0s autopkgtest [06:44:20]: starting date and time: 2025-10-21 06:44:20+0000 0s autopkgtest [06:44:20]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [06:44:20]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.etvw04_v/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:node-jquery --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-5.secgroup --name adt-resolute-amd64-apbs-20251021-064419-juju-7f2275-prod-proposed-migration-environment-15-0cb33e81-5bc9-4279-bfd2-030bf6e51e65 --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-20251021-064419-juju-7f2275-prod-proposed-migration-environment-15-0cb33e81-5bc9-4279-bfd2-030bf6e51e65 from image adt/ubuntu-resolute-amd64-server-20251020.img (UUID 058eb65a-2f1f-4603-be3f-91b3fbc0088c)... 29s autopkgtest [06:44:49]: testbed dpkg architecture: amd64 29s autopkgtest [06:44:49]: testbed apt version: 3.1.8ubuntu1 29s autopkgtest [06:44:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [06:44:49]: testbed release detected to be: None 30s autopkgtest [06:44:50]: updating testbed package index (apt update) 30s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 30s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 30s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 30s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 30s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [67.3 kB] 30s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [585 kB] 31s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 31s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 31s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [135 kB] 31s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [82.5 kB] 31s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 31s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 31s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [142 kB] 31s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [404 kB] 31s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3156 B] 31s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [6744 B] 31s Fetched 1560 kB in 1s (1642 kB/s) 31s Reading package lists... 32s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 32s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 32s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 32s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 33s Reading package lists... 33s Reading package lists... 33s Building dependency tree... 33s Reading state information... 33s Calculating upgrade... 33s The following packages will be upgraded: 33s libbrotli1 libjson-c5 python3-dbus python3-inflect python3-markupsafe 33s python3-oauthlib python3-zipp 33s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 33s Need to get 642 kB of archives. 33s After this operation, 236 kB of additional disk space will be used. 33s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libjson-c5 amd64 0.18+ds-1.1 [37.7 kB] 33s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dbus amd64 1.4.0-1build1 [118 kB] 33s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libbrotli1 amd64 1.1.0-2build6 [334 kB] 33s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-inflect all 7.5.0-1 [33.9 kB] 33s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markupsafe amd64 2.1.5-1build5 [13.8 kB] 33s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-oauthlib all 3.3.1-1 [93.5 kB] 33s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-zipp all 3.23.0-1 [10.4 kB] 33s dpkg-preconfigure: unable to re-open stdin: No such file or directory 33s Fetched 642 kB in 0s (62.7 MB/s) 33s (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 ... 78444 files and directories currently installed.) 33s Preparing to unpack .../0-libjson-c5_0.18+ds-1.1_amd64.deb ... 33s Unpacking libjson-c5:amd64 (0.18+ds-1.1) over (0.18+ds-1) ... 33s Preparing to unpack .../1-python3-dbus_1.4.0-1build1_amd64.deb ... 33s Unpacking python3-dbus (1.4.0-1build1) over (1.4.0-1) ... 34s Preparing to unpack .../2-libbrotli1_1.1.0-2build6_amd64.deb ... 34s Unpacking libbrotli1:amd64 (1.1.0-2build6) over (1.1.0-2build5) ... 34s Preparing to unpack .../3-python3-inflect_7.5.0-1_all.deb ... 34s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 34s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build5_amd64.deb ... 34s Unpacking python3-markupsafe (2.1.5-1build5) over (2.1.5-1build4) ... 34s Preparing to unpack .../5-python3-oauthlib_3.3.1-1_all.deb ... 34s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 34s Preparing to unpack .../6-python3-zipp_3.23.0-1_all.deb ... 