E-01 169s Surface tension*area energy for atom 9: 1.409521830808E-01 169s Surface tension*area energy for atom 10: 1.409521830808E-01 169s Surface tension*area energy for atom 11: 1.823253254433E-01 169s Surface tension*area energy for atom 12: 1.574305652637E-01 169s Surface tension*area energy for atom 13: 1.577849390741E-01 169s 169s Total surface tension energy: 1.64777 kJ/mol 169s 169s Total solvent accessible volume: 217.863 A^3 169s 169s Total pressure*volume energy: 52.1564 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.728858147814E+00 169s WCA energy for atom 1: -6.204037472587E+00 169s WCA energy for atom 2: -6.202937735018E+00 169s WCA energy for atom 3: -6.728762249931E+00 169s WCA energy for atom 4: -1.623549989062E+00 169s WCA energy for atom 5: -1.709092300778E+00 169s WCA energy for atom 6: -1.625196457114E+00 169s WCA energy for atom 7: -1.484289341167E+00 169s WCA energy for atom 8: -1.485410538626E+00 169s WCA energy for atom 9: -1.485593139015E+00 169s WCA energy for atom 10: -1.484878734279E+00 169s WCA energy for atom 11: -1.708585062695E+00 169s WCA energy for atom 12: -1.625094916482E+00 169s WCA energy for atom 13: -1.624416805392E+00 169s 169s Total WCA energy: -41.7207 kJ/mol 169s 169s Total non-polar energy = 1.208346456826E+01 kJ/mol 169s ---------------------------------------- 169s CALCULATION #3 (solvated-cyclohexane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 7.840324549863E-01 169s SASA for atom 1: 8.064333822716E-01 169s SASA for atom 2: 8.288343095569E-01 169s SASA for atom 3: 7.840324549863E-01 169s SASA for atom 4: 7.989664065098E-01 169s SASA for atom 5: 8.363012853187E-01 169s SASA for atom 6: 2.001169752764E+01 169s SASA for atom 7: 1.616048802948E+01 169s SASA for atom 8: 2.001169752764E+01 169s SASA for atom 9: 1.619175630687E+01 169s SASA for atom 10: 1.616048802948E+01 169s SASA for atom 11: 1.993352683418E+01 169s SASA for atom 12: 2.001169752764E+01 169s SASA for atom 13: 1.618133354774E+01 169s SASA for atom 14: 1.617091078861E+01 169s SASA for atom 15: 2.001690890721E+01 169s SASA for atom 16: 1.993873821374E+01 169s SASA for atom 17: 1.617091078861E+01 169s 169s Total solvent accessible surface area: 221.799 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 6.664275867383E-03 169s Surface tension*area energy for atom 1: 6.854683749309E-03 169s Surface tension*area energy for atom 2: 7.045091631234E-03 169s Surface tension*area energy for atom 3: 6.664275867383E-03 169s Surface tension*area energy for atom 4: 6.791214455333E-03 169s Surface tension*area energy for atom 5: 7.108560925209E-03 169s Surface tension*area energy for atom 6: 1.700994289850E-01 169s Surface tension*area energy for atom 7: 1.373641482506E-01 169s Surface tension*area energy for atom 8: 1.700994289850E-01 169s Surface tension*area energy for atom 9: 1.376299286084E-01 169s Surface tension*area energy for atom 10: 1.373641482506E-01 169s Surface tension*area energy for atom 11: 1.694349780905E-01 169s Surface tension*area energy for atom 12: 1.700994289850E-01 169s Surface tension*area energy for atom 13: 1.375413351558E-01 169s Surface tension*area energy for atom 14: 1.374527417032E-01 169s Surface tension*area energy for atom 15: 1.701437257113E-01 169s Surface tension*area energy for atom 16: 1.694792748168E-01 169s Surface tension*area energy for atom 17: 1.374527417032E-01 169s 169s Total surface tension energy: 1.88529 kJ/mol 169s 169s Total solvent accessible volume: 267.435 A^3 169s 169s Total pressure*volume energy: 64.0239 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -5.793234697241E+00 169s WCA energy for atom 1: -5.784370526583E+00 169s WCA energy for atom 2: -5.791799130412E+00 169s WCA energy for atom 3: -5.788504399087E+00 169s WCA energy for atom 4: -5.797319672490E+00 169s WCA energy for atom 5: -5.787358035342E+00 169s WCA energy for atom 6: -1.523887929614E+00 169s WCA energy for atom 7: -1.413678912317E+00 169s WCA energy for atom 8: -1.521751604392E+00 169s WCA energy for atom 9: -1.414741802525E+00 169s WCA energy for atom 10: -1.413367854344E+00 169s WCA energy for atom 11: -1.523407238081E+00 169s WCA energy for atom 12: -1.523000623583E+00 169s WCA energy for atom 13: -1.413922068538E+00 169s WCA energy for atom 14: -1.416316744211E+00 169s WCA energy for atom 15: -1.524577474659E+00 169s WCA energy for atom 16: -1.523300410052E+00 169s WCA energy for atom 17: -1.414522566061E+00 169s 169s Total WCA energy: -52.3691 kJ/mol 169s 169s Total non-polar energy = 1.354016672221E+01 kJ/mol 169s ---------------------------------------- 169s CALCULATION #4 (solvated-cyclopentane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 9.490526193215E+00 169s SASA for atom 1: 9.512927120500E+00 169s SASA for atom 2: 2.299828534626E+00 169s SASA for atom 3: 1.919012770776E+00 169s SASA for atom 4: 2.307295510388E+00 169s SASA for atom 5: 2.325838699632E+01 169s SASA for atom 6: 2.325838699632E+01 169s SASA for atom 7: 2.045987617019E+01 169s SASA for atom 8: 2.067875411190E+01 169s SASA for atom 9: 2.028790064456E+01 169s SASA for atom 10: 1.897463299431E+01 169s SASA for atom 11: 2.048593306801E+01 169s SASA for atom 12: 2.070481100972E+01 169s 169s Total solvent accessible surface area: 193.638 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 8.066947264233E-02 169s Surface tension*area energy for atom 1: 8.085988052425E-02 169s Surface tension*area energy for atom 2: 1.954854254432E-02 169s Surface tension*area energy for atom 3: 1.631160855160E-02 169s Surface tension*area energy for atom 4: 1.961201183830E-02 169s Surface tension*area energy for atom 5: 1.976962894687E-01 169s Surface tension*area energy for atom 6: 1.976962894687E-01 169s Surface tension*area energy for atom 7: 1.739089474466E-01 169s Surface tension*area energy for atom 8: 1.757694099511E-01 169s Surface tension*area energy for atom 9: 1.724471554788E-01 169s Surface tension*area energy for atom 10: 1.612843804516E-01 169s Surface tension*area energy for atom 11: 1.741304310781E-01 169s Surface tension*area energy for atom 12: 1.759908935826E-01 169s 169s Total surface tension energy: 1.64593 kJ/mol 169s 169s Total solvent accessible volume: 217.998 A^3 169s 169s Total pressure*volume energy: 52.1887 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.343496616804E+00 169s WCA energy for atom 1: -6.327869601807E+00 169s WCA energy for atom 2: -6.334858040579E+00 169s WCA energy for atom 3: -6.296075406417E+00 169s WCA energy for atom 4: -6.345600816761E+00 169s WCA energy for atom 5: -1.663697465126E+00 169s WCA energy for atom 6: -1.662444032853E+00 169s WCA energy for atom 7: -1.572325104493E+00 169s WCA energy for atom 8: -1.604626551065E+00 169s WCA energy for atom 9: -1.586431484963E+00 169s WCA energy for atom 10: -1.554291291374E+00 169s WCA energy for atom 11: -1.574315220751E+00 169s WCA energy for atom 12: -1.604941679892E+00 169s 169s Total WCA energy: -44.471 kJ/mol 169s 169s Total non-polar energy = 9.363673200142E+00 kJ/mol 169s ---------------------------------------- 169s CALCULATION #5 (solvated-ethane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 5.995981536705E+00 169s SASA for atom 1: 5.966113633657E+00 169s SASA for atom 2: 2.121552620704E+01 169s SASA for atom 3: 2.124158310486E+01 169s SASA for atom 4: 2.125200586399E+01 169s SASA for atom 5: 2.123116034573E+01 169s SASA for atom 6: 2.125200586399E+01 169s SASA for atom 7: 2.127285138225E+01 169s 169s Total solvent accessible surface area: 139.427 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 5.096584306199E-02 169s Surface tension*area energy for atom 1: 5.071196588609E-02 169s Surface tension*area energy for atom 2: 1.803319727598E-01 169s Surface tension*area energy for atom 3: 1.805534563913E-01 169s Surface tension*area energy for atom 4: 1.806420498439E-01 169s Surface tension*area energy for atom 5: 1.804648629387E-01 169s Surface tension*area energy for atom 6: 1.806420498439E-01 169s Surface tension*area energy for atom 7: 1.808192367491E-01 169s 169s Total surface tension energy: 1.18513 kJ/mol 169s 169s Total solvent accessible volume: 140.346 A^3 169s 169s Total pressure*volume energy: 33.5988 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -7.360066353115E+00 169s WCA energy for atom 1: -7.355483516201E+00 169s WCA energy for atom 2: -1.776106201066E+00 169s WCA energy for atom 3: -1.773973940651E+00 169s WCA energy for atom 4: -1.775401936843E+00 169s WCA energy for atom 5: -1.773464835521E+00 169s WCA energy for atom 6: -1.774382856097E+00 169s WCA energy for atom 7: -1.772366599434E+00 169s 169s Total WCA energy: -25.3612 kJ/mol 169s 169s Total non-polar energy = 9.422717598546E+00 kJ/mol 169s ---------------------------------------- 169s CALCULATION #6 (solvated-hexane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 4.405515699447E+00 169s SASA for atom 1: 8.213673337951E-01 169s SASA for atom 2: 3.285469335181E-01 169s SASA for atom 3: 2.986790304710E-01 169s SASA for atom 4: 1.855251124959E+01 169s SASA for atom 5: 2.147609518526E+01 169s SASA for atom 6: 1.852645435176E+01 169s SASA for atom 7: 1.655655287639E+01 169s SASA for atom 8: 1.655134149682E+01 169s SASA for atom 9: 1.360170066332E+01 169s SASA for atom 10: 1.357043238593E+01 169s SASA for atom 11: 1.381536722546E+01 169s SASA for atom 12: 1.384142412329E+01 169s SASA for atom 13: 7.765654792245E-01 169s SASA for atom 14: 1.684839013200E+01 169s SASA for atom 15: 1.682233323417E+01 169s SASA for atom 16: 4.166572475070E+00 169s SASA for atom 17: 2.179398933870E+01 169s SASA for atom 18: 1.877660057086E+01 169s SASA for atom 19: 1.876096643216E+01 169s 169s Total solvent accessible surface area: 250.291 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 3.744688344530E-02 169s Surface tension*area energy for atom 1: 6.981622337259E-03 169s Surface tension*area energy for atom 2: 2.792648934903E-03 169s Surface tension*area energy for atom 3: 2.538771759003E-03 169s Surface tension*area energy for atom 4: 1.576963456215E-01 169s Surface tension*area energy for atom 5: 1.825468090747E-01 169s Surface tension*area energy for atom 6: 1.574748619900E-01 169s Surface tension*area energy for atom 7: 1.407306994493E-01 169s Surface tension*area energy for atom 8: 1.406864027230E-01 169s Surface tension*area energy for atom 9: 1.156144556382E-01 169s Surface tension*area energy for atom 10: 1.153486752804E-01 169s Surface tension*area energy for atom 11: 1.174306214164E-01 169s Surface tension*area energy for atom 12: 1.176521050479E-01 169s Surface tension*area energy for atom 13: 6.600806573408E-03 169s Surface tension*area energy for atom 14: 1.432113161220E-01 169s Surface tension*area energy for atom 15: 1.429898324905E-01 169s Surface tension*area energy for atom 16: 3.541586603809E-02 169s Surface tension*area energy for atom 17: 1.852489093789E-01 169s Surface tension*area energy for atom 18: 1.596011048523E-01 169s Surface tension*area energy for atom 19: 1.594682146734E-01 169s 169s Total surface tension energy: 2.12748 kJ/mol 169s 169s Total solvent accessible volume: 298.053 A^3 169s 169s Total pressure*volume energy: 71.3539 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.635406071935E+00 169s WCA energy for atom 1: -5.957247427848E+00 169s WCA energy for atom 2: -5.524801144538E+00 169s WCA energy for atom 3: -5.522294168859E+00 169s WCA energy for atom 4: -1.605314409440E+00 169s WCA energy for atom 5: -1.701051761776E+00 169s WCA energy for atom 6: -1.606669162773E+00 169s WCA energy for atom 7: -1.442505934938E+00 169s WCA energy for atom 8: -1.443059002759E+00 169s WCA energy for atom 9: -1.328947132810E+00 169s WCA energy for atom 10: -1.328906972440E+00 169s WCA energy for atom 11: -1.331566344214E+00 169s WCA energy for atom 12: -1.328041776815E+00 169s WCA energy for atom 13: -5.937562025661E+00 169s WCA energy for atom 14: -1.442277774427E+00 169s WCA energy for atom 15: -1.442777091510E+00 169s WCA energy for atom 16: -6.602262542378E+00 169s WCA energy for atom 17: -1.698172146664E+00 169s WCA energy for atom 18: -1.600970858835E+00 169s WCA energy for atom 19: -1.600841970217E+00 169s 169s Total WCA energy: -57.0807 kJ/mol 169s 169s Total non-polar energy = 1.640068943201E+01 kJ/mol 169s ---------------------------------------- 169s CALCULATION #7 (solvated-isobutane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 3.464676753463E+00 169s SASA for atom 1: 1.984493338158E+01 169s SASA for atom 2: 1.778643845361E+01 169s SASA for atom 3: 1.671289426332E+01 169s SASA for atom 4: 0.000000000000E+00 169s SASA for atom 5: 3.531879535319E+00 169s SASA for atom 6: 1.673895116114E+01 169s SASA for atom 7: 1.793756846098E+01 169s SASA for atom 8: 1.973549441072E+01 169s SASA for atom 9: 1.710895911022E+01 169s SASA for atom 10: 4.599657069253E+00 169s SASA for atom 11: 1.937069784121E+01 169s SASA for atom 12: 1.654613011726E+01 169s SASA for atom 13: 1.936548646165E+01 169s 169s Total solvent accessible surface area: 192.744 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 2.944975240444E-02 169s Surface tension*area energy for atom 1: 1.686819337434E-01 169s Surface tension*area energy for atom 2: 1.511847268556E-01 169s Surface tension*area energy for atom 3: 1.420596012382E-01 169s Surface tension*area energy for atom 4: 0.000000000000E+00 169s Surface tension*area energy for atom 5: 3.002097605021E-02 169s Surface tension*area energy for atom 6: 1.422810848697E-01 169s Surface tension*area energy for atom 7: 1.524693319183E-01 169s Surface tension*area energy for atom 8: 1.677517024912E-01 169s Surface tension*area energy for atom 9: 1.454261524369E-01 169s Surface tension*area energy for atom 10: 3.909708508865E-02 169s Surface tension*area energy for atom 11: 1.646509316503E-01 169s Surface tension*area energy for atom 12: 1.406421059967E-01 169s Surface tension*area energy for atom 13: 1.646066349240E-01 169s 169s Total surface tension energy: 1.63832 kJ/mol 169s 169s Total solvent accessible volume: 218.943 A^3 169s 169s Total pressure*volume energy: 52.415 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.381016335247E+00 169s WCA energy for atom 1: -1.612317964554E+00 169s WCA energy for atom 2: -1.588013719598E+00 169s WCA energy for atom 3: -1.532162371190E+00 169s WCA energy for atom 4: -5.987950445279E+00 169s WCA energy for atom 5: -6.393089030861E+00 169s WCA energy for atom 6: -1.533454887042E+00 169s WCA energy for atom 7: -1.587650918485E+00 169s WCA energy for atom 8: -1.614083521570E+00 169s WCA energy for atom 9: -1.442402031577E+00 169s WCA energy for atom 10: -6.408813541353E+00 169s WCA energy for atom 11: -1.605830214390E+00 169s WCA energy for atom 12: -1.529385873788E+00 169s WCA energy for atom 13: -1.605662490385E+00 169s 169s Total WCA energy: -40.8218 kJ/mol 169s 169s Total non-polar energy = 1.323144287435E+01 kJ/mol 169s ---------------------------------------- 169s CALCULATION #8 (solvated-methane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 1.231304303117E+01 169s SASA for atom 1: 2.323233009850E+01 169s SASA for atom 2: 2.345641941977E+01 169s SASA for atom 3: 2.377431357320E+01 169s SASA for atom 4: 2.264344420771E+01 169s 169s Total solvent accessible surface area: 105.42 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 1.046608657649E-01 169s Surface tension*area energy for atom 1: 1.974748058372E-01 169s Surface tension*area energy for atom 2: 1.993795650680E-01 169s Surface tension*area energy for atom 3: 2.020816653722E-01 169s Surface tension*area energy for atom 4: 1.924692757655E-01 169s 169s Total surface tension energy: 0.896066 kJ/mol 169s 169s Total solvent accessible volume: 95.985 A^3 169s 169s Total pressure*volume energy: 22.9788 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -8.133807570805E+00 169s WCA energy for atom 1: -1.962181541765E+00 169s WCA energy for atom 2: -1.964078319162E+00 169s WCA energy for atom 3: -1.963015006647E+00 169s WCA energy for atom 4: -1.957425549100E+00 169s 169s Total WCA energy: -15.9805 kJ/mol 169s 169s Total non-polar energy = 7.894367190329E+00 kJ/mol 169s ---------------------------------------- 169s CALCULATION #9 (solvated-neopentane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 2.441701074100E+00 169s SASA for atom 1: 1.663993494942E+01 169s SASA for atom 2: 1.715586152630E+01 169s SASA for atom 3: 1.645753666466E+01 169s SASA for atom 4: 0.000000000000E+00 169s SASA for atom 5: 2.389432243768E+00 169s SASA for atom 6: 1.638457735076E+01 169s SASA for atom 7: 1.667641460637E+01 169s SASA for atom 8: 1.721839808108E+01 169s SASA for atom 9: 2.419300146815E+00 169s SASA for atom 10: 1.640021148945E+01 169s SASA for atom 11: 1.666599184724E+01 169s SASA for atom 12: 1.719234118325E+01 169s SASA for atom 13: 2.449168049862E+00 169s SASA for atom 14: 1.723403221977E+01 169s SASA for atom 15: 1.639500010989E+01 169s SASA for atom 16: 1.663472356985E+01 169s 169s Total solvent accessible surface area: 210.755 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 2.075445912985E-02 169s Surface tension*area energy for atom 1: 1.414394470700E-01 169s Surface tension*area energy for atom 2: 1.458248229736E-01 169s Surface tension*area energy for atom 3: 1.398890616496E-01 169s Surface tension*area energy for atom 4: 0.000000000000E+00 169s Surface tension*area energy for atom 5: 2.031017407203E-02 169s Surface tension*area energy for atom 6: 1.392689074814E-01 169s Surface tension*area energy for atom 7: 1.417495241541E-01 169s Surface tension*area energy for atom 8: 1.463563836891E-01 169s Surface tension*area energy for atom 9: 2.056405124793E-02 169s Surface tension*area energy for atom 10: 1.394017976603E-01 169s Surface tension*area energy for atom 11: 1.416609307015E-01 169s Surface tension*area energy for atom 12: 1.461349000577E-01 169s Surface tension*area energy for atom 13: 2.081792842383E-02 169s Surface tension*area energy for atom 14: 1.464892738680E-01 169s Surface tension*area energy for atom 15: 1.393575009340E-01 169s Surface tension*area energy for atom 16: 1.413951503437E-01 169s 169s Total surface tension energy: 1.79141 kJ/mol 169s 169s Total solvent accessible volume: 251.127 A^3 169s 169s Total pressure*volume energy: 60.1198 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.011082520236E+00 169s WCA energy for atom 1: -1.497367782613E+00 169s WCA energy for atom 2: -1.498546483218E+00 169s WCA energy for atom 3: -1.492562171495E+00 169s WCA energy for atom 4: -5.447325863939E+00 169s WCA energy for atom 5: -6.004516149175E+00 169s WCA energy for atom 6: -1.492776531092E+00 169s WCA energy for atom 7: -1.496078170066E+00 169s WCA energy for atom 8: -1.501529655270E+00 169s WCA energy for atom 9: -5.996267554365E+00 169s WCA energy for atom 10: -1.492194267752E+00 169s WCA energy for atom 11: -1.496027211216E+00 169s WCA energy for atom 12: -1.500561393960E+00 169s WCA energy for atom 13: -6.000218612907E+00 169s WCA energy for atom 14: -1.500859921426E+00 169s WCA energy for atom 15: -1.492908499790E+00 169s WCA energy for atom 16: -1.494057174414E+00 169s 169s Total WCA energy: -47.4149 kJ/mol 169s 169s Total non-polar energy = 1.449633815052E+01 kJ/mol 169s ---------------------------------------- 169s CALCULATION #10 (solvated-pentane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 4.405515699447E+00 169s SASA for atom 1: 8.213673337951E-01 169s SASA for atom 2: 3.285469335181E-01 169s SASA for atom 3: 7.466975761774E-01 169s SASA for atom 4: 1.855251124959E+01 169s SASA for atom 5: 2.147609518526E+01 169s SASA for atom 6: 1.852645435176E+01 169s SASA for atom 7: 1.655655287639E+01 169s SASA for atom 8: 1.655134149682E+01 169s SASA for atom 9: 1.360170066332E+01 169s SASA for atom 10: 1.357043238593E+01 169s SASA for atom 11: 1.685881289113E+01 169s SASA for atom 12: 1.687444702982E+01 169s SASA for atom 13: 4.196440378117E+00 169s SASA for atom 14: 1.881308022781E+01 169s SASA for atom 15: 1.882350298694E+01 169s SASA for atom 16: 2.182004623652E+01 169s 169s Total solvent accessible surface area: 222.524 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 3.744688344530E-02 169s Surface tension*area energy for atom 1: 6.981622337259E-03 169s Surface tension*area energy for atom 2: 2.792648934903E-03 169s Surface tension*area energy for atom 3: 6.346929397508E-03 169s Surface tension*area energy for atom 4: 1.576963456215E-01 169s Surface tension*area energy for atom 5: 1.825468090747E-01 169s Surface tension*area energy for atom 6: 1.574748619900E-01 169s Surface tension*area energy for atom 7: 1.407306994493E-01 169s Surface tension*area energy for atom 8: 1.406864027230E-01 169s Surface tension*area energy for atom 9: 1.156144556382E-01 169s Surface tension*area energy for atom 10: 1.153486752804E-01 169s Surface tension*area energy for atom 11: 1.432999095746E-01 169s Surface tension*area energy for atom 12: 1.434327997535E-01 169s Surface tension*area energy for atom 13: 3.566974321399E-02 169s Surface tension*area energy for atom 14: 1.599111819364E-01 169s Surface tension*area energy for atom 15: 1.599997753890E-01 169s Surface tension*area energy for atom 16: 1.854703930104E-01 169s 169s Total surface tension energy: 1.89145 kJ/mol 169s 169s Total solvent accessible volume: 258.93 A^3 169s 169s Total pressure*volume energy: 61.9878 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.655804319869E+00 169s WCA energy for atom 1: -6.027315962813E+00 169s WCA energy for atom 2: -5.696430965386E+00 169s WCA energy for atom 3: -6.016749084714E+00 169s WCA energy for atom 4: -1.608595384643E+00 169s WCA energy for atom 5: -1.703300955380E+00 169s WCA energy for atom 6: -1.609931495887E+00 169s WCA energy for atom 7: -1.457107525189E+00 169s WCA energy for atom 8: -1.457741620594E+00 169s WCA energy for atom 9: -1.354235498709E+00 169s WCA energy for atom 10: -1.354106470090E+00 169s WCA energy for atom 11: -1.456736412636E+00 169s WCA energy for atom 12: -1.455995435596E+00 169s WCA energy for atom 13: -6.633650611186E+00 169s WCA energy for atom 14: -1.605996088477E+00 169s WCA energy for atom 15: -1.606549890103E+00 169s WCA energy for atom 16: -1.700042300035E+00 169s 169s Total WCA energy: -49.4003 kJ/mol 169s 169s Total non-polar energy = 1.447900211546E+01 kJ/mol 169s ---------------------------------------- 169s CALCULATION #11 (solvated-propane): APOLAR 169s 169s Solvent Accessible Surface Area (SASA) for each atom: 169s SASA for atom 0: 3.173464698754E+00 169s SASA for atom 1: 1.931858404557E+01 169s SASA for atom 2: 2.014198201675E+01 169s SASA for atom 3: 2.149694070352E+01 169s SASA for atom 4: 1.904078819252E+00 169s SASA for atom 5: 2.067354273233E+01 169s SASA for atom 6: 1.937590922077E+01 169s SASA for atom 7: 3.098794941136E+00 169s SASA for atom 8: 1.942802301642E+01 169s SASA for atom 9: 1.973028303116E+01 169s SASA for atom 10: 2.204934693736E+01 169s 169s Total solvent accessible surface area: 170.391 A^2 169s 169s Surface tension*area energies (gamma * SASA) for each atom: 169s Surface tension*area energy for atom 0: 2.697444993941E-02 169s Surface tension*area energy for atom 1: 1.642079643873E-01 169s Surface tension*area energy for atom 2: 1.712068471424E-01 169s Surface tension*area energy for atom 3: 1.827239959799E-01 169s Surface tension*area energy for atom 4: 1.618466996365E-02 169s Surface tension*area energy for atom 5: 1.757251132248E-01 169s Surface tension*area energy for atom 6: 1.646952283766E-01 169s Surface tension*area energy for atom 7: 2.633975699966E-02 169s Surface tension*area energy for atom 8: 1.651381956396E-01 169s Surface tension*area energy for atom 9: 1.677074057649E-01 169s Surface tension*area energy for atom 10: 1.874194489675E-01 169s 169s Total surface tension energy: 1.44832 kJ/mol 169s 169s Total solvent accessible volume: 183.573 A^3 169s 169s Total pressure*volume energy: 43.9474 kJ/mol 169s 169s WCA dispersion Energies for each atom: 169s WCA energy for atom 0: -6.818670105515E+00 169s WCA energy for atom 1: -1.641297645338E+00 169s WCA energy for atom 2: -1.649584120441E+00 169s WCA energy for atom 3: -1.711408141255E+00 169s WCA energy for atom 4: -6.624720142882E+00 169s WCA energy for atom 5: -1.610117050515E+00 169s WCA energy for atom 6: -1.596858009746E+00 169s WCA energy for atom 7: -6.816460624835E+00 169s WCA energy for atom 8: -1.642782751806E+00 169s WCA energy for atom 9: -1.645779566650E+00 169s WCA energy for atom 10: -1.714436154542E+00 169s 169s Total WCA energy: -33.4721 kJ/mol 169s 169s Total non-polar energy = 1.192358496286E+01 kJ/mol 169s ---------------------------------------- 169s PRINT STATEMENTS 169s 169s print APOL energy 1 (solvated-2-methylbutane) end 169s Global net APOL energy = 1.439739455792E+01 kJ/mol 169s 169s print APOL energy 2 (solvated-butane) end 169s Global net APOL energy = 1.208346456826E+01 kJ/mol 169s 169s print APOL energy 3 (solvated-cyclohexane) end 169s Global net APOL energy = 1.354016672221E+01 kJ/mol 169s 169s print APOL energy 4 (solvated-cyclopentane) end 169s Global net APOL energy = 9.363673200142E+00 kJ/mol 169s 169s print APOL energy 5 (solvated-ethane) end 169s Global net APOL energy = 9.422717598546E+00 kJ/mol 169s 169s print APOL energy 6 (solvated-hexane) end 169s Global net APOL energy = 1.640068943201E+01 kJ/mol 169s 169s print APOL energy 7 (solvated-isobutane) end 169s Global net APOL energy = 1.323144287435E+01 kJ/mol 169s 169s print APOL energy 8 (solvated-methane) end 169s Global net APOL energy = 7.894367190329E+00 kJ/mol 169s 169s print APOL energy 9 (solvated-neopentane) end 169s Global net APOL energy = 1.449633815052E+01 kJ/mol 169s 169s print APOL energy 10 (solvated-pentane) end 169s Global net APOL energy = 1.447900211546E+01 kJ/mol 169s 169s print APOL energy 11 (solvated-propane) end 169s Global net APOL energy = 1.192358496286E+01 kJ/mol 169s ---------------------------------------- 169s CLEANING UP AND SHUTTING DOWN... 169s Destroying force arrays. 169s No energy arrays to destroy. 169s Destroying multigrid structures. 169s Destroying finite element structures. 169s Destroying 11 molecules 169s Final memory usage: 0.001 MB total, 2.267 MB high water 169s 169s 169s Thanks for using APBS! 169s 169s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 169s *** PASSED *** 169s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 169s *** PASSED *** 169s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 169s *** PASSED *** 169s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 169s *** PASSED *** 169s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 169s *** PASSED *** 169s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 169s *** PASSED *** 169s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 169s *** PASSED *** 169s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 169s *** PASSED *** 169s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 169s *** PASSED *** 169s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 169s *** PASSED *** 169s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 169s *** PASSED *** 169s Elapsed time: 5.678541 seconds 169s -------------------------------------------------------------------------------- 169s Total elapsed time: 5.678541 seconds 169s Test results have been logged 169s -------------------------------------------------------------------------------- 169s -------------------------------------------------------------------------------- 169s Testing input file 1d7h-dmso-mol.in 169s 174s Checking for intermediate energies in input file alkanes.out 174s EXPECTED COMPUTED: 11 174s EXPECTED EXPECTED: 11 174s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 174s 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'] 174s COMPUTED RESULT 14.39739455792 174s COMPUTED RESULT 12.08346456826 174s COMPUTED RESULT 13.54016672221 174s COMPUTED RESULT 9.363673200142 174s COMPUTED RESULT 9.422717598546 174s COMPUTED RESULT 16.40068943201 174s COMPUTED RESULT 13.23144287435 174s COMPUTED RESULT 7.894367190329 174s COMPUTED RESULT 14.49633815052 174s COMPUTED RESULT 14.47900211546 174s COMPUTED RESULT 11.92358496286 174s Running tests for FKBP section 174s BINARY: /usr/bin/apbs 174s INPUT: 1d7h-dmso-mol.in 174s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 174s asc_getToken: Error occurred (bailing out). 174s Vio_scanf: Format problem with input. 174s 174s 174s ---------------------------------------------------------------------- 174s APBS -- Adaptive Poisson-Boltzmann Solver 174s Version APBS 3.4.1 174s 174s Nathan A. Baker (nathan.baker@pnnl.gov) 174s Pacific Northwest National Laboratory 174s 174s Additional contributing authors listed in the code documentation. 174s 174s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 174s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 174s Northwest Division for the U.S. Department of Energy. 174s 174s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 174s Portions Copyright (c) 2002-2020, Nathan A. Baker. 174s Portions Copyright (c) 1999-2002, The Regents of the University of California. 174s Portions Copyright (c) 1995, Michael Holst. 174s All rights reserved. 174s 174s Redistribution and use in source and binary forms, with or without 174s modification, are permitted provided that the following conditions are met: 174s 174s * Redistributions of source code must retain the above copyright notice, this 174s list of conditions and the following disclaimer. 174s 174s * Redistributions in binary form must reproduce the above copyright notice, 174s this list of conditions and the following disclaimer in the documentation 174s and/or other materials provided with the distribution. 174s 174s * Neither the name of the developer nor the names of its contributors may be 174s used to endorse or promote products derived from this software without 174s specific prior written permission. 174s 174s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 174s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 174s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 174s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 174s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 174s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 174s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 174s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 174s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 174s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 174s ---------------------------------------------------------------------- 174s APBS uses FETK (the Finite Element ToolKit) to solve the 174s Poisson-Boltzmann equation numerically. FETK is a portable collection 174s of finite element modeling class libraries developed by the Michael Holst 174s research group and written in an object-oriented form of C. FEtk is 174s designed to solve general coupled systems of nonlinear partial differential 174s equations using adaptive finite element methods, inexact Newton methods, 174s and algebraic multilevel methods. More information about FEtk may be found 174s at . 