34s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 34s Setting up python3-dbus (1.4.0-1build1) ... 34s Setting up libbrotli1:amd64 (1.1.0-2build6) ... 34s Setting up python3-zipp (3.23.0-1) ... 34s Setting up python3-markupsafe (2.1.5-1build5) ... 34s Setting up python3-inflect (7.5.0-1) ... 34s Setting up python3-oauthlib (3.3.1-1) ... 34s Setting up libjson-c5:amd64 (0.18+ds-1.1) ... 34s Processing triggers for libc-bin (2.42-0ubuntu3) ... 34s autopkgtest [06:44:54]: upgrading testbed (apt dist-upgrade and autopurge) 34s Reading package lists... 35s Building dependency tree... 35s Reading state information... 35s Calculating upgrade... 35s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 35s Reading package lists... 35s Building dependency tree... 35s Reading state information... 35s Solving dependencies... 35s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 37s autopkgtest [06:44:57]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 37s autopkgtest [06:44:57]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 51s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 51s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 51s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 51s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 51s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 51s gpgv: Can't check signature: No public key 51s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 52s autopkgtest [06:45:12]: testing package apbs version 3.4.1-6build2 57s autopkgtest [06:45:17]: build not needed 66s autopkgtest [06:45:26]: test test-apbs: preparing testbed 66s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s The following NEW packages will be installed: 67s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax 67s libamd-comgr2 libamd3 libamdhip64-5 libapbs-dev libapbs3t64 libarpack2t64 67s libblas3 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdrm-amdgpu1 67s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfetk-dev 67s libfetk1.9t64 libgfortran5 libgomp1 libhsa-runtime64-1 libhsakmt1 67s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libjs-jquery libjs-mathjax 67s libjs-sphinxdoc libjs-underscore liblapack3 libllvm17t64 libmaloc-dev 67s libmaloc1 libopenmpi40 libpciaccess0 libpsm2-2 librdmacm1t64 libspqr4 67s libsuitesparseconfig7 libsuperlu7 libucx0 libumfpack6 libxnvctrl0 libze1 67s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 67s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 85.7 MB of archives. 67s After this operation, 351 MB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1 [2781 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 apbs-data all 3.4.1-6build2 [1769 kB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmaloc1 amd64 1.5-2 [90.9 kB] 67s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 67s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsuperlu7 amd64 7.0.1+dfsg1-2 [186 kB] 67s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 67s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.10.1+dfsg-1 [21.6 kB] 67s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.10.1+dfsg-1 [35.5 kB] 67s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcamd3 amd64 1:7.10.1+dfsg-1 [32.0 kB] 67s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 libccolamd3 amd64 1:7.10.1+dfsg-1 [34.1 kB] 67s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.10.1+dfsg-1 [27.2 kB] 67s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 68s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 68s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcholmod5 amd64 1:7.10.1+dfsg-1 [691 kB] 68s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 libumfpack6 amd64 1:7.10.1+dfsg-1 [290 kB] 68s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfetk1.9t64 amd64 3.4.1-6build2 [608 kB] 68s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapbs3t64 amd64 3.4.1-6build2 [271 kB] 68s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 68s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 68s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 libarpack2t64 amd64 3.9.1-6 [108 kB] 68s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build1 [98.8 kB] 68s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10build1 [8360 B] 68s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 68s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 librdmacm1t64 amd64 56.1-1ubuntu1 [71.4 kB] 68s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfabric1 amd64 2.1.0-1.1 [697 kB] 68s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc15 amd64 2.12.2-1 [181 kB] 68s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libllvm17t64 amd64 1:17.0.6-22build1 [25.9 MB] 69s Get:28 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build3 [14.3 MB] 69s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.125-1 [21.6 kB] 69s Get:30 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsakmt1 amd64 6.2.4+ds-1 [66.8 kB] 69s Get:31 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsa-runtime64-1 amd64 6.1.2-3 [564 kB] 69s Get:32 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamdhip64-5 amd64 5.7.1-6 [9698 kB] 70s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libibumad3 amd64 56.1-1ubuntu1 [31.3 kB] 70s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libibmad5 amd64 56.1-1ubuntu1 [44.0 kB] 70s Get:35 http://ftpmaster.internal/ubuntu resolute/universe amd64 libucx0 amd64 1.19.0+ds-1 [1308 kB] 70s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB] 70s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 70s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 libze1 amd64 1.24.1-2 [599 kB] 70s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [41.0 kB] 70s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc-plugins amd64 2.12.2-1 [22.2 kB] 70s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmpi40 amd64 5.0.8-8ubuntu1 [3384 kB] 70s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 libspqr4 amd64 1:7.10.1+dfsg-1 [148 kB] 70s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 apbs amd64 3.4.1-6build2 [76.5 kB] 70s Get:44 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 70s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 70s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 70s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 70s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 70s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 apbs-doc all 3.4.1-6build2 [5850 kB] 70s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapbs-dev amd64 3.4.1-6build2 [99.5 kB] 70s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmaloc-dev amd64 1.5-2 [904 kB] 70s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfetk-dev amd64 3.4.1-6build2 [144 kB] 70s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-apbslib amd64 3.4.1-6build2 [219 kB] 71s Fetched 85.7 MB in 4s (23.5 MB/s) 71s Selecting previously unselected package fonts-lato. 71s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78457 files and directories currently installed.) 71s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 71s Unpacking fonts-lato (2.015-1) ... 71s Selecting previously unselected package apbs-data. 71s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 71s Unpacking apbs-data (3.4.1-6build2) ... 71s Selecting previously unselected package libmaloc1:amd64. 71s Preparing to unpack .../02-libmaloc1_1.5-2_amd64.deb ... 71s Unpacking libmaloc1:amd64 (1.5-2) ... 71s Selecting previously unselected package libblas3:amd64. 71s Preparing to unpack .../03-libblas3_3.12.1-6build1_amd64.deb ... 71s Unpacking libblas3:amd64 (3.12.1-6build1) ... 71s Selecting previously unselected package libsuperlu7:amd64. 71s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_amd64.deb ... 71s Unpacking libsuperlu7:amd64 (7.0.1+dfsg1-2) ... 71s Selecting previously unselected package libgomp1:amd64. 71s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_amd64.deb ... 71s Unpacking libgomp1:amd64 (15.2.0-5ubuntu1) ... 71s Selecting previously unselected package libsuitesparseconfig7:amd64. 71s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_amd64.deb ... 71s Unpacking libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... 71s Selecting previously unselected package libamd3:amd64. 71s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 71s Unpacking libamd3:amd64 (1:7.10.1+dfsg-1) ... 71s Selecting previously unselected package libcamd3:amd64. 71s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 71s Unpacking libcamd3:amd64 (1:7.10.1+dfsg-1) ... 71s Selecting previously unselected package libccolamd3:amd64. 71s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 71s Unpacking libccolamd3:amd64 (1:7.10.1+dfsg-1) ... 71s Selecting previously unselected package libcolamd3:amd64. 71s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_amd64.deb ... 71s Unpacking libcolamd3:amd64 (1:7.10.1+dfsg-1) ... 71s Selecting previously unselected package libgfortran5:amd64. 71s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 71s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 71s Selecting previously unselected package liblapack3:amd64. 