174s ---------------------------------------------------------------------- 174s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 174s Aqua is a modified form of the Holst group PMG library 174s which has been modified by Patrice Koehl 174s for improved efficiency and 174s memory usage when solving the Poisson-Boltzmann equation. 174s ---------------------------------------------------------------------- 174s Please cite your use of APBS as: 174s 174s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 174s nanosystems: application to microtubules and the ribosome. Proc. 174s Natl. Acad. Sci. USA 98, 10037-10041 2001. 174s 174s 174s This executable compiled on Jan 3 2025 at 11:01:42 174s 174s Parsing input file 1d7h-dmso-mol.in... 174s rank 0 size 1... 174s Parsed input file. 174s Got paths for 3 molecules 174s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 174s asc_getToken: Error occurred (bailing out). 174s Vio_scanf: Format problem with input. 174s 1673 atoms 174s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 174s Net charge 9.91e-01 e 174s Reading PQR-format atom data from dmso-min.pqr. 174s asc_getToken: Error occurred (bailing out). 174s Vio_scanf: Format problem with input. 174s 10 atoms 174s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 174s Net charge 2.78e-17 e 174s Reading PQR-format atom data from 1d7h-min.pqr. 174s 1663 atoms 174s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 174s Net charge 9.91e-01 e 174s Preparing to run 12 PBE calculations. 174s ---------------------------------------- 174s CALCULATION #1 (complex-solv-coarse): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 30.4176 A 174s Current memory usage: 122.059 MB total, 122.059 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 1.500 x 1.500 x 1.500 174s Grid lengths: 96.000 x 96.000 x 96.000 174s Grid center: (25.875, 18.349, 19.112) 174s Multigrid levels: 5 174s Molecule ID: 1 174s Linearized traditional PBE 174s Multiple Debye-Huckel sphere boundary conditions 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 78.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 1.060899690259E+04 kJ/mol 174s Calculating forces... 174s [focusFillBound()]: WARNING: 174s Unusually large potential values 174s detected on the focusing boundary! 174s Convergence not guaranteed for NPBE/NRPBE calculations! 174s 174s ---------------------------------------- 174s CALCULATION #2 (complex-solv-fine): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 30.4176 A 174s Current memory usage: 122.059 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 0.225 x 0.225 x 0.225 174s Grid lengths: 14.400 x 14.400 x 14.400 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 1 174s Linearized traditional PBE 174s Boundary conditions from focusing 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 78.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 4.276523673491E+04 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s CALCULATION #3 (complex-ref-coarse): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 4.87072 A 174s Current memory usage: 122.059 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 1.500 x 1.500 x 1.500 174s Grid lengths: 96.000 x 96.000 x 96.000 174s Grid center: (25.875, 18.349, 19.112) 174s Multigrid levels: 5 174s Molecule ID: 1 174s Linearized traditional PBE 174s Multiple Debye-Huckel sphere boundary conditions 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 2.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 1.399234956777E+04 kJ/mol 174s Calculating forces... 174s [focusFillBound()]: WARNING: 174s Unusually large potential values 174s detected on the focusing boundary! 174s Convergence not guaranteed for NPBE/NRPBE calculations! 174s 174s ---------------------------------------- 174s CALCULATION #4 (complex-ref-fine): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 4.87072 A 174s Current memory usage: 122.059 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 0.225 x 0.225 x 0.225 174s Grid lengths: 14.400 x 14.400 x 14.400 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 1 174s Linearized traditional PBE 174s Boundary conditions from focusing 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 2.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 4.610066575192E+04 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 30.4176 A 174s Current memory usage: 62.428 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 1.500 x 1.500 x 1.500 174s Grid lengths: 96.000 x 96.000 x 96.000 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 2 174s Linearized traditional PBE 174s Multiple Debye-Huckel sphere boundary conditions 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 78.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 3.961107503213E+01 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s CALCULATION #6 (dmso-solv-fine): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 30.4176 A 174s Current memory usage: 62.428 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 0.225 x 0.225 x 0.225 174s Grid lengths: 14.400 x 14.400 x 14.400 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 2 174s Linearized traditional PBE 174s Boundary conditions from focusing 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 78.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 7.121048606059E+02 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 4.87072 A 174s Current memory usage: 62.428 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 1.500 x 1.500 x 1.500 174s Grid lengths: 96.000 x 96.000 x 96.000 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 2 174s Linearized traditional PBE 174s Multiple Debye-Huckel sphere boundary conditions 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 2.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 6.751571424823E+01 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s CALCULATION #8 (dmso-ref-fine): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 4.87072 A 174s Current memory usage: 62.428 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 0.225 x 0.225 x 0.225 174s Grid lengths: 14.400 x 14.400 x 14.400 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 2 174s Linearized traditional PBE 174s Boundary conditions from focusing 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 2.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 7.339101343121E+02 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 30.4176 A 174s Current memory usage: 121.736 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 1.500 x 1.500 x 1.500 174s Grid lengths: 96.000 x 96.000 x 96.000 174s Grid center: (25.875, 18.349, 19.112) 174s Multigrid levels: 5 174s Molecule ID: 3 174s Linearized traditional PBE 174s Multiple Debye-Huckel sphere boundary conditions 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 78.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 1.058410584089E+04 kJ/mol 174s Calculating forces... 174s [focusFillBound()]: WARNING: 174s Unusually large potential values 174s detected on the focusing boundary! 174s Convergence not guaranteed for NPBE/NRPBE calculations! 174s 174s ---------------------------------------- 174s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 30.4176 A 174s Current memory usage: 121.736 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 0.225 x 0.225 x 0.225 174s Grid lengths: 14.400 x 14.400 x 14.400 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 3 174s Linearized traditional PBE 174s Boundary conditions from focusing 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 78.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 4.205385249581E+04 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 4.87072 A 174s Current memory usage: 121.736 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 1.500 x 1.500 x 1.500 174s Grid lengths: 96.000 x 96.000 x 96.000 174s Grid center: (25.875, 18.349, 19.112) 174s Multigrid levels: 5 174s Molecule ID: 3 174s Linearized traditional PBE 174s Multiple Debye-Huckel sphere boundary conditions 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 2.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 1.395961902233E+04 kJ/mol 174s Calculating forces... 174s [focusFillBound()]: WARNING: 174s Unusually large potential values 174s detected on the focusing boundary! 174s Convergence not guaranteed for NPBE/NRPBE calculations! 174s 174s ---------------------------------------- 174s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 174s Setting up problem... 174s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 174s Debye length: 4.87072 A 174s Current memory usage: 121.736 MB total, 221.696 MB high water 174s Using linear spline charge discretization. 174s Grid dimensions: 65 x 65 x 65 174s Grid spacings: 0.225 x 0.225 x 0.225 174s Grid lengths: 14.400 x 14.400 x 14.400 174s Grid center: (17.751, 17.770, 20.492) 174s Multigrid levels: 5 174s Molecule ID: 3 174s Linearized traditional PBE 174s Boundary conditions from focusing 174s 2 ion species (0.010 M ionic strength): 174s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 174s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 174s Solute dielectric: 2.000 174s Solvent dielectric: 2.000 174s Using "molecular" surface definition; no smoothing 174s Solvent probe radius: 0.000 A 174s Temperature: 300.000 K 174s Electrostatic energies will be calculated 174s Total electrostatic energy = 4.538248433997E+04 kJ/mol 174s Calculating forces... 174s ---------------------------------------- 174s PRINT STATEMENTS 174s 174s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 174s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 174s Global net ELEC energy = -3.335429017008E+03 kJ/mol 174s 174s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 174s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 174s Global net ELEC energy = -2.180527370616E+01 kJ/mol 174s 174s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 174s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 174s Global net ELEC energy = -3.328631844166E+03 kJ/mol 174s 174s 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 174s Local net energy (PE 0) = 1.500810086371E+01 kJ/mol 174s Global net ELEC energy = 1.500810086371E+01 kJ/mol 174s ---------------------------------------- 174s CLEANING UP AND SHUTTING DOWN... 174s Destroying force arrays. 174s No energy arrays to destroy. 174s Destroying multigrid structures. 174s Destroying finite element structures. 174s Destroying 3 molecules 174s Final memory usage: 0.001 MB total, 221.696 MB high water 174s 174s 174s Thanks for using APBS! 174s 174s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 174s *** PASSED *** 174s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 174s *** PASSED *** 174s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 174s *** PASSED *** 174s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 174s *** PASSED *** 174s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 174s *** PASSED *** 174s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 174s *** PASSED *** 174s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 174s *** PASSED *** 174s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 174s *** PASSED *** 174s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 174s *** PASSED *** 174s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 174s *** PASSED *** 174s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 174s *** PASSED *** 174s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 174s *** PASSED *** 174s Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) 174s *** PASSED *** 174s Elapsed time: 4.730474 seconds 174s -------------------------------------------------------------------------------- 174s -------------------------------------------------------------------------------- 174s Testing input file 1d7h-dmso-smol.in 174s 178s Checking for intermediate energies in input file 1d7h-dmso-mol.out 178s EXPECTED COMPUTED: 16 178s EXPECTED EXPECTED: 16 178s COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086371] 178s 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'] 178s COMPUTED RESULT 10608.99690259 178s COMPUTED RESULT 42765.23673491 178s COMPUTED RESULT 13992.34956777 178s COMPUTED RESULT 46100.66575192 178s COMPUTED RESULT 39.61107503213 178s COMPUTED RESULT 712.1048606059 178s COMPUTED RESULT 67.51571424823 178s COMPUTED RESULT 733.9101343121 178s COMPUTED RESULT 10584.10584089 178s COMPUTED RESULT 42053.85249581 178s COMPUTED RESULT 13959.61902233 178s COMPUTED RESULT 45382.48433997 178s COMPUTED RESULT -3335.429017008 178s COMPUTED RESULT -21.80527370616 178s COMPUTED RESULT -3328.631844166 178s COMPUTED RESULT 15.00810086371 178s BINARY: /usr/bin/apbs 178s INPUT: 1d7h-dmso-smol.in 178s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.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 1d7h-dmso-smol.in... 178s rank 0 size 1... 178s Parsed input file. 178s Got paths for 3 molecules 178s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 178s asc_getToken: Error occurred (bailing out). 178s Vio_scanf: Format problem with input. 178s 1673 atoms 178s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 178s Net charge 9.91e-01 e 178s Reading PQR-format atom data from dmso-min.pqr. 178s asc_getToken: Error occurred (bailing out). 178s Vio_scanf: Format problem with input. 178s 10 atoms 178s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 178s Net charge 2.78e-17 e 178s Reading PQR-format atom data from 1d7h-min.pqr. 178s 1663 atoms 178s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 178s Net charge 9.91e-01 e 178s Preparing to run 12 PBE calculations. 178s ---------------------------------------- 178s CALCULATION #1 (complex-solv-coarse): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 30.4176 A 178s Current memory usage: 122.059 MB total, 122.059 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 1.500 x 1.500 x 1.500 178s Grid lengths: 96.000 x 96.000 x 96.000 178s Grid center: (25.875, 18.349, 19.112) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.074948704824E+04 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 #2 (complex-solv-fine): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 30.4176 A 178s Current memory usage: 122.059 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.225 x 0.225 x 0.225 178s Grid lengths: 14.400 x 14.400 x 14.400 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 4.289487256481E+04 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #3 (complex-ref-coarse): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 4.87072 A 178s Current memory usage: 122.059 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 1.500 x 1.500 x 1.500 178s Grid lengths: 96.000 x 96.000 x 96.000 178s Grid center: (25.875, 18.349, 19.112) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 2.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.399234956777E+04 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 #4 (complex-ref-fine): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 4.87072 A 178s Current memory usage: 122.059 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.225 x 0.225 x 0.225 178s Grid lengths: 14.400 x 14.400 x 14.400 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 2.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 4.610066575192E+04 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 30.4176 A 178s Current memory usage: 62.428 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 1.500 x 1.500 x 1.500 178s Grid lengths: 96.000 x 96.000 x 96.000 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 2 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 3.719709905887E+01 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #6 (dmso-solv-fine): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 30.4176 A 178s Current memory usage: 62.428 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.225 x 0.225 x 0.225 178s Grid lengths: 14.400 x 14.400 x 14.400 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 2 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 7.125747080979E+02 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 4.87072 A 178s Current memory usage: 62.428 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 1.500 x 1.500 x 1.500 178s Grid lengths: 96.000 x 96.000 x 96.000 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 2 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 2.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 6.751571424823E+01 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #8 (dmso-ref-fine): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 4.87072 A 178s Current memory usage: 62.428 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.225 x 0.225 x 0.225 178s Grid lengths: 14.400 x 14.400 x 14.400 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 2 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 2.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 7.339101343121E+02 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 30.4176 A 178s Current memory usage: 121.736 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 1.500 x 1.500 x 1.500 178s Grid lengths: 96.000 x 96.000 x 96.000 178s Grid center: (25.875, 18.349, 19.112) 178s Multigrid levels: 5 178s Molecule ID: 3 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.071654753674E+04 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 #10 (1d7h-solv-fine): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 30.4176 A 178s Current memory usage: 121.736 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.225 x 0.225 x 0.225 178s Grid lengths: 14.400 x 14.400 x 14.400 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 3 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 4.218178203716E+04 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 4.87072 A 178s Current memory usage: 121.736 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 1.500 x 1.500 x 1.500 178s Grid lengths: 96.000 x 96.000 x 96.000 178s Grid center: (25.875, 18.349, 19.112) 178s Multigrid levels: 5 178s Molecule ID: 3 178s Linearized traditional PBE 178s Multiple Debye-Huckel sphere boundary conditions 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 2.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.395961902233E+04 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 #12 (1d7h-ref-fine): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 4.87072 A 178s Current memory usage: 121.736 MB total, 221.696 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.225 x 0.225 x 0.225 178s Grid lengths: 14.400 x 14.400 x 14.400 178s Grid center: (17.751, 17.770, 20.492) 178s Multigrid levels: 5 178s Molecule ID: 3 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.010 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 2.000 178s Using "molecular" surface definition;harmonic average smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 300.000 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 4.538248433997E+04 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s PRINT STATEMENTS 178s 178s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 178s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 178s Global net ELEC energy = -3.205793187109E+03 kJ/mol 178s 178s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 178s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 178s Global net ELEC energy = -2.133542621421E+01 kJ/mol 178s 178s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 178s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 178s Global net ELEC energy = -3.200702302816E+03 kJ/mol 178s 178s 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 178s Local net energy (PE 0) = 1.624454192073E+01 kJ/mol 178s Global net ELEC energy = 1.624454192073E+01 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 3 molecules 178s Final memory usage: 0.001 MB total, 221.696 MB high water 178s 178s 178s Thanks for using APBS! 178s 178s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 178s *** PASSED *** 178s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 178s *** PASSED *** 178s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 178s *** PASSED *** 178s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 178s *** PASSED *** 178s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 178s *** PASSED *** 178s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 178s *** PASSED *** 178s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 178s *** PASSED *** 178s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 178s *** PASSED *** 178s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 178s *** PASSED *** 178s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 178s *** PASSED *** 178s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 178s *** PASSED *** 178s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 178s *** PASSED *** 178s Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) 178s *** PASSED *** 178s Elapsed time: 4.597382 seconds 178s -------------------------------------------------------------------------------- 178s -------------------------------------------------------------------------------- 178s Testing input file 1d7i-dss-mol.in 178s 183s Checking for intermediate energies in input file 1d7h-dmso-smol.out 183s EXPECTED COMPUTED: 16 183s EXPECTED EXPECTED: 16 183s COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192073] 183s 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'] 183s COMPUTED RESULT 10749.48704824 183s COMPUTED RESULT 42894.87256481 183s COMPUTED RESULT 13992.34956777 183s COMPUTED RESULT 46100.66575192 183s COMPUTED RESULT 37.19709905887 183s COMPUTED RESULT 712.5747080979 183s COMPUTED RESULT 67.51571424823 183s COMPUTED RESULT 733.9101343121 183s COMPUTED RESULT 10716.54753674 183s COMPUTED RESULT 42181.78203716 183s COMPUTED RESULT 13959.61902233 183s COMPUTED RESULT 45382.48433997 183s COMPUTED RESULT -3205.793187109 183s COMPUTED RESULT -21.33542621421 183s COMPUTED RESULT -3200.702302816 183s COMPUTED RESULT 16.24454192073 183s BINARY: /usr/bin/apbs 183s INPUT: 1d7i-dss-mol.in 183s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 183s asc_getToken: Error occurred (bailing out). 183s Vio_scanf: Format problem with input. 183s 183s 183s ---------------------------------------------------------------------- 183s APBS -- Adaptive Poisson-Boltzmann Solver 183s Version APBS 3.4.1 183s 183s Nathan A. Baker (nathan.baker@pnnl.gov) 183s Pacific Northwest National Laboratory 183s 183s Additional contributing authors listed in the code documentation. 183s 183s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 183s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 183s Northwest Division for the U.S. Department of Energy. 183s 183s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 183s Portions Copyright (c) 2002-2020, Nathan A. Baker. 183s Portions Copyright (c) 1999-2002, The Regents of the University of California. 183s Portions Copyright (c) 1995, Michael Holst. 183s All rights reserved. 183s 183s Redistribution and use in source and binary forms, with or without 183s modification, are permitted provided that the following conditions are met: 183s 183s * Redistributions of source code must retain the above copyright notice, this 183s list of conditions and the following disclaimer. 183s 183s * Redistributions in binary form must reproduce the above copyright notice, 183s this list of conditions and the following disclaimer in the documentation 183s and/or other materials provided with the distribution. 183s 183s * Neither the name of the developer nor the names of its contributors may be 183s used to endorse or promote products derived from this software without 183s specific prior written permission. 183s 183s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 183s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 183s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 183s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 183s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 183s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 183s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 183s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 183s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 183s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 183s ---------------------------------------------------------------------- 183s APBS uses FETK (the Finite Element ToolKit) to solve the 183s Poisson-Boltzmann equation numerically. FETK is a portable collection 183s of finite element modeling class libraries developed by the Michael Holst 183s research group and written in an object-oriented form of C. FEtk is 183s designed to solve general coupled systems of nonlinear partial differential 183s equations using adaptive finite element methods, inexact Newton methods, 183s and algebraic multilevel methods. More information about FEtk may be found 183s at . 183s ---------------------------------------------------------------------- 183s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 183s Aqua is a modified form of the Holst group PMG library 183s which has been modified by Patrice Koehl 183s for improved efficiency and 183s memory usage when solving the Poisson-Boltzmann equation. 183s ---------------------------------------------------------------------- 183s Please cite your use of APBS as: 183s 183s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 183s nanosystems: application to microtubules and the ribosome. Proc. 183s Natl. Acad. Sci. USA 98, 10037-10041 2001. 183s 183s 183s This executable compiled on Jan 3 2025 at 11:01:42 183s 183s Parsing input file 1d7i-dss-mol.in... 183s rank 0 size 1... 183s Parsed input file. 183s Got paths for 3 molecules 183s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 183s asc_getToken: Error occurred (bailing out). 183s Vio_scanf: Format problem with input. 183s 1677 atoms 183s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 183s Net charge 9.91e-01 e 183s Reading PQR-format atom data from dss-min.pqr. 183s asc_getToken: Error occurred (bailing out). 183s Vio_scanf: Format problem with input. 183s 14 atoms 183s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 183s Net charge -8.33e-17 e 183s Reading PQR-format atom data from 1d7i-min.pqr. 183s 1663 atoms 183s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 183s Net charge 9.91e-01 e 183s Preparing to run 12 PBE calculations. 183s ---------------------------------------- 183s CALCULATION #1 (complex-solv-coarse): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 30.4176 A 183s Current memory usage: 122.425 MB total, 122.425 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 1.500 x 1.500 x 1.500 183s Grid lengths: 96.000 x 96.000 x 96.000 183s Grid center: (25.264, 18.988, 19.122) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 78.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 9.160578033846E+03 kJ/mol 183s Calculating forces... 183s [focusFillBound()]: WARNING: 183s Unusually large potential values 183s detected on the focusing boundary! 183s Convergence not guaranteed for NPBE/NRPBE calculations! 183s 183s ---------------------------------------- 183s CALCULATION #2 (complex-solv-fine): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 30.4176 A 183s Current memory usage: 122.425 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.225 x 0.225 x 0.225 183s Grid lengths: 14.400 x 14.400 x 14.400 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 78.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 3.955701871716E+04 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #3 (complex-ref-coarse): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 4.87072 A 183s Current memory usage: 122.425 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 1.500 x 1.500 x 1.500 183s Grid lengths: 96.000 x 96.000 x 96.000 183s Grid center: (25.264, 18.988, 19.122) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 2.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 1.264965939588E+04 kJ/mol 183s Calculating forces... 183s [focusFillBound()]: WARNING: 183s Unusually large potential values 183s detected on the focusing boundary! 183s Convergence not guaranteed for NPBE/NRPBE calculations! 183s 183s ---------------------------------------- 183s CALCULATION #4 (complex-ref-fine): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 4.87072 A 183s Current memory usage: 122.425 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.225 x 0.225 x 0.225 183s Grid lengths: 14.400 x 14.400 x 14.400 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 2.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 4.301801664829E+04 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #5 (dss-solv-coarse): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 30.4176 A 183s Current memory usage: 62.528 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 1.500 x 1.500 x 1.500 183s Grid lengths: 96.000 x 96.000 x 96.000 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 78.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 9.431133325426E+01 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #6 (dss-solv-fine): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 30.4176 A 183s Current memory usage: 62.528 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.225 x 0.225 x 0.225 183s Grid lengths: 14.400 x 14.400 x 14.400 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 78.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 1.677348113184E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #7 (dss-ref-coarse): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 4.87072 A 183s Current memory usage: 62.528 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 1.500 x 1.500 x 1.500 183s Grid lengths: 96.000 x 96.000 x 96.000 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 2.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 1.171079106781E+02 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #8 (dss-ref-fine): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 4.87072 A 183s Current memory usage: 62.528 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.225 x 0.225 x 0.225 183s Grid lengths: 14.400 x 14.400 x 14.400 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 2.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 1.697869784185E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 30.4176 A 183s Current memory usage: 121.977 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 1.500 x 1.500 x 1.500 183s Grid lengths: 96.000 x 96.000 x 96.000 183s Grid center: (25.264, 18.988, 19.122) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 78.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 9.040108332204E+03 kJ/mol 183s Calculating forces... 183s [focusFillBound()]: WARNING: 183s Unusually large potential values 183s detected on the focusing boundary! 183s Convergence not guaranteed for NPBE/NRPBE calculations! 183s 183s ---------------------------------------- 183s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 30.4176 A 183s Current memory usage: 121.977 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.225 x 0.225 x 0.225 183s Grid lengths: 14.400 x 14.400 x 14.400 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 78.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 3.787747796627E+04 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 4.87072 A 183s Current memory usage: 121.977 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 1.500 x 1.500 x 1.500 183s Grid lengths: 96.000 x 96.000 x 96.000 183s Grid center: (25.264, 18.988, 19.122) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 2.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 1.252495566243E+04 kJ/mol 183s Calculating forces... 183s [focusFillBound()]: WARNING: 183s Unusually large potential values 183s detected on the focusing boundary! 183s Convergence not guaranteed for NPBE/NRPBE calculations! 183s 183s ---------------------------------------- 183s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 4.87072 A 183s Current memory usage: 121.977 MB total, 222.305 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.225 x 0.225 x 0.225 183s Grid lengths: 14.400 x 14.400 x 14.400 183s Grid center: (17.340, 19.211, 20.503) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.010 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 183s Solute dielectric: 2.000 183s Solvent dielectric: 2.000 183s Using "molecular" surface definition; no smoothing 183s Solvent probe radius: 0.000 A 183s Temperature: 300.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 4.133237922574E+04 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s PRINT STATEMENTS 183s 183s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 183s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 183s Global net ELEC energy = -3.460997931137E+03 kJ/mol 183s 183s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 183s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 183s Global net ELEC energy = -2.052167100108E+01 kJ/mol 183s 183s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 183s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 183s Global net ELEC energy = -3.454901259473E+03 kJ/mol 183s 183s 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 183s Local net energy (PE 0) = 1.442499933668E+01 kJ/mol 183s Global net ELEC energy = 1.442499933668E+01 kJ/mol 183s ---------------------------------------- 183s CLEANING UP AND SHUTTING DOWN... 183s Destroying force arrays. 183s No energy arrays to destroy. 183s Destroying multigrid structures. 183s Destroying finite element structures. 183s Destroying 3 molecules 183s Final memory usage: 0.001 MB total, 222.305 MB high water 183s 183s 183s Thanks for using APBS! 183s 183s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 183s *** PASSED *** 183s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 183s *** PASSED *** 183s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 183s *** PASSED *** 183s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 183s *** PASSED *** 183s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 183s *** PASSED *** 183s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 183s *** PASSED *** 183s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 183s *** PASSED *** 183s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 183s *** PASSED *** 183s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 183s *** PASSED *** 183s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 183s *** PASSED *** 183s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 183s *** PASSED *** 183s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 183s *** PASSED *** 183s Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) 183s *** PASSED *** 183s Elapsed time: 4.727081 seconds 183s -------------------------------------------------------------------------------- 183s -------------------------------------------------------------------------------- 183s Testing input file 1d7i-dss-smol.in 183s 187s Checking for intermediate energies in input file 1d7i-dss-mol.out 187s EXPECTED COMPUTED: 16 187s EXPECTED EXPECTED: 16 187s COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933668] 187s 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'] 187s COMPUTED RESULT 9160.578033846 187s COMPUTED RESULT 39557.01871716 187s COMPUTED RESULT 12649.65939588 187s COMPUTED RESULT 43018.01664829 187s COMPUTED RESULT 94.31133325426 187s COMPUTED RESULT 1677.348113184 187s COMPUTED RESULT 117.1079106781 187s COMPUTED RESULT 1697.869784185 187s COMPUTED RESULT 9040.108332204 187s COMPUTED RESULT 37877.47796627 187s COMPUTED RESULT 12524.95566243 187s COMPUTED RESULT 41332.37922574 187s COMPUTED RESULT -3460.997931137 187s COMPUTED RESULT -20.52167100108 187s COMPUTED RESULT -3454.901259473 187s COMPUTED RESULT 14.42499933668 187s BINARY: /usr/bin/apbs 187s INPUT: 1d7i-dss-smol.in 187s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 187s asc_getToken: Error occurred (bailing out). 187s Vio_scanf: Format problem with input. 187s 187s 187s ---------------------------------------------------------------------- 187s APBS -- Adaptive Poisson-Boltzmann Solver 187s Version APBS 3.4.1 187s 187s Nathan A. Baker (nathan.baker@pnnl.gov) 187s Pacific Northwest National Laboratory 187s 187s Additional contributing authors listed in the code documentation. 187s 187s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 187s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 187s Northwest Division for the U.S. Department of Energy. 187s 187s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 187s Portions Copyright (c) 2002-2020, Nathan A. Baker. 187s Portions Copyright (c) 1999-2002, The Regents of the University of California. 187s Portions Copyright (c) 1995, Michael Holst. 187s All rights reserved. 187s 187s Redistribution and use in source and binary forms, with or without 187s modification, are permitted provided that the following conditions are met: 187s 187s * Redistributions of source code must retain the above copyright notice, this 187s list of conditions and the following disclaimer. 187s 187s * Redistributions in binary form must reproduce the above copyright notice, 187s this list of conditions and the following disclaimer in the documentation 187s and/or other materials provided with the distribution. 187s 187s * Neither the name of the developer nor the names of its contributors may be 187s used to endorse or promote products derived from this software without 187s specific prior written permission. 187s 187s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 187s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 187s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 187s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 187s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 187s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 187s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 187s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 187s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 187s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 187s ---------------------------------------------------------------------- 187s APBS uses FETK (the Finite Element ToolKit) to solve the 187s Poisson-Boltzmann equation numerically. FETK is a portable collection 187s of finite element modeling class libraries developed by the Michael Holst 187s research group and written in an object-oriented form of C. FEtk is 187s designed to solve general coupled systems of nonlinear partial differential 187s equations using adaptive finite element methods, inexact Newton methods, 187s and algebraic multilevel methods. More information about FEtk may be found 187s at . 187s ---------------------------------------------------------------------- 187s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 187s Aqua is a modified form of the Holst group PMG library 187s which has been modified by Patrice Koehl 187s for improved efficiency and 187s memory usage when solving the Poisson-Boltzmann equation. 187s ---------------------------------------------------------------------- 187s Please cite your use of APBS as: 187s 187s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 187s nanosystems: application to microtubules and the ribosome. Proc. 187s Natl. Acad. Sci. USA 98, 10037-10041 2001. 187s 187s 187s This executable compiled on Jan 3 2025 at 11:01:42 187s 187s Parsing input file 1d7i-dss-smol.in... 187s rank 0 size 1... 187s Parsed input file. 187s Got paths for 3 molecules 187s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 187s asc_getToken: Error occurred (bailing out). 187s Vio_scanf: Format problem with input. 187s 1677 atoms 187s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 187s Net charge 9.91e-01 e 187s Reading PQR-format atom data from dss-min.pqr. 187s asc_getToken: Error occurred (bailing out). 187s Vio_scanf: Format problem with input. 187s 14 atoms 187s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 187s Net charge -8.33e-17 e 187s Reading PQR-format atom data from 1d7i-min.pqr. 187s 1663 atoms 187s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 187s Net charge 9.91e-01 e 187s Preparing to run 12 PBE calculations. 187s ---------------------------------------- 187s CALCULATION #1 (complex-solv-coarse): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 30.4176 A 187s Current memory usage: 122.425 MB total, 122.425 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 1.500 x 1.500 x 1.500 187s Grid lengths: 96.000 x 96.000 x 96.000 187s Grid center: (25.264, 18.988, 19.122) 187s Multigrid levels: 5 187s Molecule ID: 1 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 78.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 9.634884642408E+03 kJ/mol 187s Calculating forces... 187s [focusFillBound()]: WARNING: 187s Unusually large potential values 187s detected on the focusing boundary! 187s Convergence not guaranteed for NPBE/NRPBE calculations! 187s 187s ---------------------------------------- 187s CALCULATION #2 (complex-solv-fine): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 30.4176 A 187s Current memory usage: 122.425 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.225 x 0.225 x 0.225 187s Grid lengths: 14.400 x 14.400 x 14.400 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 1 187s Linearized traditional PBE 187s Boundary conditions from focusing 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 78.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 4.003177540425E+04 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s CALCULATION #3 (complex-ref-coarse): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 4.87072 A 187s Current memory usage: 122.425 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 1.500 x 1.500 x 1.500 187s Grid lengths: 96.000 x 96.000 x 96.000 187s Grid center: (25.264, 18.988, 19.122) 187s Multigrid levels: 5 187s Molecule ID: 1 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 2.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 1.264965939588E+04 kJ/mol 187s Calculating forces... 187s [focusFillBound()]: WARNING: 187s Unusually large potential values 187s detected on the focusing boundary! 187s Convergence not guaranteed for NPBE/NRPBE calculations! 187s 187s ---------------------------------------- 187s CALCULATION #4 (complex-ref-fine): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 4.87072 A 187s Current memory usage: 122.425 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.225 x 0.225 x 0.225 187s Grid lengths: 14.400 x 14.400 x 14.400 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 1 187s Linearized traditional PBE 187s Boundary conditions from focusing 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 2.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 4.301801664829E+04 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s CALCULATION #5 (dss-solv-coarse): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 30.4176 A 187s Current memory usage: 62.528 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 1.500 x 1.500 x 1.500 187s Grid lengths: 96.000 x 96.000 x 96.000 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 2 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 78.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 7.942232645345E+01 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s CALCULATION #6 (dss-solv-fine): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 30.4176 A 187s Current memory usage: 62.528 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.225 x 0.225 x 0.225 187s Grid lengths: 14.400 x 14.400 x 14.400 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 2 187s Linearized traditional PBE 187s Boundary conditions from focusing 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 78.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 1.677798535473E+03 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s CALCULATION #7 (dss-ref-coarse): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 4.87072 A 187s Current memory usage: 62.528 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 1.500 x 1.500 x 1.500 187s Grid lengths: 96.000 x 96.000 x 96.000 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 2 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 2.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 1.171079106781E+02 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s CALCULATION #8 (dss-ref-fine): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 4.87072 A 187s Current memory usage: 62.528 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.225 x 0.225 x 0.225 187s Grid lengths: 14.400 x 14.400 x 14.400 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 2 187s Linearized traditional PBE 187s Boundary conditions from focusing 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 2.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 1.697869784185E+03 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 30.4176 A 187s Current memory usage: 121.977 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 1.500 x 1.500 x 1.500 187s Grid lengths: 96.000 x 96.000 x 96.000 187s Grid center: (25.264, 18.988, 19.122) 187s Multigrid levels: 5 187s Molecule ID: 3 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 78.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 9.507068451372E+03 kJ/mol 187s Calculating forces... 187s [focusFillBound()]: WARNING: 187s Unusually large potential values 187s detected on the focusing boundary! 187s Convergence not guaranteed for NPBE/NRPBE calculations! 187s 187s ---------------------------------------- 187s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 30.4176 A 187s Current memory usage: 121.977 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.225 x 0.225 x 0.225 187s Grid lengths: 14.400 x 14.400 x 14.400 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 3 187s Linearized traditional PBE 187s Boundary conditions from focusing 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 78.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 3.835075772299E+04 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 4.87072 A 187s Current memory usage: 121.977 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 1.500 x 1.500 x 1.500 187s Grid lengths: 96.000 x 96.000 x 96.000 187s Grid center: (25.264, 18.988, 19.122) 187s Multigrid levels: 5 187s Molecule ID: 3 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 2.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 1.252495566243E+04 kJ/mol 187s Calculating forces... 187s [focusFillBound()]: WARNING: 187s Unusually large potential values 187s detected on the focusing boundary! 187s Convergence not guaranteed for NPBE/NRPBE calculations! 187s 187s ---------------------------------------- 187s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 187s Debye length: 4.87072 A 187s Current memory usage: 121.977 MB total, 222.305 MB high water 187s Using linear spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.225 x 0.225 x 0.225 187s Grid lengths: 14.400 x 14.400 x 14.400 187s Grid center: (17.340, 19.211, 20.503) 187s Multigrid levels: 5 187s Molecule ID: 3 187s Linearized traditional PBE 187s Boundary conditions from focusing 187s 2 ion species (0.010 M ionic strength): 187s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 187s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 187s Solute dielectric: 2.000 187s Solvent dielectric: 2.000 187s Using "molecular" surface definition;harmonic average smoothing 187s Solvent probe radius: 0.000 A 187s Temperature: 300.000 K 187s Electrostatic energies will be calculated 187s Total electrostatic energy = 4.133237922574E+04 kJ/mol 187s Calculating forces... 187s ---------------------------------------- 187s PRINT STATEMENTS 187s 187s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 187s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 187s Global net ELEC energy = -2.986241244040E+03 kJ/mol 187s 187s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 187s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 187s Global net ELEC energy = -2.007124871262E+01 kJ/mol 187s 187s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 187s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 187s Global net ELEC energy = -2.981621502756E+03 kJ/mol 187s 187s 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 187s Local net energy (PE 0) = 1.545150742844E+01 kJ/mol 187s Global net ELEC energy = 1.545150742844E+01 kJ/mol 187s ---------------------------------------- 187s CLEANING UP AND SHUTTING DOWN... 187s Destroying force arrays. 187s No energy arrays to destroy. 187s Destroying multigrid structures. 187s Destroying finite element structures. 187s Destroying 3 molecules 187s Final memory usage: 0.001 MB total, 222.305 MB high water 187s 187s 187s Thanks for using APBS! 187s 187s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 187s *** PASSED *** 187s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 187s *** PASSED *** 187s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 187s *** PASSED *** 187s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 187s *** PASSED *** 187s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 187s *** PASSED *** 187s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 187s *** PASSED *** 187s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 187s *** PASSED *** 187s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 187s *** PASSED *** 187s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 187s *** PASSED *** 187s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 187s *** PASSED *** 187s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 187s *** PASSED *** 187s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 187s *** PASSED *** 187s Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) 187s *** PASSED *** 187s Elapsed time: 4.598029 seconds 187s -------------------------------------------------------------------------------- 187s Total elapsed time: 18.652966 seconds 187s Test results have been logged 187s -------------------------------------------------------------------------------- 187s -------------------------------------------------------------------------------- 187s Testing input file apbs-mol.in 187s 192s Checking for intermediate energies in input file 1d7i-dss-smol.out 192s EXPECTED COMPUTED: 16 192s EXPECTED EXPECTED: 16 192s COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742844] 192s 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'] 192s COMPUTED RESULT 9634.884642408 192s COMPUTED RESULT 40031.77540425 192s COMPUTED RESULT 12649.65939588 192s COMPUTED RESULT 43018.01664829 192s COMPUTED RESULT 79.42232645345 192s COMPUTED RESULT 1677.798535473 192s COMPUTED RESULT 117.1079106781 192s COMPUTED RESULT 1697.869784185 192s COMPUTED RESULT 9507.068451372 192s COMPUTED RESULT 38350.75772299 192s COMPUTED RESULT 12524.95566243 192s COMPUTED RESULT 41332.37922574 192s COMPUTED RESULT -2986.24124404 192s COMPUTED RESULT -20.07124871262 192s COMPUTED RESULT -2981.621502756 192s COMPUTED RESULT 15.45150742844 192s Running tests for hca-bind section 192s BINARY: /usr/bin/apbs 192s INPUT: apbs-mol.in 192s COMMAND: ['/usr/bin/apbs', 'apbs-mol.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.in... 192s rank 0 size 1... 192s Parsed input file. 192s Got paths for 3 molecules 192s Reading PQR-format atom data from acet.pqr. 192s asc_getToken: Error occurred (bailing out). 192s Vio_scanf: Format problem with input. 192s 18 atoms 192s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 192s Net charge -1.00e+00 e 192s Reading PQR-format atom data from hca.pqr. 192s asc_getToken: Error occurred (bailing out). 192s Vio_scanf: Format problem with input. 192s 2482 atoms 192s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 192s Net charge 1.00e+00 e 192s Reading PQR-format atom data from complex.pqr. 192s 2500 atoms 192s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 192s Net charge -1.02e-14 e 192s Preparing to run 9 PBE calculations. 192s ---------------------------------------- 192s CALCULATION #1 (acet): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 62.727 MB total, 62.727 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 1.500 x 1.500 x 1.500 192s Grid lengths: 96.000 x 96.000 x 96.000 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Single Debye-Huckel sphere boundary conditions 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 2.213600726771E+02 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s CALCULATION #2 (acet): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 62.727 MB total, 123.701 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.581 x 0.581 x 0.581 192s Grid lengths: 37.181 x 37.181 x 37.181 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 1.825764811255E+03 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s CALCULATION #3 (acet): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 62.727 MB total, 123.701 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.225 x 0.Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 192s *** PASSED *** 192s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 192s *** PASSED *** 192s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 192s *** PASSED *** 192s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 192s *** PASSED *** 192s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 192s *** PASSED *** 192s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 192s *** PASSED *** 192s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 192s *** PASSED *** 192s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 192s *** PASSED *** 192s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 192s *** PASSED *** 192s Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) 192s *** PASSED *** 192s Elapsed time: 4.247074 seconds 192s -------------------------------------------------------------------------------- 192s -------------------------------------------------------------------------------- 192s Testing input file apbs-smol.in 192s 192s 225 x 0.225 192s Grid lengths: 14.400 x 14.400 x 14.400 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 1 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 6.458471211905E+03 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s CALCULATION #4 (hca): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 146.516 MB total, 146.516 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 1.500 x 1.500 x 1.500 192s Grid lengths: 96.000 x 96.000 x 96.000 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 2 192s Linearized traditional PBE 192s Single Debye-Huckel sphere boundary conditions 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 2.093606095527E+04 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 #5 (hca): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 146.516 MB total, 245.092 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.581 x 0.581 x 0.581 192s Grid lengths: 37.181 x 37.181 x 37.181 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 2 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 1.515433544464E+05 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 (hca): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 146.516 MB total, 245.092 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.225 x 0.225 x 0.225 192s Grid lengths: 14.400 x 14.400 x 14.400 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 2 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 1.786369323561E+05 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s CALCULATION #7 (complex): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 146.926 MB total, 245.092 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 1.500 x 1.500 x 1.500 192s Grid lengths: 96.000 x 96.000 x 96.000 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 3 192s Linearized traditional PBE 192s Single Debye-Huckel sphere boundary conditions 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 2.105322784838E+04 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 #8 (complex): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 146.926 MB total, 245.725 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.581 x 0.581 x 0.581 192s Grid lengths: 37.181 x 37.181 x 37.181 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 3 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 1.533304996252E+05 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 #9 (complex): MULTIGRID 192s Setting up problem... 192s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 192s Debye length: 0 A 192s Current memory usage: 146.926 MB total, 245.725 MB high water 192s Using linear spline charge discretization. 192s Grid dimensions: 65 x 65 x 65 192s Grid spacings: 0.225 x 0.225 x 0.225 192s Grid lengths: 14.400 x 14.400 x 14.400 192s Grid center: (-6.028, 3.898, 15.179) 192s Multigrid levels: 5 192s Molecule ID: 3 192s Linearized traditional PBE 192s Boundary conditions from focusing 192s 2 ion species (0.000 M ionic strength): 192s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 192s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 192s Solute dielectric: 2.000 192s Solvent dielectric: 78.540 192s Using "molecular" surface definition; no smoothing 192s Solvent probe radius: 0.000 A 192s Temperature: 298.150 K 192s Electrostatic energies will be calculated 192s Total electrostatic energy = 1.850429388099E+05 kJ/mol 192s Calculating forces... 192s ---------------------------------------- 192s PRINT STATEMENTS 192s 192s print energy 3 (complex) - 1 (acet) - 2 (hca) end 192s Local net energy (PE 0) = -5.246475812665E+01 kJ/mol 192s Global net ELEC energy = -5.246475812665E+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 3 molecules 192s Final memory usage: 0.001 MB total, 245.725 MB high water 192s 192s 192s Thanks for using APBS! 192s 196s Checking for intermediate energies in input file apbs-mol.out 196s EXPECTED COMPUTED: 10 196s EXPECTED EXPECTED: 10 196s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] 196s 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'] 196s COMPUTED RESULT 221.3600726771 196s COMPUTED RESULT 1825.764811255 196s COMPUTED RESULT 6458.471211905 196s COMPUTED RESULT 20936.06095527 196s COMPUTED RESULT 151543.3544464 196s COMPUTED RESULT 178636.9323561 196s COMPUTED RESULT 21053.22784838 196s COMPUTED RESULT 153330.4996252 196s COMPUTED RESULT 185042.9388099 196s COMPUTED RESULT -52.46475812665 196s BINARY: /usr/bin/apbs 196s INPUT: apbs-smol.in 196s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 196s asc_getToken: Error occurred (bailing out). 196s Vio_scanf: Format problem with input. 196s 196s 196s ---------------------------------------------------------------------- 196s APBS -- Adaptive Poisson-Boltzmann Solver 196s Version APBS 3.4.1 196s 196s Nathan A. Baker (nathan.baker@pnnl.gov) 196s Pacific Northwest National Laboratory 196s 196s Additional contributing authors listed in the code documentation. 196s 196s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 196s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 196s Northwest Division for the U.S. Department of Energy. 196s 196s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 196s Portions Copyright (c) 2002-2020, Nathan A. Baker. 196s Portions Copyright (c) 1999-2002, The Regents of the University of California. 196s Portions Copyright (c) 1995, Michael Holst. 196s All rights reserved. 196s 196s Redistribution and use in source and binary forms, with or without 196s modification, are permitted provided that the following conditions are met: 196s 196s * Redistributions of source code must retain the above copyright notice, this 196s list of conditions and the following disclaimer. 196s 196s * Redistributions in binary form must reproduce the above copyright notice, 196s this list of conditions and the following disclaimer in the documentation 196s and/or other materials provided with the distribution. 196s 196s * Neither the name of the developer nor the names of its contributors may be 196s used to endorse or promote products derived from this software without 196s specific prior written permission. 196s 196s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 196s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 196s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 196s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 196s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 196s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 196s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 196s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 196s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 196s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 196s ---------------------------------------------------------------------- 196s APBS uses FETK (the Finite Element ToolKit) to solve the 196s Poisson-Boltzmann equation numerically. FETK is a portable collection 196s of finite element modeling class libraries developed by the Michael Holst 196s research group and written in an object-oriented form of C. FEtk is 196s designed to solve general coupled systems of nonlinear partial differential 196s equations using adaptive finite element methods, inexact Newton methods, 196s and algebraic multilevel methods. More information about FEtk may be found 196s at . 