71s Preparing to unpack .../12-liblapack3_3.12.1-6build1_amd64.deb ... 71s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 71s Selecting previously unselected package libcholmod5:amd64. 71s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_amd64.deb ... 71s Unpacking libcholmod5:amd64 (1:7.10.1+dfsg-1) ... 71s Selecting previously unselected package libumfpack6:amd64. 71s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_amd64.deb ... 71s Unpacking libumfpack6:amd64 (1:7.10.1+dfsg-1) ... 71s Selecting previously unselected package libfetk1.9t64:amd64. 71s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_amd64.deb ... 71s Unpacking libfetk1.9t64:amd64 (3.4.1-6build2) ... 71s Selecting previously unselected package libapbs3t64:amd64. 71s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_amd64.deb ... 71s Unpacking libapbs3t64:amd64 (3.4.1-6build2) ... 71s Selecting previously unselected package fonts-mathjax. 71s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 71s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 71s Selecting previously unselected package libjs-mathjax. 71s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 71s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 71s Selecting previously unselected package libarpack2t64:amd64. 71s Preparing to unpack .../19-libarpack2t64_3.9.1-6_amd64.deb ... 71s Unpacking libarpack2t64:amd64 (3.9.1-6) ... 71s Selecting previously unselected package libevent-core-2.1-7t64:amd64. 71s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_amd64.deb ... 71s Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 71s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 71s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_amd64.deb ... 71s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 71s Selecting previously unselected package libpsm2-2. 71s Preparing to unpack .../22-libpsm2-2_11.2.185-2.1_amd64.deb ... 71s Unpacking libpsm2-2 (11.2.185-2.1) ... 71s Selecting previously unselected package librdmacm1t64:amd64. 71s Preparing to unpack .../23-librdmacm1t64_56.1-1ubuntu1_amd64.deb ... 71s Unpacking librdmacm1t64:amd64 (56.1-1ubuntu1) ... 71s Selecting previously unselected package libfabric1:amd64. 71s Preparing to unpack .../24-libfabric1_2.1.0-1.1_amd64.deb ... 71s Unpacking libfabric1:amd64 (2.1.0-1.1) ... 71s Selecting previously unselected package libhwloc15:amd64. 71s Preparing to unpack .../25-libhwloc15_2.12.2-1_amd64.deb ... 71s Unpacking libhwloc15:amd64 (2.12.2-1) ... 71s Selecting previously unselected package libllvm17t64:amd64. 71s Preparing to unpack .../26-libllvm17t64_1%3a17.0.6-22build1_amd64.deb ... 71s Unpacking libllvm17t64:amd64 (1:17.0.6-22build1) ... 72s Selecting previously unselected package libamd-comgr2:amd64. 72s Preparing to unpack .../27-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build3_amd64.deb ... 72s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build3) ... 72s Selecting previously unselected package libdrm-amdgpu1:amd64. 72s Preparing to unpack .../28-libdrm-amdgpu1_2.4.125-1_amd64.deb ... 72s Unpacking 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libucx0:amd64. 72s Preparing to unpack .../34-libucx0_1.19.0+ds-1_amd64.deb ... 72s Unpacking libucx0:amd64 (1.19.0+ds-1) ... 72s Selecting previously unselected package libpciaccess0:amd64. 72s Preparing to unpack .../35-libpciaccess0_0.18.1-1ubuntu2_amd64.deb ... 72s Unpacking libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 72s Selecting previously unselected package libxnvctrl0:amd64. 72s Preparing to unpack .../36-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 72s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 72s Selecting previously unselected package libze1:amd64. 72s Preparing to unpack .../37-libze1_1.24.1-2_amd64.deb ... 72s Unpacking libze1:amd64 (1.24.1-2) ... 72s Selecting previously unselected package ocl-icd-libopencl1:amd64. 72s Preparing to unpack .../38-ocl-icd-libopencl1_2.3.3-1_amd64.deb ... 72s Unpacking ocl-icd-libopencl1:amd64 (2.3.3-1) ... 72s Selecting previously unselected package libhwloc-plugins:amd64. 72s Preparing to unpack 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(3.4.1-6build2) ... 72s Selecting previously unselected package libmaloc-dev. 72s Preparing to unpack .../50-libmaloc-dev_1.5-2_amd64.deb ... 72s Unpacking libmaloc-dev (1.5-2) ... 72s Selecting previously unselected package libfetk-dev:amd64. 72s Preparing to unpack .../51-libfetk-dev_3.4.1-6build2_amd64.deb ... 72s Unpacking libfetk-dev:amd64 (3.4.1-6build2) ... 72s Selecting previously unselected package python3-apbslib. 