196s ---------------------------------------------------------------------- 196s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 196s Aqua is a modified form of the Holst group PMG library 196s which has been modified by Patrice Koehl 196s for improved efficiency and 196s memory usage when solving the Poisson-Boltzmann equation. 196s ---------------------------------------------------------------------- 196s Please cite your use of APBS as: 196s 196s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 196s nanosystems: application to microtubules and the ribosome. Proc. 196s Natl. Acad. Sci. USA 98, 10037-10041 2001. 196s 196s 196s This executable compiled on Jan 3 2025 at 11:01:42 196s 196s Parsing input file apbs-smol.in... 196s rank 0 size 1... 196s Parsed input file. 196s Got paths for 3 molecules 196s Reading PQR-format atom data from acet.pqr. 196s asc_getToken: Error occurred (bailing out). 196s Vio_scanf: Format problem with input. 196s 18 atoms 196s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 196s Net charge -1.00e+00 e 196s Reading PQR-format atom data from hca.pqr. 196s asc_getToken: Error occurred (bailing out). 196s Vio_scanf: Format problem with input. 196s 2482 atoms 196s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 196s Net charge 1.00e+00 e 196s Reading PQR-format atom data from complex.pqr. 196s 2500 atoms 196s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 196s Net charge -1.02e-14 e 196s Preparing to run 9 PBE calculations. 196s ---------------------------------------- 196s CALCULATION #1 (acet): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 62.727 MB total, 62.727 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 1.500 x 1.500 x 1.500 196s Grid lengths: 96.000 x 96.000 x 96.000 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Single Debye-Huckel sphere boundary conditions 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.884888131017E+02 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s CALCULATION #2 (acet): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 62.727 MB total, 123.701 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.581 x 0.581 x 0.581 196s Grid lengths: 37.181 x 37.181 x 37.181 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.820045922544E+03 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s CALCULATION #3 (acet): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 62.727 MB total, 123.701 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.225 x 0.225 x 0.225 196s Grid lengths: 14.400 x 14.400 x 14.400 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 6.460002606908E+03 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s CALCULATION #4 (hca): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 146.516 MB total, 146.516 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 1.500 x 1.500 x 1.500 196s Grid lengths: 96.000 x 96.000 x 96.000 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 2 196s Linearized traditional PBE 196s Single Debye-Huckel sphere boundary conditions 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 2.189161497021E+04 kJ/mol 196s Calculating forces... 196s [focusFillBound()]: WARNING: 196s Unusually large potential values 196s detected on the focusing boundary! 196s Convergence not guaranteed for NPBE/NRPBE calculations! 196s 196s ---------------------------------------- 196s CALCULATION #5 (hca): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 146.516 MB total, 245.092 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.581 x 0.581 x 0.581 196s Grid lengths: 37.181 x 37.181 x 37.181 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 2 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.520000494925E+05 kJ/mol 196s Calculating forces... 196s [focusFillBound()]: WARNING: 196s Unusually large potential values 196s detected on the focusing boundary! 196s Convergence not guaranteed for NPBE/NRPBE calculations! 196s 196s ---------------------------------------- 196s CALCULATION #6 (hca): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 146.516 MB total, 245.092 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.225 x 0.225 x 0.225 196s Grid lengths: 14.400 x 14.400 x 14.400 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 2 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.790436191580E+05 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s CALCULATION #7 (complex): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 146.926 MB total, 245.092 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 1.500 x 1.500 x 1.500 196s Grid lengths: 96.000 x 96.000 x 96.000 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 3 196s Linearized traditional PBE 196s Single Debye-Huckel sphere boundary conditions 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 2.195842512312E+04 kJ/mol 196s Calculating forces... 196s [focusFillBound()]: WARNING: 196s Unusually large potential values 196s detected on the focusing boundary! 196s Convergence not guaranteed for NPBE/NRPBE calculations! 196s 196s ---------------------------------------- 196s CALCULATION #8 (complex): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 146.926 MB total, 245.725 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.581 x 0.581 x 0.581 196s Grid lengths: 37.181 x 37.181 x 37.181 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 3 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.537771604355E+05 kJ/mol 196s Calculating forces... 196s [focusFillBound()]: WARNING: 196s Unusually large potential values 196s detected on the focusing boundary! 196s Convergence not guaranteed for NPBE/NRPBE calculations! 196s 196s ---------------------------------------- 196s CALCULATION #9 (complex): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 146.926 MB total, 245.725 MB high water 196s Using linear spline charge discretization. 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.225 x 0.225 x 0.225 196s Grid lengths: 14.400 x 14.400 x 14.400 196s Grid center: (-6.028, 3.898, 15.179) 196s Multigrid levels: 5 196s Molecule ID: 3 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 2 ion species (0.000 M ionic strength): 196s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 196s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 196s Solute dielectric: 2.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition;harmonic average smoothing 196s Solvent probe radius: 0.000 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.854495619747E+05 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s PRINT STATEMENTS 196s 196s print energy 3 (complex) - 1 (acet) - 2 (hca) end 196s Local net energy (PE 0) = -5.405979017066E+01 kJ/mol 196s Global net ELEC energy = -5.405979017066E+01 kJ/mol 196s ---------------------------------------- 196s CLEANING UP AND SHUTTING DOWN... 196s Destroying force arrays. 196s No energy arrays to destroy. 196s Destroying multigrid structures. 196s Destroying finite element structures. 196s Destroying 3 molecules 196s Final memory usage: 0.001 MB total, 245.725 MB high water 196s 196s 196s Thanks for using APBS! 196s 196s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 196s *** PASSED *** 196s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 196s *** PASSED *** 196s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 196s *** PASSED *** 196s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 196s *** PASSED *** 196s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 196s *** PASSED *** 196s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 196s *** PASSED *** 196s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 196s *** PASSED *** 196s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 196s *** PASSED *** 196s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 196s *** PASSED *** 196s Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) 196s *** PASSED *** 196s Elapsed time: 4.013162 seconds 196s -------------------------------------------------------------------------------- 196s Total elapsed time: 8.260236 seconds 196s Test results have been logged 196s -------------------------------------------------------------------------------- 196s -------------------------------------------------------------------------------- 196s Testing input file apbs-mol.in 196s 197s Checking for intermediate energies in input file apbs-smol.out 197s EXPECTED COMPUTED: 10 197s EXPECTED EXPECTED: 10 197s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] 197s 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'] 197s COMPUTED RESULT 188.4888131017 197s COMPUTED RESULT 1820.045922544 197s COMPUTED RESULT 6460.002606908 197s COMPUTED RESULT 21891.61497021 197s COMPUTED RESULT 152000.0494925 197s COMPUTED RESULT 179043.619158 197s COMPUTED RESULT 21958.42512312 197s COMPUTED RESULT 153777.1604355 197s COMPUTED RESULT 185449.5619747 197s COMPUTED RESULT -54.05979017066 197s Running tests for ionize section 197s BINARY: /usr/bin/apbs 197s INPUT: apbs-mol.in 197s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 197s asc_getToken: Error occurred (bailing out). 197s Vio_scanf: Format problem with input. 197s 197s 197s ---------------------------------------------------------------------- 197s APBS -- Adaptive Poisson-Boltzmann Solver 197s Version APBS 3.4.1 197s 197s Nathan A. Baker (nathan.baker@pnnl.gov) 197s Pacific Northwest National Laboratory 197s 197s Additional contributing authors listed in the code documentation. 197s 197s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 197s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 197s Northwest Division for the U.S. Department of Energy. 197s 197s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 197s Portions Copyright (c) 2002-2020, Nathan A. Baker. 197s Portions Copyright (c) 1999-2002, The Regents of the University of California. 197s Portions Copyright (c) 1995, Michael Holst. 197s All rights reserved. 197s 197s Redistribution and use in source and binary forms, with or without 197s modification, are permitted provided that the following conditions are met: 197s 197s * Redistributions of source code must retain the above copyright notice, this 197s list of conditions and the following disclaimer. 197s 197s * Redistributions in binary form must reproduce the above copyright notice, 197s this list of conditions and the following disclaimer in the documentation 197s and/or other materials provided with the distribution. 197s 197s * Neither the name of the developer nor the names of its contributors may be 197s used to endorse or promote products derived from this software without 197s specific prior written permission. 197s 197s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 197s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 197s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 197s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 197s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 197s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 197s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 197s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 197s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 197s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 197s ---------------------------------------------------------------------- 197s APBS uses FETK (the Finite Element ToolKit) to solve the 197s Poisson-Boltzmann equation numerically. FETK is a portable collection 197s of finite element modeling class libraries developed by the Michael Holst 197s research group and written in an object-oriented form of C. FEtk is 197s designed to solve general coupled systems of nonlinear partial differential 197s equations using adaptive finite element methods, inexact Newton methods, 197s and algebraic multilevel methods. More information about FEtk may be found 197s at . 197s ---------------------------------------------------------------------- 197s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 197s Aqua is a modified form of the Holst group PMG library 197s which has been modified by Patrice Koehl 197s for improved efficiency and 197s memory usage when solving the Poisson-Boltzmann equation. 197s ---------------------------------------------------------------------- 197s Please cite your use of APBS as: 197s 197s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 197s nanosystems: application to microtubules and the ribosome. Proc. 197s Natl. Acad. Sci. USA 98, 10037-10041 2001. 197s 197s 197s This executable compiled on Jan 3 2025 at 11:01:42 197s 197s Parsing input file apbs-mol.in... 197s rank 0 size 1... 197s Parsed input file. 197s Got paths for 3 molecules 197s Reading PQR-format atom data from acetic-acid.pqr. 197s asc_getToken: Error occurred (bailing out). 197s Vio_scanf: Format problem with input. 197s 8 atoms 197s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 197s Net charge -1.67e-16 e 197s Reading PQR-format atom data from acetate.pqr. 197s asc_getToken: Error occurred (bailing out). 197s Vio_scanf: Format problem with input. 197s 8 atoms 197s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 197s Net charge -1.00e+00 e 197s Reading PQR-format atom data from proton.pqr. 197s 1 atoms 197s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 197s Net charge 1.00e+00 e 197s Preparing to run 12 PBE calculations. 197s ---------------------------------------- 197s CALCULATION #1 (acetic-solv): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 7.76163 A 197s Current memory usage: 61.598 MB total, 61.598 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.188 x 0.188 x 0.188 197s Grid lengths: 12.000 x 12.000 x 12.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 1 197s Linearized traditional PBE 197s Multiple Debye-Huckel sphere boundary conditions 197s 2 ion species (0.150 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 78.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 5.823898055191E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #2 (acetic-solv): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 7.76163 A 197s Current memory usage: 61.598 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.094 x 0.094 x 0.094 197s Grid lengths: 6.000 x 6.000 x 6.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 1 197s Linearized traditional PBE 197s Boundary conditions from focusing 197s 2 ion species (0.150 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 78.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 9.793274462353E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #3 (acetic-ref): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 0 A 197s Current memory usage: 61.422 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.188 x 0.188 x 0.188 197s Grid lengths: 12.000 x 12.000 x 12.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 1 197s Linearized traditional PBE 197s Multiple Debye-Huckel sphere boundary conditions 197s 2 ion species (0.000 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 2.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 5.846917564309E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #4 (acetic-ref): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 0 A 197s Current memory usage: 61.422 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.094 x 0.094 x 0.094 197s Grid lengths: 6.000 x 6.000 x 6.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 1 197s Linearized traditional PBE 197s Boundary conditions from focusing 197s 2 ion species (0.000 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 2.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 9.815953282539E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #5 (acetate-solv): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 7.76163 A 197s Current memory usage: 61.598 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.188 x 0.188 x 0.188 197s Grid lengths: 12.000 x 12.000 x 12.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 2 197s Linearized traditional PBE 197s Multiple Debye-Huckel sphere boundary conditions 197s 2 ion species (0.150 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 78.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 8.219846763777E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #6 (acetate-solv): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 7.76163 A 197s Current memory usage: 61.598 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.094 x 0.094 x 0.094 197s Grid lengths: 6.000 x 6.000 x 6.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 2 197s Linearized traditional PBE 197s Boundary conditions from focusing 197s 2 ion species (0.150 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 78.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 1.392741988698E+04 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #7 (acetate-ref): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 0 A 197s Current memory usage: 61.422 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.188 x 0.188 x 0.188 197s Grid lengths: 12.000 x 12.000 x 12.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 2 197s Linearized traditional PBE 197s Multiple Debye-Huckel sphere boundary conditions 197s 2 ion species (0.000 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 2.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 8.420373979905E+03 kJ/mol 197s Calculating forces... 197s [focusFillBound()]: WARNING: 197s Unusually large potential values 197s detected on the focusing boundary! 197s Convergence not guaranteed for NPBE/NRPBE calculations! 197s 197s ---------------------------------------- 197s CALCULATION #8 (acetate-ref): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 0 A 197s Current memory usage: 61.422 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.094 x 0.094 x 0.094 197s Grid lengths: 6.000 x 6.000 x 6.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 2 197s Linearized traditional PBE 197s Boundary conditions from focusing 197s 2 ion species (0.000 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 2.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 1.412716615065E+04 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #9 (proton-solv): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 7.76163 A 197s Current memory usage: 61.412 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.188 x 0.188 x 0.188 197s Grid lengths: 12.000 x 12.000 x 12.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 3 197s Linearized traditional PBE 197s Multiple Debye-Huckel sphere boundary conditions 197s 2 ion species (0.150 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 78.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 3.862359524598E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #10 (proton-solv): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 7.76163 A 197s Current memory usage: 61.412 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.094 x 0.094 x 0.094 197s Grid lengths: 6.000 x 6.000 x 6.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 3 197s Linearized traditional PBE 197s Boundary conditions from focusing 197s 2 ion species (0.150 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 78.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 6.288156251610E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s CALCULATION #11 (proton-ref): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 0 A 197s Current memory usage: 61.373 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.188 x 0.188 x 0.188 197s Grid lengths: 12.000 x 12.000 x 12.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 3 197s Linearized traditional PBE 197s Multiple Debye-Huckel sphere boundary conditions 197s 2 ion species (0.000 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 2.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 4.162533113906E+03 kJ/mol 197s Calculating forces... 197s [focusFillBound()]: WARNING: 197s Unusually large potential values 197s detected on the focusing boundary! 197s Convergence not guaranteed for NPBE/NRPBE calculations! 197s 197s ---------------------------------------- 197s CALCULATION #12 (proton-ref): MULTIGRID 197s Setting up problem... 197s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 197s Debye length: 0 A 197s Current memory usage: 61.373 MB total, 122.404 MB high water 197s Using linear spline charge discretization. 197s Grid dimensions: 65 x 65 x 65 197s Grid spacings: 0.094 x 0.094 x 0.094 197s Grid lengths: 6.000 x 6.000 x 6.000 197s Grid center: (0.000, -0.154, 1.287) 197s Multigrid levels: 5 197s Molecule ID: 3 197s Linearized traditional PBE 197s Boundary conditions from focusing 197s 2 ion species (0.000 M ionic strength): 197s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 197s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 197s Solute dielectric: 2.000 197s Solvent dielectric: 2.000 197s Using "molecular" surface definition; no smoothing 197s Solvent probe radius: 0.000 A 197s Temperature: 293.000 K 197s Electrostatic energies will be calculated 197s Total electrostatic energy = 6.585616091973E+03 kJ/mol 197s Calculating forces... 197s ---------------------------------------- 197s PRINT STATEMENTS 197s 197s print energy 1 (acetic-solv) - 2 (acetic-ref) end 197s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 197s Global net ELEC energy = -2.267882018629E+01 kJ/mol 197s 197s print energy 3 (acetate-solv) - 4 (acetate-ref) end 197s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 197s Global net ELEC energy = -1.997462636633E+02 kJ/mol 197s 197s print energy 5 (proton-solv) - 6 (proton-ref) end 197s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 197s Global net ELEC energy = -2.974598403628E+02 kJ/mol 197s 197s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 197s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 197s Global net ELEC energy = -4.745272838398E+02 kJ/mol 197s ---------------------------------------- 197s CLEANING UP AND SHUTTING DOWN... 197s Destroying force arrays. 197s No energy arrays to destroy. 197s Destroying multigrid structures. 197s Destroying finite element structures. 197s Destroying 3 molecules 197s Final memory usage: 0.001 MB total, 122.404 MB high water 197s 197s 197s Thanks for using APBS! 197s 197s Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 197s *** PASSED *** 197s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 197s *** PASSED *** 197s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 197s *** PASSED *** 197s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 197s *** PASSED *** 197s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 197s *** PASSED *** 197s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 197s *** PASSED *** 197s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 197s *** PASSED *** 197s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 197s *** PASSED *** 197s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 197s *** PASSED *** 197s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 197s *** PASSED *** 197s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 197s *** PASSED *** 197s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 197s *** PASSED *** 197s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 197s *** PASSED *** 197s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 197s *** PASSED *** 197s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 197s *** PASSED *** 197s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 197s *** PASSED *** 197s Elapsed time: 1.128822 seconds 197s -------------------------------------------------------------------------------- 197s -------------------------------------------------------------------------------- 197s Testing input file apbs-smol.in 197s 198s Checking for intermediate energies in input file apbs-mol.out 198s EXPECTED COMPUTED: 16 198s EXPECTED EXPECTED: 16 198s 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] 198s 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'] 198s COMPUTED RESULT 5823.898055191 198s COMPUTED RESULT 9793.274462353 198s COMPUTED RESULT 5846.917564309 198s COMPUTED RESULT 9815.953282539 198s COMPUTED RESULT 8219.846763777 198s COMPUTED RESULT 13927.41988698 198s COMPUTED RESULT 8420.373979905 198s COMPUTED RESULT 14127.16615065 198s COMPUTED RESULT 3862.359524598 198s COMPUTED RESULT 6288.15625161 198s COMPUTED RESULT 4162.533113906 198s COMPUTED RESULT 6585.616091973 198s COMPUTED RESULT -22.67882018629 198s COMPUTED RESULT -199.7462636633 198s COMPUTED RESULT -297.4598403628 198s COMPUTED RESULT -474.5272838398 198s BINARY: /usr/bin/apbs 198s INPUT: apbs-smol.in 198s COMMAND: ['/usr/bin/apbs', 'apbs-smol.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.in... 198s rank 0 size 1... 198s Parsed input file. 198s Got paths for 3 molecules 198s Reading PQR-format atom data from acetic-acid.pqr. 198s asc_getToken: Error occurred (bailing out). 198s Vio_scanf: Format problem with input. 198s 8 atoms 198s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 198s Net charge -1.67e-16 e 198s Reading PQR-format atom data from acetate.pqr. 198s asc_getToken: Error occurred (bailing out). 198s Vio_scanf: Format problem with input. 198s 8 atoms 198s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 198s Net charge -1.00e+00 e 198s Reading PQR-format atom data from proton.pqr. 198s 1 atoms 198s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 198s Net charge 1.00e+00 e 198s Preparing to run 12 PBE calculations. 198s ---------------------------------------- 198s CALCULATION #1 (acetic-solv): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 7.76163 A 198s Current memory usage: 61.598 MB total, 61.598 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.188 x 0.188 x 0.188 198s Grid lengths: 12.000 x 12.000 x 12.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 2 ion species (0.150 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 5.824172730822E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #2 (acetic-solv): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 7.76163 A 198s Current memory usage: 61.598 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.094 x 0.094 x 0.094 198s Grid lengths: 6.000 x 6.000 x 6.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 2 ion species (0.150 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 9.793622759239E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #3 (acetic-ref): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.422 MB total, 122.404 MB high water 198s Using linear spline chaTesting computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 198s *** PASSED *** 198s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 198s *** PASSED *** 198s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 198s *** PASSED *** 198s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 198s *** PASSED *** 198s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 198s *** PASSED *** 198s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 198s *** PASSED *** 198s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 198s *** PASSED *** 198s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 198s *** PASSED *** 198s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 198s *** PASSED *** 198s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 198s *** PASSED *** 198s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 198s *** PASSED *** 198s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 198s *** PASSED *** 198s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 198s *** PASSED *** 198s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 198s *** PASSED *** 198s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 198s *** PASSED *** 198s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 198s *** PASSED *** 198s Elapsed time: 1.092811 seconds 198s -------------------------------------------------------------------------------- 198s Total elapsed time: 2.221633 seconds 198s Test results have been logged 198s -------------------------------------------------------------------------------- 198s -------------------------------------------------------------------------------- 198s Testing input file ion-pmf.in 198s 198s rge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.188 x 0.188 x 0.188 198s Grid lengths: 12.000 x 12.000 x 12.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 2 ion species (0.000 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 2.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 5.846917564309E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #4 (acetic-ref): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.422 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.094 x 0.094 x 0.094 198s Grid lengths: 6.000 x 6.000 x 6.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 1 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 2 ion species (0.000 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 2.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 9.815953282539E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #5 (acetate-solv): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 7.76163 A 198s Current memory usage: 61.598 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.188 x 0.188 x 0.188 198s Grid lengths: 12.000 x 12.000 x 12.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 2 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 2 ion species (0.150 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 8.221328580569E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #6 (acetate-solv): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 7.76163 A 198s Current memory usage: 61.598 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.094 x 0.094 x 0.094 198s Grid lengths: 6.000 x 6.000 x 6.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 2 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 2 ion species (0.150 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 1.392867783119E+04 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #7 (acetate-ref): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.422 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.188 x 0.188 x 0.188 198s Grid lengths: 12.000 x 12.000 x 12.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 2 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 2 ion species (0.000 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 2.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 8.420373979905E+03 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 #8 (acetate-ref): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.422 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.094 x 0.094 x 0.094 198s Grid lengths: 6.000 x 6.000 x 6.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 2 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 2 ion species (0.000 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 2.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 1.412716615065E+04 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #9 (proton-solv): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 7.76163 A 198s Current memory usage: 61.412 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.188 x 0.188 x 0.188 198s Grid lengths: 12.000 x 12.000 x 12.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 3 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 2 ion species (0.150 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 3.863066835285E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #10 (proton-solv): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 7.76163 A 198s Current memory usage: 61.412 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.094 x 0.094 x 0.094 198s Grid lengths: 6.000 x 6.000 x 6.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 3 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 2 ion species (0.150 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 6.289649216644E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #11 (proton-ref): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.373 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.188 x 0.188 x 0.188 198s Grid lengths: 12.000 x 12.000 x 12.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 3 198s Linearized traditional PBE 198s Multiple Debye-Huckel sphere boundary conditions 198s 2 ion species (0.000 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 2.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 4.162533113906E+03 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 #12 (proton-ref): MULTIGRID 198s Setting up problem... 198s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 198s Debye length: 0 A 198s Current memory usage: 61.373 MB total, 122.404 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 65 x 65 x 65 198s Grid spacings: 0.094 x 0.094 x 0.094 198s Grid lengths: 6.000 x 6.000 x 6.000 198s Grid center: (0.000, -0.154, 1.287) 198s Multigrid levels: 5 198s Molecule ID: 3 198s Linearized traditional PBE 198s Boundary conditions from focusing 198s 2 ion species (0.000 M ionic strength): 198s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 198s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 198s Solute dielectric: 2.000 198s Solvent dielectric: 2.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 293.000 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 6.585616091973E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s PRINT STATEMENTS 198s 198s print energy 1 (acetic-solv) - 2 (acetic-ref) end 198s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 198s Global net ELEC energy = -2.233052329981E+01 kJ/mol 198s 198s print energy 3 (acetate-solv) - 4 (acetate-ref) end 198s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 198s Global net ELEC energy = -1.984883194538E+02 kJ/mol 198s 198s print energy 5 (proton-solv) - 6 (proton-ref) end 198s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 198s Global net ELEC energy = -2.959668753288E+02 kJ/mol 198s 198s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 198s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 198s Global net ELEC energy = -4.721246714828E+02 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 3 molecules 198s Final memory usage: 0.001 MB total, 122.404 MB high water 198s 198s 198s Thanks for using APBS! 198s 201s Checking for intermediate energies in input file apbs-smol.out 201s EXPECTED COMPUTED: 16 201s EXPECTED EXPECTED: 16 201s 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] 201s 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'] 201s COMPUTED RESULT 5824.172730822 201s COMPUTED RESULT 9793.622759239 201s COMPUTED RESULT 5846.917564309 201s COMPUTED RESULT 9815.953282539 201s COMPUTED RESULT 8221.328580569 201s COMPUTED RESULT 13928.67783119 201s COMPUTED RESULT 8420.373979905 201s COMPUTED RESULT 14127.16615065 201s COMPUTED RESULT 3863.066835285 201s COMPUTED RESULT 6289.649216644 201s COMPUTED RESULT 4162.533113906 201s COMPUTED RESULT 6585.616091973 201s COMPUTED RESULT -22.33052329981 201s COMPUTED RESULT -198.4883194538 201s COMPUTED RESULT -295.9668753288 201s COMPUTED RESULT -472.1246714828 201s Running tests for ion-pmf section 201s BINARY: /usr/bin/apbs 201s INPUT: ion-pmf.in 201s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 201s asc_getToken: Error occurred (bailing out). 201s Vio_scanf: Format problem with input. 201s asc_getToken: Error occurred (bailing out). 201s Vio_scanf: Format problem with input. 201s 201s 201s ---------------------------------------------------------------------- 201s APBS -- Adaptive Poisson-Boltzmann Solver 201s Version APBS 3.4.1 201s 201s Nathan A. Baker (nathan.baker@pnnl.gov) 201s Pacific Northwest National Laboratory 201s 201s Additional contributing authors listed in the code documentation. 201s 201s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 201s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 201s Northwest Division for the U.S. Department of Energy. 201s 201s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 201s Portions Copyright (c) 2002-2020, Nathan A. Baker. 201s Portions Copyright (c) 1999-2002, The Regents of the University of California. 201s Portions Copyright (c) 1995, Michael Holst. 201s All rights reserved. 201s 201s Redistribution and use in source and binary forms, with or without 201s modification, are permitted provided that the following conditions are met: 201s 201s * Redistributions of source code must retain the above copyright notice, this 201s list of conditions and the following disclaimer. 201s 201s * Redistributions in binary form must reproduce the above copyright notice, 201s this list of conditions and the following disclaimer in the documentation 201s and/or other materials provided with the distribution. 201s 201s * Neither the name of the developer nor the names of its contributors may be 201s used to endorse or promote products derived from this software without 201s specific prior written permission. 201s 201s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 201s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 201s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 201s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 201s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 201s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 201s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 201s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 201s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 201s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 201s ---------------------------------------------------------------------- 201s APBS uses FETK (the Finite Element ToolKit) to solve the 201s Poisson-Boltzmann equation numerically. FETK is a portable collection 201s of finite element modeling class libraries developed by the Michael Holst 201s research group and written in an object-oriented form of C. FEtk is 201s designed to solve general coupled systems of nonlinear partial differential 201s equations using adaptive finite element methods, inexact Newton methods, 201s and algebraic multilevel methods. More information about FEtk may be found 201s at . 201s ---------------------------------------------------------------------- 201s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 201s Aqua is a modified form of the Holst group PMG library 201s which has been modified by Patrice Koehl 201s for improved efficiency and 201s memory usage when solving the Poisson-Boltzmann equation. 201s ---------------------------------------------------------------------- 201s Please cite your use of APBS as: 201s 201s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 201s nanosystems: application to microtubules and the ribosome. Proc. 201s Natl. Acad. Sci. USA 98, 10037-10041 2001. 201s 201s 201s This executable compiled on Jan 3 2025 at 11:01:42 201s 201s Parsing input file ion-pmf.in... 201s rank 0 size 1... 201s Parsed input file. 201s Reading parameter data from parm.dat. 201s Got paths for 1 molecules 201s Reading PDB-format atom data from ion-pmf.pdb. 201s Vpmg_ibForce: No force for zero ionic strength! 201s Vpmg_ibForce: No force for zero ionic strength! 201s 2 atoms 201s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 201s Net charge 2.00e+00 e 201s Preparing to run 3 PBE calculations. 201s ---------------------------------------- 201s CALCULATION #1 (solv): MULTIGRID 201s Setting up problem... 201s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 201s Debye length: 0 A 201s Current memory usage: 61.106 MB total, 61.106 MB high water 201s Using cubic spline charge discretization. 201s Grid dimensions: 65 x 65 x 65 201s Grid spacings: 0.210 x 0.210 x 0.210 201s Grid lengths: 13.440 x 13.440 x 13.440 201s Grid center: (0.000, 0.000, 0.000) 201s Multigrid levels: 5 201s Molecule ID: 1 201s Linearized traditional PBE 201s Multiple Debye-Huckel sphere boundary conditions 201s 0 ion species (0.000 M ionic strength): 201s Solute dielectric: 1.000 201s Solvent dielectric: 78.540 201s Using spline-based surface definition;window = 0.300 201s Temperature: 298.150 K 201s Electrostatic energies will be calculated 201s All-atom solvent forces will be calculated 201s Total electrostatic energy = 7.839535983197E+03 kJ/mol 201s Calculating forces... 201s Printing per-atom forces for molecule 1 (kJ/mol/A) 201s Legend: 201s tot n -- total force for atom n 201s qf n -- fixed charge force for atom n 201s db n -- dielectric boundary force for atom n 201s ib n -- ionic boundary force for atom n 201s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 201s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 201s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 201s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 201s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 201s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 201s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 201s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 201s Vpmg_ibForce: No force for zero ionic strength! 201s Vpmg_ibForce: No force for zero ionic strength! 201s ---------------------------------------- 201s CALCULATION #2 (ref): MULTIGRID 201s Setting up problem... 201s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 201s Debye length: 0 A 201s Current memory usage: 61.106 MB total, 61.155 MB high water 201s Using cubic spline charge discretization. 201s Grid dimensions: 65 x 65 x 65 201s Grid spacings: 0.210 x 0.210 x 0.210 201s Grid lengths: 13.440 x 13.440 x 13.440 201s Grid center: (0.000, 0.000, 0.000) 201s Multigrid levels: 5 201s Molecule ID: 1 201s Linearized traditional PBE 201s Multiple Debye-Huckel sphere boundary conditions 201s 0 ion species (0.000 M ionic strength): 201s Solute dielectric: 1.000 201s Solvent dielectric: 1.000 201s Using spline-based surface definition;window = 0.300 201s Temperature: 298.150 K 201s Electrostatic energies will be calculated 201s All-atom solvent forces will be calculated 201s Total electrostatic energy = 8.964727588811E+03 kJ/mol 201s Calculating forces... 201s Printing per-atom forces for molecule 1 (kJ/mol/A) 201s Legend: 201s tot n -- total force for atom n 201s qf n -- fixed charge force for atom n 201s db n -- dielectric boundary force for atom n 201s ib n -- ionic boundary force for atom n 201s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 201s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 201s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 201s mgF db 0 0.000e+00 0.000e+00 0.000e+00 201s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 201s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 201s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 201s mgF db 1 0.000e+00 0.000e+00 0.000e+00 201s ---------------------------------------- 201s CALCULATION #3 (asolv): APOLAR 201s Printing per atom forces (kJ/mol/A) 201s Legend: 201s tot n -- Total force for atom n 201s sasa n -- SASA force for atom n 201s sav n -- SAV force for atom n 201s wca n -- WCA force for atom n 201s 201s gamma 0.000720 201s pressure 0.000000 201s bconc 0.033000 201s 201s tot 0 2.715e-02 9.130e-07 9.130e-07 201s sasa 0 -1.100e+01 0.000e+00 0.000e+00 201s sav 0 0.000e+00 0.000e+00 0.000e+00 201s wca 0 -5.827e-01 -2.767e-05 -2.767e-05 201s tot 1 -2.723e-02 9.133e-07 9.133e-07 201s sasa 1 1.112e+01 0.000e+00 0.000e+00 201s sav 1 0.000e+00 0.000e+00 0.000e+00 201s wca 1 5.827e-01 -2.767e-05 -2.767e-05 201s 201s 201s Solvent Accessible Surface Area (SASA) for each atom: 201s SASA for atom 0: 1.153275282828E+02 201s SASA for atom 1: 1.153114143344E+02 201s 201s Total solvent accessible surface area: 230.639 A^2 201s 201s Surface tension*area energies (gamma * SASA) for each atom: 201s Surface tension*area energy for atom 0: 8.303582036361E-02 201s Surface tension*area energy for atom 1: 8.302421832080E-02 201s 201s Total surface tension energy: 0.16606 kJ/mol 201s 201s Total solvent accessible volume: 0 A^3 201s 201s Total pressure*volume energy: 0 kJ/mol 201s 201s WCA dispersion Energies for each atom: 201s WCA energy for atom 0: -6.909718359932E+00 201s WCA energy for atom 1: -6.909422551724E+00 201s 201s Total WCA energy: -13.8191 kJ/mol 201s 201s Total non-polar energy = -1.365308087297E+01 kJ/mol 201s ---------------------------------------- 201s PRINT STATEMENTS 201s 201s print energy 1 (solv) - 2 (ref) end 201s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 201s Global net ELEC energy = -1.125191605614E+03 kJ/mol 201s print force 1 (solv) - 2 (ref) end 201s Printing per-atom forces (kJ/mol/A). 201s Legend: 201s tot n -- Total force for atom n 201s qf n -- Fixed charge force for atom n 201s db n -- Dielectric boundary force for atom n 201s ib n -- Ionic boundary force for atom n 201s tot all -- Total force for system 201s qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 201s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 201s db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 201s tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 201s qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 201s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 201s db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 201s tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 201s tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 201s 201s print APOL energy 1 (asolv) end 201s Global net APOL energy = -1.365308087297E+01 kJ/mol 201s 201s print APOL force 1 (asolv) end 201s Printing per atom forces (kJ/mol/A) 201s Legend: 201s tot n -- Total force for atom n 201s sasa n -- SASA force for atom n 201s sav n -- SAV force for atom n 201s wca n -- WCA force for atom n 201s tot all -- Total force for system 201s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 201s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 201s wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 201s tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 201s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 201s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 201s wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 201s tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 201s tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 201s ---------------------------------------- 201s CLEANING UP AND SHUTTING DOWN... 201s Destroying force arrays. 201s No energy arrays to destroy. 201s Destroying multigrid structures. 201s Destroying finite element structures. 201s Destroying 1 molecules 201s Final memory usage: 60.711 MB total, 62.250 MB high water 201s 201s 201s Thanks for using APBS! 201s 201s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 201s *** PASSED *** 201s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 201s *** PASSED *** 201s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 201s *** PASSED *** 201s Elapsed time: 3.480922 seconds 201s -------------------------------------------------------------------------------- 201s Total elapsed time: 3.480922 seconds 201s Test results have been logged 201s -------------------------------------------------------------------------------- 201s -------------------------------------------------------------------------------- 201s Testing input file apbs-mol-vdw.in 201s 207s Checking for intermediate energies in input file ion-pmf.out 207s EXPECTED COMPUTED: 4 207s EXPECTED EXPECTED: 4 207s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] 207s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 207s COMPUTED RESULT 7839.535983197 207s COMPUTED RESULT 8964.727588811 207s COMPUTED RESULT -1125.191605614 207s COMPUTED RESULT -13.65308087297 207s Running tests for pka-lig section 207s BINARY: /usr/bin/apbs 207s INPUT: apbs-mol-vdw.in 207s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 207s asc_getToken: Error occurred (bailing out). 207s Vio_scanf: Format problem with input. 207s 207s 207s ---------------------------------------------------------------------- 207s APBS -- Adaptive Poisson-Boltzmann Solver 207s Version APBS 3.4.1 207s 207s Nathan A. Baker (nathan.baker@pnnl.gov) 207s Pacific Northwest National Laboratory 207s 207s Additional contributing authors listed in the code documentation. 207s 207s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 207s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 207s Northwest Division for the U.S. Department of Energy. 207s 207s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 207s Portions Copyright (c) 2002-2020, Nathan A. Baker. 207s Portions Copyright (c) 1999-2002, The Regents of the University of California. 207s Portions Copyright (c) 1995, Michael Holst. 207s All rights reserved. 207s 207s Redistribution and use in source and binary forms, with or without 207s modification, are permitted provided that the following conditions are met: 207s 207s * Redistributions of source code must retain the above copyright notice, this 207s list of conditions and the following disclaimer. 207s 207s * Redistributions in binary form must reproduce the above copyright notice, 207s this list of conditions and the following disclaimer in the documentation 207s and/or other materials provided with the distribution. 207s 207s * Neither the name of the developer nor the names of its contributors may be 207s used to endorse or promote products derived from this software without 207s specific prior written permission. 207s 207s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 207s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 207s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 207s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 207s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 207s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 207s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 207s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 207s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 207s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 207s ---------------------------------------------------------------------- 207s APBS uses FETK (the Finite Element ToolKit) to solve the 207s Poisson-Boltzmann equation numerically. FETK is a portable collection 207s of finite element modeling class libraries developed by the Michael Holst 207s research group and written in an object-oriented form of C. FEtk is 207s designed to solve general coupled systems of nonlinear partial differential 207s equations using adaptive finite element methods, inexact Newton methods, 207s and algebraic multilevel methods. More information about FEtk may be found 207s at . 207s ---------------------------------------------------------------------- 207s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 207s Aqua is a modified form of the Holst group PMG library 207s which has been modified by Patrice Koehl 207s for improved efficiency and 207s memory usage when solving the Poisson-Boltzmann equation. 207s ---------------------------------------------------------------------- 207s Please cite your use of APBS as: 207s 207s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 207s nanosystems: application to microtubules and the ribosome. Proc. 207s Natl. Acad. Sci. USA 98, 10037-10041 2001. 207s 207s 207s This executable compiled on Jan 3 2025 at 11:01:42 207s 207s Parsing input file apbs-mol-vdw.in... 207s rank 0 size 1... 207s Parsed input file. 207s Got paths for 3 molecules 207s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 207s asc_getToken: Error occurred (bailing out). 207s Vio_scanf: Format problem with input. 207s 47 atoms 207s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 207s Net charge 1.11e-16 e 207s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 207s asc_getToken: Error occurred (bailing out). 207s Vio_scanf: Format problem with input. 207s 3423 atoms 207s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 207s Net charge 1.00e+00 e 207s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 207s 3470 atoms 207s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 207s Net charge 1.00e+00 e 207s Preparing to run 6 PBE calculations. 207s ---------------------------------------- 207s CALCULATION #1 (lig-coarse): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 204.292 MB total, 204.292 MB high water 207s Using linear spline charge discretization. 207s Grid dimensions: 97 x 97 x 97 207s Grid spacings: 0.729 x 0.729 x 0.729 207s Grid lengths: 70.000 x 70.000 x 70.000 207s Grid center: (28.969, -32.507, 27.022) 207s Multigrid levels: 4 207s Molecule ID: 1 207s Linearized traditional PBE 207s Single Debye-Huckel sphere boundary conditions 207s 2 ion species (0.000 M ionic strength): 207s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 207s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 207s Solute dielectric: 2.000 207s Solvent dielectric: 78.000 207s Using "molecular" surface definition; no smoothing 207s Solvent probe radius: 0.000 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 2.224988750664E+03 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s CALCULATION #2 (lig-fine): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 204.292 MB total, 406.001 MB high water 207s Using linear spline charge discretization. 207s Grid dimensions: 97 x 97 x 97 207s Grid spacings: 0.250 x 0.250 x 0.250 207s Grid lengths: 24.000 x 24.000 x 24.000 207s Grid center: (24.822, -33.153, 21.545) 207s Multigrid levels: 4 207s Molecule ID: 1 207s Linearized traditional PBE 207s Boundary conditions from focusing 207s 2 ion species (0.000 M ionic strength): 207s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 207s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 207s Solute dielectric: 2.000 207s Solvent dielectric: 78.000 207s Using "molecular" surface definition; no smoothing 207s Solvent probe radius: 0.000 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 1.049695084686E+04 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s CALCULATION #3 (pka-coarse): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 291.151 MB total, 406.001 MB high water 207s Using linear spline charge discretization. 207s Grid dimensions: 97 x 97 x 97 207s Grid spacings: 0.729 x 0.729 x 0.729 207s Grid lengths: 70.000 x 70.000 x 70.000 207s Grid center: (28.969, -32.507, 27.022) 207s Multigrid levels: 4 207s Molecule ID: 2 207s Linearized traditional PBE 207s Single Debye-Huckel sphere boundary conditions 207s 2 ion species (0.000 M ionic strength): 207s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 207s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 207s Solute dielectric: 2.000 207s Solvent dielectric: 78.000 207s Using "molecular" surface definition; no smoothing 207s Solvent probe radius: 0.000 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 1.818450789522E+05 kJ/mol 207s Calculating forces... 207s [focusFillBound()]: WARNING: 207s Unusually large potential values 207s detectedTesting computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 207s *** PASSED *** 207s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 207s *** PASSED *** 207s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 207s *** PASSED *** 207s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 207s on the focusing boundary! 207s Convergence not guaranteed for NPBE/NRPBE calculations! 207s 207s ---------------------------------------- 207s CALCULATION #4 (pka-fine): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 291.151 MB total, 533.426 MB high water 207s Using linear spline charge discretization. 207s Grid dimensions: 97 x 97 x 97 207s Grid spacings: 0.250 x 0.250 x 0.250 207s Grid lengths: 24.000 x 24.000 x 24.000 207s Grid center: (24.822, -33.153, 21.545) 207s Multigrid levels: 4 207s Molecule ID: 2 207s Linearized traditional PBE 207s Boundary conditions from focusing 207s 2 ion species (0.000 M ionic strength): 207s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 207s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 207s Solute dielectric: 2.000 207s Solvent dielectric: 78.000 207s Using "molecular" surface definition; no smoothing 207s Solvent probe radius: 0.000 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 3.008254338259E+05 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s CALCULATION #5 (complex-coarse): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 292.063 MB total, 533.426 MB high water 207s Using linear spline charge discretization. 207s Grid dimensions: 97 x 97 x 97 207s Grid spacings: 0.729 x 0.729 x 0.729 207s Grid lengths: 70.000 x 70.000 x 70.000 207s Grid center: (28.969, -32.507, 27.022) 207s Multigrid levels: 4 207s Molecule ID: 3 207s Linearized traditional PBE 207s Single Debye-Huckel sphere boundary conditions 207s 2 ion species (0.000 M ionic strength): 207s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 207s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 207s Solute dielectric: 2.000 207s Solvent dielectric: 78.000 207s Using "molecular" surface definition; no smoothing 207s Solvent probe radius: 0.000 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 1.840918409896E+05 kJ/mol 207s Calculating forces... 207s [focusFillBound()]: WARNING: 207s Unusually large potential values 207s detected on the focusing boundary! 207s Convergence not guaranteed for NPBE/NRPBE calculations! 207s 207s ---------------------------------------- 207s CALCULATION #6 (complex-fine): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 292.063 MB total, 534.806 MB high water 207s Using linear spline charge discretization. 207s Grid dimensions: 97 x 97 x 97 207s Grid spacings: 0.250 x 0.250 x 0.250 207s Grid lengths: 24.000 x 24.000 x 24.000 207s Grid center: (24.822, -33.153, 21.545) 207s Multigrid levels: 4 207s Molecule ID: 3 207s Linearized traditional PBE 207s Boundary conditions from focusing 207s 2 ion species (0.000 M ionic strength): 207s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 207s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 207s Solute dielectric: 2.000 207s Solvent dielectric: 78.000 207s Using "molecular" surface definition; no smoothing 207s Solvent probe radius: 0.000 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 3.113304681884E+05 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s PRINT STATEMENTS 207s 207s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 207s Local net energy (PE 0) = 8.083515648730E+00 kJ/mol 207s Global net ELEC energy = 8.083515648730E+00 kJ/mol 207s ---------------------------------------- 207s CLEANING UP AND SHUTTING DOWN... 207s Destroying force arrays. 207s No energy arrays to destroy. 207s Destroying multigrid structures. 207s Destroying finite element structures. 207s Destroying 3 molecules 207s Final memory usage: 0.001 MB total, 534.806 MB high water 207s 207s 207s Thanks for using APBS! 207s 207s *** PASSED *** 207s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 207s *** PASSED *** 207s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 207s *** PASSED *** 207s Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) 207s *** PASSED *** 207s Elapsed time: 5.749284 seconds 207s -------------------------------------------------------------------------------- 207s -------------------------------------------------------------------------------- 207s Testing input file apbs-smol-vdw.in 207s 212s Checking for intermediate energies in input file apbs-mol-vdw.out 212s EXPECTED COMPUTED: 7 212s EXPECTED EXPECTED: 7 212s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] 212s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 212s COMPUTED RESULT 2224.988750664 212s COMPUTED RESULT 10496.95084686 212s COMPUTED RESULT 181845.0789522 212s COMPUTED RESULT 300825.4338259 212s COMPUTED RESULT 184091.8409896 212s COMPUTED RESULT 311330.4681884 212s COMPUTED RESULT 8.08351564873 212s BINARY: /usr/bin/apbs 212s INPUT: apbs-smol-vdw.in 212s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 212s asc_getToken: Error occurred (bailing out). 212s Vio_scanf: Format problem with input. 212s 212s 212s ---------------------------------------------------------------------- 212s APBS -- Adaptive Poisson-Boltzmann Solver 212s Version APBS 3.4.1 212s 212s Nathan A. Baker (nathan.baker@pnnl.gov) 212s Pacific Northwest National Laboratory 212s 212s Additional contributing authors listed in the code documentation. 212s 212s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 212s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 212s Northwest Division for the U.S. Department of Energy. 212s 212s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 212s Portions Copyright (c) 2002-2020, Nathan A. Baker. 212s Portions Copyright (c) 1999-2002, The Regents of the University of California. 212s Portions Copyright (c) 1995, Michael Holst. 212s All rights reserved. 212s 212s Redistribution and use in source and binary forms, with or without 212s modification, are permitted provided that the following conditions are met: 212s 212s * Redistributions of source code must retain the above copyright notice, this 212s list of conditions and the following disclaimer. 212s 212s * Redistributions in binary form must reproduce the above copyright notice, 212s this list of conditions and the following disclaimer in the documentation 212s and/or other materials provided with the distribution. 212s 212s * Neither the name of the developer nor the names of its contributors may be 212s used to endorse or promote products derived from this software without 212s specific prior written permission. 212s 212s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 212s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 212s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 212s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 212s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 212s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 212s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 212s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 212s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 212s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 212s ---------------------------------------------------------------------- 212s APBS uses FETK (the Finite Element ToolKit) to solve the 212s Poisson-Boltzmann equation numerically. FETK is a portable collection 212s of finite element modeling class libraries developed by the Michael Holst 212s research group and written in an object-oriented form of C. FEtk is 212s designed to solve general coupled systems of nonlinear partial differential 212s equations using adaptive finite element methods, inexact Newton methods, 212s and algebraic multilevel methods. More information about FEtk may be found 212s at . 212s ---------------------------------------------------------------------- 212s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 212s Aqua is a modified form of the Holst group PMG library 212s which has been modified by Patrice Koehl 212s for improved efficiency and 212s memory usage when solving the Poisson-Boltzmann equation. 212s ---------------------------------------------------------------------- 212s Please cite your use of APBS as: 212s 212s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 212s nanosystems: application to microtubules and the ribosome. Proc. 212s Natl. Acad. Sci. USA 98, 10037-10041 2001. 212s 212s 212s This executable compiled on Jan 3 2025 at 11:01:42 212s 212s Parsing input file apbs-smol-vdw.in... 212s rank 0 size 1... 212s Parsed input file. 212s Got paths for 3 molecules 212s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 212s asc_getToken: Error occurred (bailing out). 212s Vio_scanf: Format problem with input. 212s 47 atoms 212s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 212s Net charge 1.11e-16 e 212s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 212s asc_getToken: Error occurred (bailing out). 212s Vio_scanf: Format problem with input. 212s 3423 atoms 212s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 212s Net charge 1.00e+00 e 212s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 212s 3470 atoms 212s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 212s Net charge 1.00e+00 e 212s Preparing to run 6 PBE calculations. 212s ---------------------------------------- 212s CALCULATION #1 (lig-coarse): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 204.292 MB total, 204.292 MB high water 212s Using linear spline charge discretization. 212s Grid dimensions: 97 x 97 x 97 212s Grid spacings: 0.729 x 0.729 x 0.729 212s Grid lengths: 70.000 x 70.000 x 70.000 212s Grid center: (28.969, -32.507, 27.022) 212s Multigrid levels: 4 212s Molecule ID: 1 212s Linearized traditional PBE 212s Single Debye-Huckel sphere boundary conditions 212s 2 ion species (0.000 M ionic strength): 212s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 212s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 212s Solute dielectric: 2.000 212s Solvent dielectric: 78.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 0.000 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 2.226793167046E+03 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s CALCULATION #2 (lig-fine): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 204.292 MB total, 406.001 MB high water 212s Using linear spline charge discretization. 212s Grid dimensions: 97 x 97 x 97 212s Grid spacings: 0.250 x 0.250 x 0.250 212s Grid lengths: 24.000 x 24.000 x 24.000 212s Grid center: (24.822, -33.153, 21.545) 212s Multigrid levels: 4 212s Molecule ID: 1 212s Linearized traditional PBE 212s Boundary conditions from focusing 212s 2 ion species (0.000 M ionic strength): 212s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 212s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 212s Solute dielectric: 2.000 212s Solvent dielectric: 78.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 0.000 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 1.050504485887E+04 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s CALCULATION #3 (pka-coarse): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 291.151 MB total, 406.001 MB high water 212s Using linear spline charge discretization. 212s Grid dimensions: 97 x 97 x 97 212s Grid spacings: 0.729 x 0.729 x 0.729 212s Grid lengths: 70.000 x 70.000 x 70.000 212s Grid center: (28.969, -32.507, 27.022) 212s Multigrid levels: 4 212s Molecule ID: 2 212s Linearized traditional PBE 212s Single Debye-Huckel sphere boundary conditions 212s 2 ion species (0.000 M ionic strength): 212s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 212s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 212s Solute dielectric: 2.000 212s Solvent dielectric: 78.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 0.000 ATesting computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 212s *** PASSED *** 212s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 212s *** PASSED *** 212s 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 1.827976621645E+05 kJ/mol 212s Calculating forces... 212s [focusFillBound()]: WARNING: 212s Unusually large potential values 212s detected on the focusing boundary! 212s Convergence not guaranteed for NPBE/NRPBE calculations! 212s 212s ---------------------------------------- 212s CALCULATION #4 (pka-fine): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 291.151 MB total, 533.426 MB high water 212s Using linear spline charge discretization. 212s Grid dimensions: 97 x 97 x 97 212s Grid spacings: 0.250 x 0.250 x 0.250 212s Grid lengths: 24.000 x 24.000 x 24.000 212s Grid center: (24.822, -33.153, 21.545) 212s Multigrid levels: 4 212s Molecule ID: 2 212s Linearized traditional PBE 212s Boundary conditions from focusing 212s 2 ion species (0.000 M ionic strength): 212s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 212s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 212s Solute dielectric: 2.000 212s Solvent dielectric: 78.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 0.000 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 3.017228546773E+05 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s CALCULATION #5 (complex-coarse): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 292.063 MB total, 533.426 MB high water 212s Using linear spline charge discretization. 212s Grid dimensions: 97 x 97 x 97 212s Grid spacings: 0.729 x 0.729 x 0.729 212s Grid lengths: 70.000 x 70.000 x 70.000 212s Grid center: (28.969, -32.507, 27.022) 212s Multigrid levels: 4 212s Molecule ID: 3 212s Linearized traditional PBE 212s Single Debye-Huckel sphere boundary conditions 212s 2 ion species (0.000 M ionic strength): 212s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 212s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 212s Solute dielectric: 2.000 212s Solvent dielectric: 78.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 0.000 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 1.850819075387E+05 kJ/mol 212s Calculating forces... 212s [focusFillBound()]: WARNING: 212s Unusually large potential values 212s detected on the focusing boundary! 212s Convergence not guaranteed for NPBE/NRPBE calculations! 212s 212s ---------------------------------------- 212s CALCULATION #6 (complex-fine): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 292.063 MB total, 534.806 MB high water 212s Using linear spline charge discretization. 212s Grid dimensions: 97 x 97 x 97 212s Grid spacings: 0.250 x 0.250 x 0.250 212s Grid lengths: 24.000 x 24.000 x 24.000 212s Grid center: (24.822, -33.153, 21.545) 212s Multigrid levels: 4 212s Molecule ID: 3 212s Linearized traditional PBE 212s Boundary conditions from focusing 212s 2 ion species (0.000 M ionic strength): 212s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 212s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 212s Solute dielectric: 2.000 212s Solvent dielectric: 78.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 0.000 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 3.122488625388E+05 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s PRINT STATEMENTS 212s 212s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 212s Local net energy (PE 0) = 2.096300255723E+01 kJ/mol 212s Global net ELEC energy = 2.096300255723E+01 kJ/mol 212s ---------------------------------------- 212s CLEANING UP AND SHUTTING DOWN... 212s Destroying force arrays. 212s No energy arrays to destroy. 212s Destroying multigrid structures. 212s Destroying finite element structures. 212s Destroying 3 molecules 212s Final memory usage: 0.001 MB total, 534.806 MB high water 212s 212s 212s Thanks for using APBS! 212s 212s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 212s *** PASSED *** 212s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 212s *** PASSED *** 212s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 212s *** PASSED *** 212s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 212s *** PASSED *** 212s Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01) 212s *** PASSED *** 212s Elapsed time: 5.047735 seconds 212s -------------------------------------------------------------------------------- 212s -------------------------------------------------------------------------------- 212s Testing input file apbs-mol-surf.in 212s 217s Checking for intermediate energies in input file apbs-smol-vdw.out 217s EXPECTED COMPUTED: 7 217s EXPECTED EXPECTED: 7 217s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] 217s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 217s COMPUTED RESULT 2226.793167046 217s COMPUTED RESULT 10505.04485887 217s COMPUTED RESULT 182797.6621645 217s COMPUTED RESULT 301722.8546773 217s COMPUTED RESULT 185081.9075387 217s COMPUTED RESULT 312248.8625388 217s COMPUTED RESULT 20.96300255723 217s BINARY: /usr/bin/apbs 217s INPUT: apbs-mol-surf.in 217s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 217s asc_getToken: Error occurred (bailing out). 217s Vio_scanf: Format problem with input. 217s 217s 217s ---------------------------------------------------------------------- 217s APBS -- Adaptive Poisson-Boltzmann Solver 217s Version APBS 3.4.1 217s 217s Nathan A. Baker (nathan.baker@pnnl.gov) 217s Pacific Northwest National Laboratory 217s 217s Additional contributing authors listed in the code documentation. 217s 217s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 217s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 217s Northwest Division for the U.S. Department of Energy. 217s 217s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 217s Portions Copyright (c) 2002-2020, Nathan A. Baker. 217s Portions Copyright (c) 1999-2002, The Regents of the University of California. 217s Portions Copyright (c) 1995, Michael Holst. 217s All rights reserved. 217s 217s Redistribution and use in source and binary forms, with or without 217s modification, are permitted provided that the following conditions are met: 217s 217s * Redistributions of source code must retain the above copyright notice, this 217s list of conditions and the following disclaimer. 217s 217s * Redistributions in binary form must reproduce the above copyright notice, 217s this list of conditions and the following disclaimer in the documentation 217s and/or other materials provided with the distribution. 217s 217s * Neither the name of the developer nor the names of its contributors may be 217s used to endorse or promote products derived from this software without 217s specific prior written permission. 217s 217s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 217s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 217s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 217s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 217s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 217s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 217s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 217s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 217s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 217s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 217s ---------------------------------------------------------------------- 217s APBS uses FETK (the Finite Element ToolKit) to solve the 217s Poisson-Boltzmann equation numerically. FETK is a portable collection 217s of finite element modeling class libraries developed by the Michael Holst 217s research group and written in an object-oriented form of C. FEtk is 217s designed to solve general coupled systems of nonlinear partial differential 217s equations using adaptive finite element methods, inexact Newton methods, 217s and algebraic multilevel methods. More information about FEtk may be found 217s at . 217s ---------------------------------------------------------------------- 217s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 217s Aqua is a modified form of the Holst group PMG library 217s which has been modified by Patrice Koehl 217s for improved efficiency and 217s memory usage when solving the Poisson-Boltzmann equation. 217s ---------------------------------------------------------------------- 217s Please cite your use of APBS as: 217s 217s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 217s nanosystems: application to microtubules and the ribosome. Proc. 217s Natl. Acad. Sci. USA 98, 10037-10041 2001. 217s 217s 217s This executable compiled on Jan 3 2025 at 11:01:42 217s 217s Parsing input file apbs-mol-surf.in... 217s rank 0 size 1... 217s Parsed input file. 217s Got paths for 3 molecules 217s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 217s asc_getToken: Error occurred (bailing out). 217s Vio_scanf: Format problem with input. 217s 47 atoms 217s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 217s Net charge 1.11e-16 e 217s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 217s asc_getToken: Error occurred (bailing out). 217s Vio_scanf: Format problem with input. 217s 3423 atoms 217s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 217s Net charge 1.00e+00 e 217s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 217s 3470 atoms 217s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 217s Net charge 1.00e+00 e 217s Preparing to run 6 PBE calculations. 217s ---------------------------------------- 217s CALCULATION #1 (lig-coarse): MULTIGRID 217s Setting up problem... 217s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 217s Debye length: 0 A 217s Current memory usage: 203.877 MB total, 203.877 MB high water 217s Using linear spline charge discretization. 217s Grid dimensions: 97 x 97 x 97 217s Grid spacings: 0.729 x 0.729 x 0.729 217s Grid lengths: 70.000 x 70.000 x 70.000 217s Grid center: (28.969, -32.507, 27.022) 217s Multigrid levels: 4 217s Molecule ID: 1 217s Linearized traditional PBE 217s Single Debye-Huckel sphere boundary conditions 217s 2 ion species (0.000 M ionic strength): 217s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 217s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 217s Solute dielectric: 2.000 217s Solvent dielectric: 78.000 217s Using "molecular" surface definition; no smoothing 217s Solvent probe radius: 1.400 A 217s Temperature: 298.150 K 217s Electrostatic energies will be calculated 217s Total electrostatic energy = 2.244350164274E+03 kJ/mol 217s Calculating forces... 217s ---------------------------------------- 217s CALCULATION #2 (lig-fine): MULTIGRID 217s Setting up problem... 217s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 217s Debye length: 0 A 217s Current memory usage: 203.877 MB total, 405.586 MB high water 217s Using linear spline charge discretization. 217s Grid dimensions: 97 x 97 x 97 217s Grid spacings: 0.250 x 0.250 x 0.250 217s Grid lengths: 24.000 x 24.000 x 24.000 217s Grid center: (24.822, -33.153, 21.545) 217s Multigrid levels: 4 217s Molecule ID: 1 217s Linearized traditional PBE 217s Boundary conditions from focusing 217s 2 ion species (0.000 M ionic strength): 217s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 217s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 217s Solute dielectric: 2.000 217s Solvent dielectric: 78.000 217s Using "molecular" surface definition; no smoothing 217s Solvent probe radius: 1.400 A 217s Temperature: 298.150 K 217s Electrostatic energies will be calculated 217s Total electrostatic energy = 1.052149475373E+04 kJ/mol 217s Calculating forces... 217s ---------------------------------------- 217s CALCULATION #3 (pka-coarse): MULTIGRID 217s Setting up problem... 217s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 217s Debye length: 0 A 217s Current memory usage: 251.521 MB total, 405.586 MB high water 217s Using linear spline charge discretization. 217s Grid dimensions: 97 x 97 x 97 217s Grid spacings: 0.729 x 0.729 x 0.729 217s Grid lengths: 70.000 x 70.000 x 70.000 217s Grid center: (28.969, -32.507, 27.022) 217s Multigrid levels: 4 217s Molecule ID: 2 217s Linearized traditional PBE 217s Single Debye-Huckel sphere boundary conditions 217s 2 ion species (0.000 M ionic strength): 217s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 217s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 217s Solute dielectric: 2.000 217s Solvent dielectric: 78.000 217s Using "molecular" surface definition; no smoothing 217s Solvent probe radius: 1.400 A 217s Temperature: 298.150 K 217s Electrostatic energies will be calculated 217s Total electrostatic energy = 1.862615690066E+05 kJ/mol 217s Calculating forces... 217s [focusFillBound()]: WARNING: 217s Unusually large potential values 217s detected on the focusing boundary! 217s Convergence not guaranteed for NPBE/NRPBE calculations! 217s 217s ---------------------------------------- 217s CALCULATION #4 (pka-fine): MULTIGRID 217s Setting up problem... 217s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 217s Debye length: 0 A 217s Current memory usage: 251.521 MB total, 493.795 MB high water 217s Using linear spline charge discretization. 217s Grid dimensions: 97 x 97 x 97 217s Grid spacings: 0.250 x 0.250 x 0.250 217s Grid lengths: 24.000 x 24.000 x 24.000 217s Grid center: (24.822, -33.153, 21.545) 217s Multigrid levels: 4 217s Molecule ID: 2 217s Linearized traditional PBE 217s Boundary conditions from focusing 217s 2 ion species (0.000 M ionic strength): 217s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 217s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 217s Solute dielectric: 2.000 217s Solvent dielectric: 78.000 217s Using "molecular" surface definition; no smoothing 217s Solvent probe radius: 1.400 A 217s Temperature: 298.150 K 217s Electrostatic energies will be calculated 217s Total electrostatic energy = 3.051810884053E+05 kJ/mol 217s Calculating forces... 217s ---------------------------------------- 217s CALCULATION #5 (complex-coarse): MULTIGRID 217s Setting up problem... 217s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 217s Debye length: 0 A 217s Current memory usage: 251.858 MB total, 493.795 MB high water 217s Using linear spline charge discretization. 217s Grid dimensions: 97 x 97 x 97 217s Grid spacings: 0.729 x 0.729 x 0.729 217s Grid lengths: 70.000 x 70.000 x 70.000 217s Grid center: (28.969, -32.507, 27.022) 217s Multigrid levels: 4 217s Molecule ID: 3 217s Linearized traditional PBE 217s Single Debye-Huckel sphere boundary conditions 217s 2 ion species (0.000 M ionic strength): 217s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 217s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 217s Solute dielectric: 2.000 217s Solvent dielectric: 78.000 217s Using "molecular" surface definition; no smoothing 217s Solvent probe radius: 1.400 A 217s Temperature: 298.150 K 217s Electrostatic energies will be calculated 217s Total electrostatic energy = 1.886625455219E+05 kJ/mol 217s Calculating forces... 217s [focusFillBound()]: WARNING: 217s Unusually large potential values 217s detected on the focusing boundary! 217s Convergence not guaranteed for NPBE/NRPBE calculations! 217s 217s ---------------------------------------- 217s CALCULATION #6 (complex-fine): MULTIGRID 217s Setting up problem... 217s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 217s Debye length: 0 A 217s Current memory usage: 251.858 MB total, 494.601 MB high water 217s Using linear spline charge discretization. 217s Grid dimensions: 97 x 97 x 97 217s Grid spacings: 0.250 x 0.250 x 0.250 217s Grid lengths: 24.000 x 24.000 x 24.000 217s Grid center: (24.822, -33.153, 21.545) 217s Multigrid levels: 4 217s Molecule ID: 3 217s Linearized traditional PBE 217s Boundary conditions from focusing 217s 2 ion species (0.000 M ionic strength): 217s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 217s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 217s Solute dielectric: 2.000 217s Solvent dielectric: 78.000 217s Using "molecular" surface definition; no smoothing 217s Solvent probe radius: 1.400 A 217s Temperature: 298.150 K 217s Electrostatic energies will be calculated 217s Total electrostatic energy = 3.158218439277E+05 kJ/mol 217s Calculating forces... 217s ---------------------------------------- 217s PRINT STATEMENTS 217s 217s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 217s Local net energy (PE 0) = 1.192607686581E+02 kJ/mol 217s Global net ELEC energy = 1.192607686581E+02 kJ/mol 217s ---------------------------------------- 217s CLEANING UP AND SHUTTING DOWN... 217s Destroying force arrays. 217s No energy arrays to destroy. 217s Destroying multigrid structures. 217s Destroying finite element structures. 217s Destroying 3 molecules 217s Final memory usage: 0.001 MB total, 494.601 MB high water 217s 217s 217s Thanks for using APBS! 217s 217s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 217s *** PASSED *** 217s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 217s *** PASSED *** 217s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 217s *** PASSED *** 217s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 217s *** PASSED *** 217s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 217s *** PASSED *** 217s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 217s *** PASSED *** 217s Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) 217s *** PASSED *** 217s Elapsed time: 5.194028 seconds 217s -------------------------------------------------------------------------------- 217s -------------------------------------------------------------------------------- 217s Testing input file apbs-smol-surf.in 217s 222s Checking for intermediate energies in input file apbs-mol-surf.out 222s EXPECTED COMPUTED: 7 222s EXPECTED EXPECTED: 7 222s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] 222s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 222s COMPUTED RESULT 2244.350164274 222s COMPUTED RESULT 10521.49475373 222s COMPUTED RESULT 186261.5690066 222s COMPUTED RESULT 305181.0884053 222s COMPUTED RESULT 188662.5455219 222s COMPUTED RESULT 315821.8439277 222s COMPUTED RESULT 119.2607686581 222s BINARY: /usr/bin/apbs 222s INPUT: apbs-smol-surf.in 222s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 222s asc_getToken: Error occurred (bailing out). 222s Vio_scanf: Format problem with input. 222s 222s 222s ---------------------------------------------------------------------- 222s APBS -- Adaptive Poisson-Boltzmann Solver 222s Version APBS 3.4.1 222s 222s Nathan A. Baker (nathan.baker@pnnl.gov) 222s Pacific Northwest National Laboratory 222s 222s Additional contributing authors listed in the code documentation. 222s 222s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 222s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 222s Northwest Division for the U.S. Department of Energy. 222s 222s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 222s Portions Copyright (c) 2002-2020, Nathan A. Baker. 222s Portions Copyright (c) 1999-2002, The Regents of the University of California. 222s Portions Copyright (c) 1995, Michael Holst. 222s All rights reserved. 222s 222s Redistribution and use in source and binary forms, with or without 222s modification, are permitted provided that the following conditions are met: 222s 222s * Redistributions of source code must retain the above copyright notice, this 222s list of conditions and the following disclaimer. 222s 222s * Redistributions in binary form must reproduce the above copyright notice, 222s this list of conditions and the following disclaimer in the documentation 222s and/or other materials provided with the distribution. 222s 222s * Neither the name of the developer nor the names of its contributors may be 222s used to endorse or promote products derived from this software without 222s specific prior written permission. 222s 222s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 222s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 222s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 222s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 222s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 222s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 222s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 222s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 222s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 222s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 222s ---------------------------------------------------------------------- 222s APBS uses FETK (the Finite Element ToolKit) to solve the 222s Poisson-Boltzmann equation numerically. FETK is a portable collection 222s of finite element modeling class libraries developed by the Michael Holst 222s research group and written in an object-oriented form of C. FEtk is 222s designed to solve general coupled systems of nonlinear partial differential 222s equations using adaptive finite element methods, inexact Newton methods, 222s and algebraic multilevel methods. More information about FEtk may be found 222s at . 222s ---------------------------------------------------------------------- 222s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 222s Aqua is a modified form of the Holst group PMG library 222s which has been modified by Patrice Koehl 222s for improved efficiency and 222s memory usage when solving the Poisson-Boltzmann equation. 222s ---------------------------------------------------------------------- 222s Please cite your use of APBS as: 222s 222s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 222s nanosystems: application to microtubules and the ribosome. Proc. 222s Natl. Acad. Sci. USA 98, 10037-10041 2001. 222s 222s 222s This executable compiled on Jan 3 2025 at 11:01:42 222s 222s Parsing input file apbs-smol-surf.in... 222s rank 0 size 1... 222s Parsed input file. 222s Got paths for 3 molecules 222s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 222s asc_getToken: Error occurred (bailing out). 222s Vio_scanf: Format problem with input. 222s 47 atoms 222s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 222s Net charge 1.11e-16 e 222s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 222s asc_getToken: Error occurred (bailing out). 222s Vio_scanf: Format problem with input. 222s 3423 atoms 222s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 222s Net charge 1.00e+00 e 222s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 222s 3470 atoms 222s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 222s Net charge 1.00e+00 e 222s Preparing to run 6 PBE calculations. 222s ---------------------------------------- 222s CALCULATION #1 (lig-coarse): MULTIGRID 222s Setting up problem... 222s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 222s Debye length: 0 A 222s Current memory usage: 203.877 MB total, 203.877 MB high water 222s Using linear spline charge discretization. 222s Grid dimensions: 97 x 97 x 97 222s Grid spacings: 0.729 x 0.729 x 0.729 222s Grid lengths: 70.000 x 70.000 x 70.000 222s Grid center: (28.969, -32.507, 27.022) 222s Multigrid levels: 4 222s Molecule ID: 1 222s Linearized traditional PBE 222s Single Debye-Huckel sphere boundary conditions 222s 2 ion species (0.000 M ionic strength): 222s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 222s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 222s Solute dielectric: 2.000 222s Solvent dielectric: 78.000 222s Using "molecular" surface definition;harmonic average smoothing 222s Solvent probe radius: 1.400 A 222s Temperature: 298.150 K 222s Electrostatic energies will be calculated 222s Total electrostatic energy = 2.251466789420E+03 kJ/mol 222s Calculating forces... 222s ---------------------------------------- 222s CALCULATION #2 (lig-fine): MULTIGRID 222s Setting up problem... 222s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 222s Debye length: 0 A 222s Current memory usage: 203.877 MB total, 405.586 MB high water 222s Using linear spline charge discretization. 222s Grid dimensions: 97 x 97 x 97 222s Grid spacings: 0.250 x 0.250 x 0.250 222s Grid lengths: 24.000 x 24.000 x 24.000 222s Grid center: (24.822, -33.153, 21.545) 222s Multigrid levels: 4 222s Molecule ID: 1 222s Linearized traditional PBE 222s Boundary conditions from focusing 222s 2 ion species (0.000 M ionic strength): 222s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 222s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 222s Solute dielectric: 2.000 222s Solvent dielectric: 78.000 222s Using "molecular" surface definition;harmonic average smoothing 222s Solvent probe radius: 1.400 A 222s Temperature: 298.150 K 222s Electrostatic energies will be calculated 222s Total electrostatic energy = 1.052814502873E+04 kJ/mol 222s Calculating forces... 222s ---------------------------------------- 222s CALCULATION #3 (pka-coarse): MULTIGRID 222s Setting up problem... 222s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 222s Debye length: 0 A 222s Current memory usage: 251.521 MB total, 405.586 MB high water 222s Using linear spline charge discretization. 222s Grid dimensions: 97 x 97 x 97 222s Grid spacings: 0.729 x 0.729 x 0.729 222s Grid lengths: 70.000 x 70.000 x 70.000 222s Grid center: (28.969, -32.507, 27.022) 222s Multigrid levels: 4 222s Molecule ID: 2 222s Linearized traditional PBE 222s Single Debye-Huckel sphere boundary conditions 222s 2 ion species (0.000 M ionic strength): 222s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 222s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 222s Solute dielectric: 2.000 222s Solvent dielectric: 78.000 222s Using "molecular" surface definition;harmonic average smoothing 222s Solvent probe radius: 1.400 A 222s Temperature: 298.150 K 222s Electrostatic energies will be calculated 222s Total electrostatic energy = 1.864071689626E+05 kJ/mol 222s Calculating forces... 222s [focusFillBound()]: WARNING: 222s Unusually large potential values 222s detected on the focusing boundary! 222s Convergence not guaranteed for NPBE/NRPBE calculations! 222s 222s ---------------------------------------- 222s CALCULATION #4 (pka-fine): MULTIGRID 222s Setting up problem... 222s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 222s Debye length: 0 A 222s Current memory usage: 251.521 MB total, 493.795 MB high water 222s Using linear spline charge discretization. 222s Grid dimensions: 97 x 97 x 97 222s Grid spacings: 0.250 x 0.250 x 0.250 222s Grid lengths: 24.000 x 24.000 x 24.000 222s Grid center: (24.822, -33.153, 21.545) 222s Multigrid levels: 4 222s Molecule ID: 2 222s Linearized traditional PBE 222s Boundary conditions from focusing 222s 2 ion species (0.000 M ionic strength): 222s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 222s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 222s Solute dielectric: 2.000 222s Solvent dielectric: 78.000 222s Using "molecular" surface definition;harmonic average smoothing 222s Solvent probe radius: 1.400 A 222s Temperature: 298.150 K 222s Electrostatic energies will be calculated 222s Total electrostatic energy = 3.053319953673E+05 kJ/mol 222s Calculating forces... 222s ---------------------------------------- 222s CALCULATION #5 (complex-coarse): MULTIGRID 222s Setting up problem... 222s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 222s Debye length: 0 A 222s Current memory usage: 251.858 MB total, 493.795 MB high water 222s Using linear spline charge discretization. 222s Grid dimensions: 97 x 97 x 97 222s Grid spacings: 0.729 x 0.729 x 0.729 222s Grid lengths: 70.000 x 70.000 x 70.000 222s Grid center: (28.969, -32.507, 27.022) 222s Multigrid levels: 4 222s Molecule ID: 3 222s Linearized traditional PBE 222s Single Debye-Huckel sphere boundary conditions 222s 2 ion species (0.000 M ionic strength): 222s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 222s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 222s Solute dielectric: 2.000 222s Solvent dielectric: 78.000 222s Using "molecular" surface definition;harmonic average smoothing 222s Solvent probe radius: 1.400 A 222s Temperature: 298.150 K 222s Electrostatic energies will be calculated 222s Total electrostatic energy = 1.888027142979E+05 kJ/mol 222s Calculating forces... 222s [focusFillBound()]: WARNING: 222s Unusually large potential values 222s detected on the focusing boundary! 222s Convergence not guaranteed for NPBE/NRPBE calculations! 222s 222s ---------------------------------------- 222s CALCULATION #6 (complex-fine): MULTIGRID 222s Setting up problem... 222s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 222s Debye length: 0 A 222s Current memory usage: 251.858 MB total, 494.601 MB high water 222s Using linear spline charge discretization. 222s Grid dimensions: 97 x 97 x 97 222s Grid spacings: 0.250 x 0.250 x 0.250 222s Grid lengths: 24.000 x 24.000 x 24.000 222s Grid center: (24.822, -33.153, 21.545) 222s Multigrid levels: 4 222s Molecule ID: 3 222s Linearized traditional PBE 222s Boundary conditions from focusing 222s 2 ion species (0.000 M ionic strength): 222s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 222s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 222s Solute dielectric: 2.000 222s Solvent dielectric: 78.000 222s Using "molecular" surface definition;harmonic average smoothing 222s Solvent probe radius: 1.400 A 222s Temperature: 298.150 K 222s Electrostatic energies will be calculated 222s Total electrostatic energy = 3.159690177241E+05 kJ/mol 222s Calculating forces... 222s ---------------------------------------- 222s PRINT STATEMENTS 222s 222s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 222s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 222s Global net ELEC energy = 1.088773280806E+02 kJ/mol 222s ---------------------------------------- 222s CLEANING UP AND SHUTTING DOWN... 222s Destroying force arrays. 222s No energy arrays to destroy. 222s Destroying multigrid structures. 222s Destroying finite element structures. 222s Destroying 3 molecules 222s Final memory usage: 0.001 MB total, 494.601 MB high water 222s 222s 222s Thanks for using APBS! 222s 222s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 222s *** PASSED *** 222s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 222s *** PASSED *** 222s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 222s *** PASSED *** 222s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 222s *** PASSED *** 222s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 222s *** PASSED *** 222s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 222s *** PASSED *** 222s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 222s *** PASSED *** 222s Elapsed time: 4.90818 seconds 222s -------------------------------------------------------------------------------- 222s Total elapsed time: 20.899227 seconds 222s Test results have been logged 222s -------------------------------------------------------------------------------- 222s -------------------------------------------------------------------------------- 222s Testing input file complex-0_1.in 222s 223s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 223s *** PASSED *** 223s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 223s *** PASSED *** 223s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 223s *** PASSED *** 223s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 223s *** PASSED *** 223s Checking for intermediate energies in input file apbs-smol-surf.out 223s EXPECTED COMPUTED: 7 223s EXPECTED EXPECTED: 7 223s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 223s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 223s COMPUTED RESULT 2251.46678942 223s COMPUTED RESULT 10528.14502873 223s COMPUTED RESULT 186407.1689626 223s COMPUTED RESULT 305331.9953673 223s COMPUTED RESULT 188802.7142979 223s COMPUTED RESULT 315969.0177241 223s COMPUTED RESULT 108.8773280806 223s Running tests for point-pmf section 223s BINARY: /usr/bin/apbs 223s INPUT: complex-0_1.in 223s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 223s 223s ---------------------------------------------------------------------- 223s APBS -- Adaptive Poisson-Boltzmann Solver 223s Version APBS 3.4.1 223s 223s Nathan A. Baker (nathan.baker@pnnl.gov) 223s Pacific Northwest National Laboratory 223s 223s Additional contributing authors listed in the code documentation. 223s 223s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 223s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 223s Northwest Division for the U.S. Department of Energy. 223s 223s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 223s Portions Copyright (c) 2002-2020, Nathan A. Baker. 223s Portions Copyright (c) 1999-2002, The Regents of the University of California. 223s Portions Copyright (c) 1995, Michael Holst. 223s All rights reserved. 223s 223s Redistribution and use in source and binary forms, with or without 223s modification, are permitted provided that the following conditions are met: 223s 223s * Redistributions of source code must retain the above copyright notice, this 223s list of conditions and the following disclaimer. 223s 223s * Redistributions in binary form must reproduce the above copyright notice, 223s this list of conditions and the following disclaimer in the documentation 223s and/or other materials provided with the distribution. 223s 223s * Neither the name of the developer nor the names of its contributors may be 223s used to endorse or promote products derived from this software without 223s specific prior written permission. 223s 223s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 223s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 223s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 223s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 223s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 223s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 223s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 223s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 223s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 223s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 223s ---------------------------------------------------------------------- 223s APBS uses FETK (the Finite Element ToolKit) to solve the 223s Poisson-Boltzmann equation numerically. FETK is a portable collection 223s of finite element modeling class libraries developed by the Michael Holst 223s research group and written in an object-oriented form of C. FEtk is 223s designed to solve general coupled systems of nonlinear partial differential 223s equations using adaptive finite element methods, inexact Newton methods, 223s and algebraic multilevel methods. More information about FEtk may be found 223s at . 223s ---------------------------------------------------------------------- 223s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 223s Aqua is a modified form of the Holst group PMG library 223s which has been modified by Patrice Koehl 223s for improved efficiency and 223s memory usage when solving the Poisson-Boltzmann equation. 223s ---------------------------------------------------------------------- 223s Please cite your use of APBS as: 223s 223s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 223s nanosystems: application to microtubules and the ribosome. Proc. 223s Natl. Acad. Sci. USA 98, 10037-10041 2001. 223s 223s 223s This executable compiled on Jan 3 2025 at 11:01:42 223s 223s Parsing input file complex-0_1.in... 223s rank 0 size 1... 223s Parsed input file. 223s Got paths for 3 molecules 223s Reading PQR-format atom data from mol0.pqr. 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 1 atoms 223s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 223s Net charge 1.00e+00 e 223s Reading PQR-format atom data from mol1.pqr. 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 1 atoms 223s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 223s Net charge 1.00e+00 e 223s Reading PQR-format atom data from complex-0_1.pqr. 223s 2 atoms 223s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 223s Net charge 2.00e+00 e 223s Preparing to run 3 PBE calculations. 223s ---------------------------------------- 223s CALCULATION #1 (point1): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.060 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 1 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 9.776035707281E+01 kJ/mol 223s Fixed charge energy = 97.7604 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 96.5336 kJ/mol 223s Per-atom energies: 223s Atom 0: 9.776035707281E+01 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s CALCULATION #2 (point2): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.067 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 2 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 8.975920687031E+01 kJ/mol 223s Fixed charge energy = 89.7592 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 88.6151 kJ/mol 223s Per-atom energies: 223s Atom 0: 8.975920687031E+01 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s CALCULATION #3 (complex): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.067 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 3 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 2.058277719334E+02 kJ/mol 223s Fixed charge energy = 205.828 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 201.106 kJ/mol 223s Per-atom energies: 223s Atom 0: 1.069144350786E+02 kJ/mol 223s Atom 1: 9.891333685475E+01 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s PRINT STATEMENTS 223s 223s print energy 3 (complex) - 1 (point1) - 2 (point2) end 223s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 223s Global net ELEC energy = 1.830820799027E+01 kJ/mol 223s ---------------------------------------- 223s CLEANING UP AND SHUTTING DOWN... 223s Destroying force arrays. 223s No energy arrays to destroy. 223s Destroying multigrid structures. 223s Destroying finite element structures. 223s Destroying 3 molecules 223s Final memory usage: 0.001 MB total, 61.067 MB high water 223s 223s 223s Thanks for using APBS! 223s 223s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 223s *** PASSED *** 223s Elapsed time: 0.360466 seconds 223s -------------------------------------------------------------------------------- 223s -------------------------------------------------------------------------------- 223s Testing input file complex-0_2.in 223s 223s Checking for intermediate energies in input file complex-0_1.out 223s EXPECTED COMPUTED: 13 223s EXPECTED EXPECTED: 13 223s 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] 223s 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'] 223s COMPUTED RESULT 97.76035707281 223s COMPUTED RESULT 89.75920687031 223s COMPUTED RESULT 205.8277719334 223s COMPUTED RESULT 0.0 223s COMPUTED RESULT 0.0 223s COMPUTED RESULT 0.0 223s COMPUTED RESULT 97.7604 223s COMPUTED RESULT 89.7592 223s COMPUTED RESULT 205.828 223s COMPUTED RESULT 96.5336 223s COMPUTED RESULT 88.6151 223s COMPUTED RESULT 201.106 223s COMPUTED RESULT 18.30820799027 223s BINARY: /usr/bin/apbs 223s INPUT: complex-0_2.in 223s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 223s 223s ---------------------------------------------------------------------- 223s APBS -- Adaptive Poisson-Boltzmann Solver 223s Version APBS 3.4.1 223s 223s Nathan A. Baker (nathan.baker@pnnl.gov) 223s Pacific Northwest National Laboratory 223s 223s Additional contributing authors listed in the code documentation. 223s 223s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 223s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 223s Northwest Division for the U.S. Department of Energy. 223s 223s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 223s Portions Copyright (c) 2002-2020, Nathan A. Baker. 223s Portions Copyright (c) 1999-2002, The Regents of the University of California. 223s Portions Copyright (c) 1995, Michael Holst. 223s All rights reserved. 223s 223s Redistribution and use in source and binary forms, with or without 223s modification, are permitted provided that the following conditions are met: 223s 223s * Redistributions of source code must retain the above copyright notice, this 223s list of conditions and the following disclaimer. 223s 223s * Redistributions in binary form must reproduce the above copyright notice, 223s this list of conditions and the following disclaimer in the documentation 223s and/or other materials provided with the distribution. 223s 223s * Neither the name of the developer nor the names of its contributors may be 223s used to endorse or promote products derived from this software without 223s specific prior written permission. 223s 223s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 223s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 223s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 223s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 223s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 223s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 223s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 223s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 223s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 223s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 223s ---------------------------------------------------------------------- 223s APBS uses FETK (the Finite Element ToolKit) to solve the 223s Poisson-Boltzmann equation numerically. FETK is a portable collection 223s of finite element modeling class libraries developed by the Michael Holst 223s research group and written in an object-oriented form of C. FEtk is 223s designed to solve general coupled systems of nonlinear partial differential 223s equations using adaptive finite element methods, inexact Newton methods, 223s and algebraic multilevel methods. More information about FEtk may be found 223s at . 223s ---------------------------------------------------------------------- 223s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 223s Aqua is a modified form of the Holst group PMG library 223s which has been modified by Patrice Koehl 223s for improved efficiency and 223s memory usage when solving the Poisson-Boltzmann equation. 223s ---------------------------------------------------------------------- 223s Please cite your use of APBS as: 223s 223s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 223s nanosystems: application to microtubules and the ribosome. Proc. 223s Natl. Acad. Sci. USA 98, 10037-10041 2001. 223s 223s 223s This executable compiled on Jan 3 2025 at 11:01:42 223s 223s Parsing input file complex-0_2.in... 223s rank 0 size 1... 223s Parsed input file. 223s Got paths for 3 molecules 223s Reading PQR-format atom data from mol0.pqr. 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 1 atoms 223s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 223s Net charge 1.00e+00 e 223s Reading PQR-format atom data from mol2.pqr. 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 1 atoms 223s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 223s Net charge 1.00e+00 e 223s Reading PQR-format atom data from complex-0_2.pqr. 223s 2 atoms 223s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 223s Net charge 2.00e+00 e 223s Preparing to run 3 PBE calculations. 223s ---------------------------------------- 223s CALCULATION #1 (point1): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.060 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 1 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 9.776035707281E+01 kJ/mol 223s Fixed charge energy = 97.7604 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 96.5336 kJ/mol 223s Per-atom energies: 223s Atom 0: 9.776035707281E+01 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s CALCULATION #2 (point2): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.067 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 2 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 1.017611498797E+02 kJ/mol 223s Fixed charge energy = 101.761 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 100.656 kJ/mol 223s Per-atom energies: 223s Atom 0: 1.017611498797E+02 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s CALCULATION #3 (complex): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.068 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 3 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 2.084282010393E+02 kJ/mol 223s Fixed charge energy = 208.428 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 203.83 kJ/mol 223s Per-atom energies: 223s Atom 0: 1.022136878480E+02 kJ/mol 223s Atom 1: 1.062145131913E+02 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s PRINT STATEMENTS 223s 223s print energy 3 (complex) - 1 (point1) - 2 (point2) end 223s Local net energy (PE 0) = 8.906694086750E+00 kJ/mol 223s Global net ELEC energy = 8.906694086750E+00 kJ/mol 223s ---------------------------------------- 223s CLEANING UP AND SHUTTING DOWN... 223s Destroying force arrays. 223s No energy arrays to destroy. 223s Destroying multigrid structures. 223s Destroying finite element structures. 223s Destroying 3 molecules 223s Final memory usage: 0.001 MB total, 61.068 MB high water 223s 223s 223s Thanks for using APBS! 223s 223s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 223s *** PASSED *** 223s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 223s *** PASSED *** 223s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 223s *** PASSED *** 223s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) 223s *** PASSED *** 223s Elapsed time: 0.361631 seconds 223s -------------------------------------------------------------------------------- 223s -------------------------------------------------------------------------------- 223s Testing input file complex-0_3.in 223s 223s Checking for intermediate energies in input file complex-0_2.out 223s EXPECTED COMPUTED: 13 223s EXPECTED EXPECTED: 13 223s COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.90669408675] 223s 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'] 223s COMPUTED RESULT 97.76035707281 223s COMPUTED RESULT 101.7611498797 223s COMPUTED RESULT 208.4282010393 223s COMPUTED RESULT 0.0 223s COMPUTED RESULT 0.0 223s COMPUTED RESULT 0.0 223s COMPUTED RESULT 97.7604 223s COMPUTED RESULT 101.761 223s COMPUTED RESULT 208.428 223s COMPUTED RESULT 96.5336 223s COMPUTED RESULT 100.656 223s COMPUTED RESULT 203.83 223s COMPUTED RESULT 8.90669408675 223s BINARY: /usr/bin/apbs 223s INPUT: complex-0_3.in 223s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 223s 223s ---------------------------------------------------------------------- 223s APBS -- Adaptive Poisson-Boltzmann Solver 223s Version APBS 3.4.1 223s 223s Nathan A. Baker (nathan.baker@pnnl.gov) 223s Pacific Northwest National Laboratory 223s 223s Additional contributing authors listed in the code documentation. 223s 223s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 223s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 223s Northwest Division for the U.S. Department of Energy. 223s 223s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 223s Portions Copyright (c) 2002-2020, Nathan A. Baker. 223s Portions Copyright (c) 1999-2002, The Regents of the University of California. 223s Portions Copyright (c) 1995, Michael Holst. 223s All rights reserved. 223s 223s Redistribution and use in source and binary forms, with or without 223s modification, are permitted provided that the following conditions are met: 223s 223s * Redistributions of source code must retain the above copyright notice, this 223s list of conditions and the following disclaimer. 223s 223s * Redistributions in binary form must reproduce the above copyright notice, 223s this list of conditions and the following disclaimer in the documentation 223s and/or other materials provided with the distribution. 223s 223s * Neither the name of the developer nor the names of its contributors may be 223s used to endorse or promote products derived from this software without 223s specific prior written permission. 223s 223s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 223s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 223s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 223s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 223s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 223s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 223s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 223s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 223s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 223s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 223s ---------------------------------------------------------------------- 223s APBS uses FETK (the Finite Element ToolKit) to solve the 223s Poisson-Boltzmann equation numerically. FETK is a portable collection 223s of finite element modeling class libraries developed by the Michael Holst 223s research group and written in an object-oriented form of C. FEtk is 223s designed to solve general coupled systems of nonlinear partial differential 223s equations using adaptive finite element methods, inexact Newton methods, 223s and algebraic multilevel methods. More information about FEtk may be found 223s at . 223s ---------------------------------------------------------------------- 223s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 223s Aqua is a modified form of the Holst group PMG library 223s which has been modified by Patrice Koehl 223s for improved efficiency and 223s memory usage when solving the Poisson-Boltzmann equation. 223s ---------------------------------------------------------------------- 223s Please cite your use of APBS as: 223s 223s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 223s nanosystems: application to microtubules and the ribosome. Proc. 223s Natl. Acad. Sci. USA 98, 10037-10041 2001. 223s 223s 223s This executable compiled on Jan 3 2025 at 11:01:42 223s 223s Parsing input file complex-0_3.in... 223s rank 0 size 1... 223s Parsed input file. 223s Got paths for 3 molecules 223s Reading PQR-format atom data from mol0.pqr. 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 1 atoms 223s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 223s Net charge 1.00e+00 e 223s Reading PQR-format atom data from mol3.pqr. 223s asc_getToken: Error occurred (bailing out). 223s Vio_scanf: Format problem with input. 223s 1 atoms 223s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 223s Net charge 1.00e+00 e 223s Reading PQR-format atom data from complex-0_3.pqr. 223s 2 atoms 223s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 223s Net charge 2.00e+00 e 223s Preparing to run 3 PBE calculations. 223s ---------------------------------------- 223s CALCULATION #1 (point1): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.060 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 1 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 9.776035707281E+01 kJ/mol 223s Fixed charge energy = 97.7604 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 96.5336 kJ/mol 223s Per-atom energies: 223s Atom 0: 9.776035707281E+01 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s CALCULATION #2 (point2): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.067 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 2 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 1.337661883222E+02 kJ/mol 223s Fixed charge energy = 133.766 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 132.672 kJ/mol 223s Per-atom energies: 223s Atom 0: 1.337661883222E+02 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s CALCULATION #3 (complex): MULTIGRID 223s Setting up problem... 223s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 223s Debye length: 0 A 223s Current memory usage: 61.060 MB total, 61.068 MB high water 223s Using linear spline charge discretization. 223s Grid dimensions: 65 x 65 x 65 223s Grid spacings: 0.210 x 0.210 x 0.210 223s Grid lengths: 13.440 x 13.440 x 13.440 223s Grid center: (0.000, 0.000, 0.000) 223s Multigrid levels: 5 223s Molecule ID: 3 223s Linearized traditional PBE 223s Multiple Debye-Huckel sphere boundary conditions 223s 0 ion species (0.000 M ionic strength): 223s Solute dielectric: 78.540 223s Solvent dielectric: 78.540 223s Using spline-based surface definition;window = 0.300 223s Temperature: 298.150 K 223s Electrostatic energies will be calculated 223s Total electrostatic energy = 2.374361452120E+02 kJ/mol 223s Fixed charge energy = 237.436 kJ/mol 223s Mobile charge energy = 0 kJ/mol 223s Dielectric energy = 232.924 kJ/mol 223s Per-atom energies: 223s Atom 0: 1.007151570480E+02 kJ/mol 223s Atom 1: 1.367209881640E+02 kJ/mol 223s Calculating forces... 223s ---------------------------------------- 223s PRINT STATEMENTS 223s 223s print energy 3 (complex) - 1 (point1) - 2 (point2) end 223s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 223s Global net ELEC energy = 5.909599816984E+00 kJ/mol 223s ---------------------------------------- 223s CLEANING UP AND SHUTTING DOWN... 223s Destroying force arrays. 223s No energy arrays to destroy. 223s Destroying multigrid structures. 223s Destroying finite element structures. 223s Destroying 3 molecules 223s Final memory usage: 0.001 MB total, 61.068 MB high water 223s 223s 223s Thanks for using APBS! 223s 223s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 223s *** PASSED *** 223s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 223s *** PASSED *** 223s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 223s *** PASSED *** 223s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 223s *** PASSED *** 223s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 223s *** PASSED *** 223s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 223s *** PASSED *** 223s Elapsed time: 0.349215 seconds 223s -------------------------------------------------------------------------------- 223s -------------------------------------------------------------------------------- 223s Testing input file complex-0_4.in 223s 224s Checking for intermediate energies in input file complex-0_3.out 224s EXPECTED COMPUTED: 13 224s EXPECTED EXPECTED: 13 224s 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] 224s 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'] 224s COMPUTED RESULT 97.76035707281 224s COMPUTED RESULT 133.7661883222 224s COMPUTED RESULT 237.436145212 224s COMPUTED RESULT 0.0 224s COMPUTED RESULT 0.0 224s COMPUTED RESULT 0.0 224s COMPUTED RESULT 97.7604 224s COMPUTED RESULT 133.766 224s COMPUTED RESULT 237.436 224s COMPUTED RESULT 96.5336 224s COMPUTED RESULT 132.672 224s COMPUTED RESULT 232.924 224s COMPUTED RESULT 5.909599816984 224s BINARY: /usr/bin/apbs 224s INPUT: complex-0_4.in 224s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 224s asc_getToken: Error occurred (bailing out). 224s Vio_scanf: Format problem with input. 224s 224s 224s ---------------------------------------------------------------------- 224s APBS -- Adaptive Poisson-Boltzmann Solver 224s Version APBS 3.4.1 224s 224s Nathan A. Baker (nathan.baker@pnnl.gov) 224s Pacific Northwest National Laboratory 224s 224s Additional contributing authors listed in the code documentation. 224s 224s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 224s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 224s Northwest Division for the U.S. Department of Energy. 224s 224s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 224s Portions Copyright (c) 2002-2020, Nathan A. Baker. 224s Portions Copyright (c) 1999-2002, The Regents of the University of California. 224s Portions Copyright (c) 1995, Michael Holst. 224s All rights reserved. 224s 224s Redistribution and use in source and binary forms, with or without 224s modification, are permitted provided that the following conditions are met: 224s 224s * Redistributions of source code must retain the above copyright notice, this 224s list of conditions and the following disclaimer. 224s 224s * Redistributions in binary form must reproduce the above copyright notice, 224s this list of conditions and the following disclaimer in the documentation 224s and/or other materials provided with the distribution. 224s 224s * Neither the name of the developer nor the names of its contributors may be 224s used to endorse or promote products derived from this software without 224s specific prior written permission. 224s 224s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 224s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 224s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 224s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 224s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 224s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 224s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 224s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 224s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 224s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 224s ---------------------------------------------------------------------- 224s APBS uses FETK (the Finite Element ToolKit) to solve the 224s Poisson-Boltzmann equation numerically. FETK is a portable collection 224s of finite element modeling class libraries developed by the Michael Holst 224s research group and written in an object-oriented form of C. FEtk is 224s designed to solve general coupled systems of nonlinear partial differential 224s equations using adaptive finite element methods, inexact Newton methods, 224s and algebraic multilevel methods. More information about FEtk may be found 224s at . 224s ---------------------------------------------------------------------- 224s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 224s Aqua is a modified form of the Holst group PMG library 224s which has been modified by Patrice Koehl 224s for improved efficiency and 224s memory usage when solving the Poisson-Boltzmann equation. 224s ---------------------------------------------------------------------- 224s Please cite your use of APBS as: 224s 224s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 224s nanosystems: application to microtubules and the ribosome. Proc. 224s Natl. Acad. Sci. USA 98, 10037-10041 2001. 224s 224s 224s This executable compiled on Jan 3 2025 at 11:01:42 224s 224s Parsing input file complex-0_4.in... 224s rank 0 size 1... 224s Parsed input file. 224s Got paths for 3 molecules 224s Reading PQR-format atom data from mol0.pqr. 224s asc_getToken: Error occurred (bailing out). 224s Vio_scanf: Format problem with input. 224s 1 atoms 224s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 224s Net charge 1.00e+00 e 224s Reading PQR-format atom data from mol4.pqr. 224s asc_getToken: Error occurred (bailing out). 224s Vio_scanf: Format problem with input. 224s 1 atoms 224s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 224s Net charge 1.00e+00 e 224s Reading PQR-format atom data from complex-0_4.pqr. 224s 2 atoms 224s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 224s Net charge 2.00e+00 e 224s Preparing to run 3 PBE calculations. 224s ---------------------------------------- 224s CALCULATION #1 (point1): MULTIGRID 224s Setting up problem... 224s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 224s Debye length: 0 A 224s Current memory usage: 61.060 MB total, 61.060 MB high water 224s Using linear spline charge discretization. 224s Grid dimensions: 65 x 65 x 65 224s Grid spacings: 0.210 x 0.210 x 0.210 224s Grid lengths: 13.440 x 13.440 x 13.440 224s Grid center: (0.000, 0.000, 0.000) 224s Multigrid levels: 5 224s Molecule ID: 1 224s Linearized traditional PBE 224s Multiple Debye-Huckel sphere boundary conditions 224s 0 ion species (0.000 M ionic strength): 224s Solute dielectric: 78.540 224s Solvent dielectric: 78.540 224s Using spline-based surface definition;window = 0.300 224s Temperature: 298.150 K 224s Electrostatic energies will be calculated 224s Total electrostatic energy = 9.776035707281E+01 kJ/mol 224s Fixed charge energy = 97.7604 kJ/mol 224s Mobile charge energy = 0 kJ/mol 224s Dielectric energy = 96.5336 kJ/mol 224s Per-atom energies: 224s Atom 0: 9.776035707281E+01 kJ/mol 224s Calculating forces... 224s ---------------------------------------- 224s CALCULATION #2 (point2): MULTIGRID 224s Setting up problem... 224s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 224s Debye length: 0 A 224s Current memory usage: 61.060 MB total, 61.067 MB high water 224s Using linear spline charge discretization. 224s Grid dimensions: 65 x 65 x 65 224s Grid spacings: 0.210 x 0.210 x 0.210 224s Grid lengths: 13.440 x 13.440 x 13.440 224s Grid center: (0.000, 0.000, 0.000) 224s Multigrid levels: 5 224s Molecule ID: 2 224s Linearized traditional PBE 224s Multiple Debye-Huckel sphere boundary conditions 224s 0 ion species (0.000 M ionic strength): 224s Solute dielectric: 78.540 224s Solvent dielectric: 78.540 224s Using spline-based surface definition;window = 0.300 224s Temperature: 298.150 K 224s Electrostatic energies will be calculated 224s Total electrostatic energy = 1.017611498797E+02 kJ/mol 224s Fixed charge energy = 101.761 kJ/mol 224s Mobile charge energy = 0 kJ/mol 224s Dielectric energy = 100.654 kJ/mol 224s Per-atom energies: 224s Atom 0: 1.017611498797E+02 kJ/mol 224s Calculating forces... 224s ---------------------------------------- 224s CALCULATION #3 (complex): MULTIGRID 224s Setting up problem... 224s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 224s Debye length: 0 A 224s Current memory usage: 61.061 MB total, 61.068 MB high water 224s Using linear spline charge discretization. 224s Grid dimensions: 65 x 65 x 65 224s Grid spacings: 0.210 x 0.210 x 0.210 224s Grid lengths: 13.440 x 13.440 x 13.440 224s Grid center: (0.000, 0.000, 0.000) 224s Multigrid levels: 5 224s Molecule ID: 3 224s Linearized traditional PBE 224s Multiple Debye-Huckel sphere boundary conditions 224s 0 ion species (0.000 M ionic strength): 224s Solute dielectric: 78.540 224s Solvent dielectric: 78.540 224s Using spline-based surface definition;window = 0.300 224s Temperature: 298.150 K 224s Electrostatic energies will be calculated 224s Total electrostatic energy = 2.039516519000E+02 kJ/mol 224s Fixed charge energy = 203.952 kJ/mol 224s Mobile charge energy = 0 kJ/mol 224s Dielectric energy = 199.493 kJ/mol 224s Per-atom energies: 224s Atom 0: 9.997541697022E+01 kJ/mol 224s Atom 1: 1.039762349297E+02 kJ/mol 224s Calculating forces... 224s ---------------------------------------- 224s PRINT STATEMENTS 224s 224s print energy 3 (complex) - 1 (point1) - 2 (point2) end 224s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 224s Global net ELEC energy = 4.430144947418E+00 kJ/mol 224s ---------------------------------------- 224s CLEANING UP AND SHUTTING DOWN... 224s Destroying force arrays. 224s No energy arrays to destroy. 224s Destroying multigrid structures. 224s Destroying finite element structures. 224s Destroying 3 molecules 224s Final memory usage: 0.001 MB total, 61.068 MB high water 224s 224s 224s Thanks for using APBS! 224s 224s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 224s *** PASSED *** 224s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 224s *** PASSED *** 224s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 224s *** PASSED *** 224s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 224s *** PASSED *** 224s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 224s *** PASSED *** 224s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 224s *** PASSED *** 224s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 224s *** PASSED *** 224s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 224s *** PASSED *** 224s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 224s *** PASSED *** 224s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 224s *** PASSED *** 224s Elapsed time: 0.34797 seconds 224s -------------------------------------------------------------------------------- 224s Total elapsed time: 1.419282 seconds 224s Test results have been logged 224s -------------------------------------------------------------------------------- 224s -------------------------------------------------------------------------------- 224s Testing input file apbs-mol.in 224s 224s Checking for intermediate energies in input file complex-0_4.out 224s EXPECTED COMPUTED: 13 224s EXPECTED EXPECTED: 13 224s 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] 224s 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'] 224s COMPUTED RESULT 97.76035707281 224s COMPUTED RESULT 101.7611498797 224s COMPUTED RESULT 203.9516519 224s COMPUTED RESULT 0.0 224s COMPUTED RESULT 0.0 224s COMPUTED RESULT 0.0 224s COMPUTED RESULT 97.7604 224s COMPUTED RESULT 101.761 224s COMPUTED RESULT 203.952 224s COMPUTED RESULT 96.5336 224s COMPUTED RESULT 100.654 224s COMPUTED RESULT 199.493 224s COMPUTED RESULT 4.430144947418 224s Running tests for solv section 224s BINARY: /usr/bin/apbs 224s INPUT: apbs-mol.in 224s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 224s asc_getToken: Error occurred (bailing out). 224s Vio_scanf: Format problem with input. 224s 224s 224s ---------------------------------------------------------------------- 224s APBS -- Adaptive Poisson-Boltzmann Solver 224s Version APBS 3.4.1 224s 224s Nathan A. Baker (nathan.baker@pnnl.gov) 224s Pacific Northwest National Laboratory 224s 224s Additional contributing authors listed in the code documentation. 224s 224s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 224s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 224s Northwest Division for the U.S. Department of Energy. 224s 224s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 224s Portions Copyright (c) 2002-2020, Nathan A. Baker. 224s Portions Copyright (c) 1999-2002, The Regents of the University of California. 224s Portions Copyright (c) 1995, Michael Holst. 224s All rights reserved. 224s 224s Redistribution and use in source and binary forms, with or without 224s modification, are permitted provided that the following conditions are met: 224s 224s * Redistributions of source code must retain the above copyright notice, this 224s list of conditions and the following disclaimer. 224s 224s * Redistributions in binary form must reproduce the above copyright notice, 224s this list of conditions and the following disclaimer in the documentation 224s and/or other materials provided with the distribution. 224s 224s * Neither the name of the developer nor the names of its contributors may be 224s used to endorse or promote products derived from this software without 224s specific prior written permission. 224s 224s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 224s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 224s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 224s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 224s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 224s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 224s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 224s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 224s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 224s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 224s ---------------------------------------------------------------------- 224s APBS uses FETK (the Finite Element ToolKit) to solve the 224s Poisson-Boltzmann equation numerically. FETK is a portable collection 224s of finite element modeling class libraries developed by the Michael Holst 224s research group and written in an object-oriented form of C. FEtk is 224s designed to solve general coupled systems of nonlinear partial differential 224s equations using adaptive finite element methods, inexact Newton methods, 224s and algebraic multilevel methods. More information about FEtk may be found 224s at . 224s ---------------------------------------------------------------------- 224s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 224s Aqua is a modified form of the Holst group PMG library 224s which has been modified by Patrice Koehl 224s for improved efficiency and 224s memory usage when solving the Poisson-Boltzmann equation. 224s ---------------------------------------------------------------------- 224s Please cite your use of APBS as: 224s 224s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 224s nanosystems: application to microtubules and the ribosome. Proc. 224s Natl. Acad. Sci. USA 98, 10037-10041 2001. 224s 224s 224s This executable compiled on Jan 3 2025 at 11:01:42 224s 224s Parsing input file apbs-mol.in... 224s rank 0 size 1... 224s Parsed input file. 224s Got paths for 2 molecules 224s Reading PQR-format atom data from methanol.pqr. 224s asc_getToken: Error occurred (bailing out). 224s Vio_scanf: Format problem with input. 224s 3 atoms 224s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 224s Net charge 5.55e-17 e 224s Reading PQR-format atom data from methoxide.pqr. 224s 2 atoms 224s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 224s Net charge -1.00e+00 e 224s Preparing to run 4 PBE calculations. 224s ---------------------------------------- 224s CALCULATION #1 (methanol-solv): MULTIGRID 224s Setting up problem... 224s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 224s Debye length: 0 A 224s Current memory usage: 61.253 MB total, 61.253 MB high water 224s Using linear spline charge discretization. 224s Grid dimensions: 65 x 65 x 65 224s Grid spacings: 0.250 x 0.250 x 0.250 224s Grid lengths: 16.000 x 16.000 x 16.000 224s Grid center: (0.309, 0.000, -0.242) 224s Multigrid levels: 5 224s Molecule ID: 1 224s Linearized traditional PBE 224s Multiple Debye-Huckel sphere boundary conditions 224s 2 ion species (0.000 M ionic strength): 224s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 224s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 224s Solute dielectric: 2.000 224s Solvent dielectric: 78.000 224s Using "molecular" surface definition; no smoothing 224s Solvent probe radius: 0.000 A 224s Temperature: 300.000 K 224s Electrostatic energies will be calculated 224s Total electrostatic energy = 1.847663548071E+03 kJ/mol 224s Calculating forces... 224s ---------------------------------------- 224s CALCULATION #2 (methanol-ref): MULTIGRID 224s Setting up problem... 224s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 224s Debye length: 0 A 224s Current memory usage: 61.253 MB total, 61.328 MB high water 224s Using linear spline charge discretization. 224s Grid dimensions: 65 x 65 x 65 224s Grid spacings: 0.250 x 0.250 x 0.250 224s Grid lengths: 16.000 x 16.000 x 16.000 224s Grid center: (0.309, 0.000, -0.242) 224s Multigrid levels: 5 224s Molecule ID: 1 224s Linearized traditional PBE 224s Multiple Debye-Huckel sphere boundary conditions 224s 2 ion species (0.000 M ionic strength): 224s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 224s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 224s Solute dielectric: 2.000 224s Solvent dielectric: 1.000 224s Using "molecular" surface definition; no smoothing 224s Solvent probe radius: 0.000 A 224s Temperature: 300.000 K 224s Electrostatic energies will be calculated 224s Total electrostatic energy = 1.883912182952E+03 kJ/mol 224s Calculating forces... 224s ---------------------------------------- 224s CALCULATION #3 (methoxide-solv): MULTIGRID 224s Setting up problem... 224s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 224s Debye length: 0 A 224s Current memory usage: 61.250 MB total, 61.328 MB high water 224s Using linear spline charge discretization. 224s Grid dimensions: 65 x 65 x 65 224s Grid spacings: 0.250 x 0.250 x 0.250 224s Grid lengths: 16.000 x 16.000 x 16.000 224s Grid center: (0.000, 0.000, -0.128) 224s Multigrid levels: 5 224s Molecule ID: 2 224s Linearized traditional PBE 224s Multiple Debye-Huckel sphere boundary conditions 224s 2 ion species (0.000 M ionic strength): 224s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 224s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 224s Solute dielectric: 2.000 224s Solvent dielectric: 78.000 224s Using "molecular" surface definition; no smoothing 224s Solvent probe radius: 0.000 A 224s Temperature: 300.000 K 224s Electrostatic energies will be calculated 224s Total electrostatic energy = 2.732623683321E+03 kJ/mol 224s Calculating forces... 224s ---------------------------------------- 224s CALCULATION #4 (methoxide-ref): MULTIGRID 224s Setting up problem... 224s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 224s Debye length: 0 A 224s Current memory usage: 61.250 MB total, 61.328 MB high water 224s Using linear spline charge discretization. 224s Grid dimensions: 65 x 65 x 65 224s Grid spacings: 0.250 x 0.250 x 0.250 224s Grid lengths: 16.000 x 16.000 x 16.000 224s Grid center: (0.000, 0.000, -0.128) 224s Multigrid levels: 5 224s Molecule ID: 2 224s Linearized traditional PBE 224s Multiple Debye-Huckel sphere boundary conditions 224s 2 ion species (0.000 M ionic strength): 224s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 224s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 224s Solute dielectric: 2.000 224s Solvent dielectric: 1.000 224s Using "molecular" surface definition; no smoothing 224s Solvent probe radius: 0.000 A 224s Temperature: 300.000 K 224s Electrostatic energies will be calculated 224s Total electrostatic energy = 3.123035854133E+03 kJ/mol 224s Calculating forces... 224s ---------------------------------------- 224s PRINT STATEMENTS 224s 224s print energy 1 (methanol-solv) - 2 (methanol-ref) end 224s Local net energy (PE 0) = -3.624863488074E+01 kJ/mol 224s Global net ELEC energy = -3.624863488074E+01 kJ/mol 224s 224s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 224s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 224s Global net ELEC energy = -3.904121708125E+02 kJ/mol 224s 224s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 224s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 224s Global net ELEC energy = -3.541635359318E+02 kJ/mol 224s ---------------------------------------- 224s CLEANING UP AND SHUTTING DOWN... 224s Destroying force arrays. 224s No energy arrays to destroy. 224s Destroying multigrid structures. 224s Destroying finite element structures. 224s Destroying 2 molecules 224s Final memory usage: 0.001 MB total, 61.328 MB high water 224s 224s 224s Thanks for using APBS! 224s 224s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 224s *** PASSED *** 224s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 224s *** PASSED *** 224s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 224s *** PASSED *** 224s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 224s *** PASSED *** 224s Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) 224s *** PASSED *** 224s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 224s *** PASSED *** 224s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 224s *** PASSED *** 224s Elapsed time: 0.440953 seconds 224s -------------------------------------------------------------------------------- 224s -------------------------------------------------------------------------------- 224s Testing input file apbs-smol.in 224s 225s Checking for intermediate energies in input file apbs-mol.out 225s EXPECTED COMPUTED: 7 225s EXPECTED EXPECTED: 7 225s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] 225s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 225s COMPUTED RESULT 1847.663548071 225s COMPUTED RESULT 1883.912182952 225s COMPUTED RESULT 2732.623683321 225s COMPUTED RESULT 3123.035854133 225s COMPUTED RESULT -36.24863488074 225s COMPUTED RESULT -390.4121708125 225s COMPUTED RESULT -354.1635359318 225s BINARY: /usr/bin/apbs 225s INPUT: apbs-smol.in 225s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 225s asc_getToken: Error occurred (bailing out). 225s Vio_scanf: Format problem with input. 225s 225s 225s ---------------------------------------------------------------------- 225s APBS -- Adaptive Poisson-Boltzmann Solver 225s Version APBS 3.4.1 225s 225s Nathan A. Baker (nathan.baker@pnnl.gov) 225s Pacific Northwest National Laboratory 225s 225s Additional contributing authors listed in the code documentation. 225s 225s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 225s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 225s Northwest Division for the U.S. Department of Energy. 225s 225s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 225s Portions Copyright (c) 2002-2020, Nathan A. Baker. 225s Portions Copyright (c) 1999-2002, The Regents of the University of California. 225s Portions Copyright (c) 1995, Michael Holst. 225s All rights reserved. 225s 225s Redistribution and use in source and binary forms, with or without 225s modification, are permitted provided that the following conditions are met: 225s 225s * Redistributions of source code must retain the above copyright notice, this 225s list of conditions and the following disclaimer. 225s 225s * Redistributions in binary form must reproduce the above copyright notice, 225s this list of conditions and the following disclaimer in the documentation 225s and/or other materials provided with the distribution. 225s 225s * Neither the name of the developer nor the names of its contributors may be 225s used to endorse or promote products derived from this software without 225s specific prior written permission. 225s 225s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 225s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 225s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 225s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 225s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 225s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 225s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 225s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 225s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 225s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 225s ---------------------------------------------------------------------- 225s APBS uses FETK (the Finite Element ToolKit) to solve the 225s Poisson-Boltzmann equation numerically. FETK is a portable collection 225s of finite element modeling class libraries developed by the Michael Holst 225s research group and written in an object-oriented form of C. FEtk is 225s designed to solve general coupled systems of nonlinear partial differential 225s equations using adaptive finite element methods, inexact Newton methods, 225s and algebraic multilevel methods. More information about FEtk may be found 225s at . 225s ---------------------------------------------------------------------- 225s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 225s Aqua is a modified form of the Holst group PMG library 225s which has been modified by Patrice Koehl 225s for improved efficiency and 225s memory usage when solving the Poisson-Boltzmann equation. 225s ---------------------------------------------------------------------- 225s Please cite your use of APBS as: 225s 225s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 225s nanosystems: application to microtubules and the ribosome. Proc. 225s Natl. Acad. Sci. USA 98, 10037-10041 2001. 225s 225s 225s This executable compiled on Jan 3 2025 at 11:01:42 225s 225s Parsing input file apbs-smol.in... 225s rank 0 size 1... 225s Parsed input file. 225s Got paths for 2 molecules 225s Reading PQR-format atom data from methanol.pqr. 225s asc_getToken: Error occurred (bailing out). 225s Vio_scanf: Format problem with input. 225s 3 atoms 225s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 225s Net charge 5.55e-17 e 225s Reading PQR-format atom data from methoxide.pqr. 225s 2 atoms 225s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 225s Net charge -1.00e+00 e 225s Preparing to run 4 PBE calculations. 225s ---------------------------------------- 225s CALCULATION #1 (methanol-solv): MULTIGRID 225s Setting up problem... 225s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 225s Debye length: 0 A 225s Current memory usage: 61.253 MB total, 61.253 MB high water 225s Using linear spline charge discretization. 225s Grid dimensions: 65 x 65 x 65 225s Grid spacings: 0.250 x 0.250 x 0.250 225s Grid lengths: 16.000 x 16.000 x 16.000 225s Grid center: (0.309, 0.000, -0.242) 225s Multigrid levels: 5 225s Molecule ID: 1 225s Linearized traditional PBE 225s Multiple Debye-Huckel sphere boundary conditions 225s 2 ion species (0.000 M ionic strength): 225s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 225s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 225s Solute dielectric: 2.000 225s Solvent dielectric: 78.000 225s Using "molecular" surface definition;harmonic average smoothing 225s Solvent probe radius: 0.000 A 225s Temperature: 300.000 K 225s Electrostatic energies will be calculated 225s Total electrostatic energy = 1.847860440020E+03 kJ/mol 225s Calculating forces... 225s ---------------------------------------- 225s CALCULATION #2 (methanol-ref): MULTIGRID 225s Setting up problem... 225s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 225s Debye length: 0 A 225s Current memory usage: 61.253 MB total, 61.328 MB high water 225s Using linear spline charge discretization. 225s Grid dimensions: 65 x 65 x 65 225s Grid spacings: 0.250 x 0.250 x 0.250 225s Grid lengths: 16.000 x 16.000 x 16.000 225s Grid center: (0.309, 0.000, -0.242) 225s Multigrid levels: 5 225s Molecule ID: 1 225s Linearized traditional PBE 225s Multiple Debye-Huckel sphere boundary conditions 225s 2 ion species (0.000 M ionic strength): 225s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 225s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 225s Solute dielectric: 2.000 225s Solvent dielectric: 1.000 225s Using "molecular" surface definition;harmonic average smoothing 225s Solvent probe radius: 0.000 A 225s Temperature: 300.000 K 225s Electrostatic energies will be calculated 225s Total electrostatic energy = 1.885436377745E+03 kJ/mol 225s Calculating forces... 225s ---------------------------------------- 225s CALCULATION #3 (methoxide-solv): MULTIGRID 225s Setting up problem... 225s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 225s Debye length: 0 A 225s Current memory usage: 61.250 MB total, 61.328 MB high water 225s Using linear spline charge discretization. 225s Grid dimensions: 65 x 65 x 65 225s Grid spacings: 0.250 x 0.250 x 0.250 225s Grid lengths: 16.000 x 16.000 x 16.000 225s Grid center: (0.000, 0.000, -0.128) 225s Multigrid levels: 5 225s Molecule ID: 2 225s Linearized traditional PBE 225s Multiple Debye-Huckel sphere boundary conditions 225s 2 ion species (0.000 M ionic strength): 225s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 225s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 225s Solute dielectric: 2.000 225s Solvent dielectric: 78.000 225s Using "molecular" surface definition;harmonic average smoothing 225s Solvent probe radius: 0.000 A 225s Temperature: 300.000 K 225s Electrostatic energies will be calculated 225s Total electrostatic energy = 2.734040568569E+03 kJ/mol 225s Calculating forces... 225s ---------------------------------------- 225s CALCULATION #4 (methoxide-ref): MULTIGRID 225s Setting up problem... 225s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 225s Debye length: 0 A 225s Current memory usage: 61.250 MB total, 61.328 MB high water 225s Using linear spline charge discretization. 225s Grid dimensions: 65 x 65 x 65 225s Grid spacings: 0.250 x 0.250 x 0.250 225s Grid lengths: 16.000 x 16.000 x 16.000 225s Grid center: (0.000, 0.000, -0.128) 225s Multigrid levels: 5 225s Molecule ID: 2 225s Linearized traditional PBE 225s Multiple Debye-Huckel sphere boundary conditions 225s 2 ion species (0.000 M ionic strength): 225s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 225s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 225s Solute dielectric: 2.000 225s Solvent dielectric: 1.000 225s Using "molecular" surface definition;harmonic average smoothing 225s Solvent probe radius: 0.000 A 225s Temperature: 300.000 K 225s Electrostatic energies will be calculated 225s Total electrostatic energy = 3.125279428954E+03 kJ/mol 225s Calculating forces... 225s ---------------------------------------- 225s PRINT STATEMENTS 225s 225s print energy 1 (methanol-solv) - 2 (methanol-ref) end 225s Local net energy (PE 0) = -3.757593772493E+01 kJ/mol 225s Global net ELEC energy = -3.757593772493E+01 kJ/mol 225s 225s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 225s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 225s Global net ELEC energy = -3.912388603848E+02 kJ/mol 225s 225s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 225s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 225s Global net ELEC energy = -3.536629226599E+02 kJ/mol 225s ---------------------------------------- 225s CLEANING UP AND SHUTTING DOWN... 225s Destroying force arrays. 225s No energy arrays to destroy. 225s Destroying multigrid structures. 225s Destroying finite element structures. 225s Destroying 2 molecules 225s Final memory usage: 0.001 MB total, 61.328 MB high water 225s 225s 225s Thanks for using APBS! 225s 225s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 225s *** PASSED *** 225s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 225s *** PASSED *** 225s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 225s *** PASSED *** 225s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 225s *** PASSED *** 225s Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) 225s *** PASSED *** 225s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 225s *** PASSED *** 225s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 225s *** PASSED *** 225s Elapsed time: 0.44992 seconds 225s -------------------------------------------------------------------------------- 225s Total elapsed time: 0.890873 seconds 225s Test results have been logged 225s -------------------------------------------------------------------------------- 225s Checking for intermediate energies in input file apbs-smol.out 225s EXPECTED COMPUTED: 7 225s EXPECTED EXPECTED: 7 225s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] 225s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 225s COMPUTED RESULT 1847.86044002 225s COMPUTED RESULT 1885.436377745 225s COMPUTED RESULT 2734.040568569 225s COMPUTED RESULT 3125.279428954 225s COMPUTED RESULT -37.57593772493 225s COMPUTED RESULT -391.2388603848 225s COMPUTED RESULT -353.6629226599 225s autopkgtest [15:23:28]: test test-apbs: -----------------------] 225s autopkgtest [15:23:28]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 225s test-apbs PASS 226s autopkgtest [15:23:29]: @@@@@@@@@@@@@@@@@@@@ summary 226s test-apbs PASS