72s Preparing to unpack .../52-python3-apbslib_3.4.1-6build2_amd64.deb ... 72s Unpacking python3-apbslib (3.4.1-6build2) ... 72s Setting up libmaloc1:amd64 (1.5-2) ... 72s Setting up libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 72s Setting up fonts-lato (2.015-1) ... 72s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 72s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 72s Setting up libibumad3:amd64 (56.1-1ubuntu1) ... 72s Setting up libibmad5:amd64 (56.1-1ubuntu1) ... 72s Setting up apbs-data (3.4.1-6build2) ... 72s Setting up libgomp1:amd64 (15.2.0-5ubuntu1) ... 72s Setting up libze1:amd64 (1.24.1-2) ... 72s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 72s Setting up libblas3:amd64 (3.12.1-6build1) ... 72s 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 72s Setting up libllvm17t64:amd64 (1:17.0.6-22build1) ... 72s Setting up libhwloc15:amd64 (2.12.2-1) ... 72s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 72s Setting up ocl-icd-libopencl1:amd64 (2.3.3-1) ... 72s Setting up libpsm2-2 (11.2.185-2.1) ... 72s Setting up libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up librdmacm1t64:amd64 (56.1-1ubuntu1) ... 72s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 72s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build3) ... 72s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 72s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 72s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 72s Setting up libmaloc-dev (1.5-2) ... 72s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 72s Setting up libdrm-amdgpu1:amd64 (2.4.125-1) ... 72s Setting up libfabric1:amd64 (2.1.0-1.1) ... 72s Setting up liblapack3:amd64 (3.12.1-6build1) ... 72s 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 72s Setting up libarpack2t64:amd64 (3.9.1-6) ... 72s Setting up libamd3:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up libcolamd3:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 72s Setting up libhwloc-plugins:amd64 (2.12.2-1) ... 72s Setting up libcamd3:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up libsuperlu7:amd64 (7.0.1+dfsg1-2) ... 72s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 72s Setting up libccolamd3:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... 72s Setting up libcholmod5:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up libspqr4:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up apbs-doc (3.4.1-6build2) ... 72s Setting up libumfpack6:amd64 (1:7.10.1+dfsg-1) ... 72s Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... 72s Setting up libfetk1.9t64:amd64 (3.4.1-6build2) ... 72s Setting up libapbs3t64:amd64 (3.4.1-6build2) ... 72s Setting up libfetk-dev:amd64 (3.4.1-6build2) ... 72s Setting up libamdhip64-5:amd64 (5.7.1-6) ... 72s Setting up libapbs-dev:amd64 (3.4.1-6build2) ... 72s Setting up python3-apbslib (3.4.1-6build2) ... 73s Setting up libucx0:amd64 (1.19.0+ds-1) ... 73s Setting up libopenmpi40:amd64 (5.0.8-8ubuntu1) ... 73s Setting up apbs (3.4.1-6build2) ... 73s Processing triggers for man-db (2.13.1-1) ... 73s Processing triggers for libc-bin (2.42-0ubuntu3) ... 75s autopkgtest [06:45:35]: test test-apbs: [----------------------- 75s TESTING WITH BINARY_NAME:apbs 75s START_DIR:/tmp/autopkgtest.mQDh5g/autopkgtest_tmp/build 75s -------------------------------------------------------------------------------- 75s Testing forces from apbs-forces.in 75s 75s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000586 seconds 75s -------------------------------------------------------------------------------- 75s -------------------------------------------------------------------------------- 75s Testing input file apbs-mol-auto.in 75s 76s CHECKING:/usr/local/sbin/apbs 76s CHECKING:/usr/local/bin/apbs 76s CHECKING:/usr/sbin/apbs 76s CHECKING:/usr/bin/apbs 76s NOTE: Using apbs binary:/usr/bin/apbs 76s Testing all sections 76s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 76s ================================================================================ 76s Running tests for born section 76s BINARY: /usr/bin/apbs 76s INPUT: apbs-mol-auto.in 76s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 76s asc_getToken: Error occurred (bailing out). 76s Vio_scanf: Format problem with input. 76s 76s 76s ---------------------------------------------------------------------- 76s APBS -- Adaptive Poisson-Boltzmann Solver 76s Version APBS 3.4.1 76s 76s Nathan A. Baker (nathan.baker@pnnl.gov) 76s Pacific Northwest National Laboratory 76s 76s Additional contributing authors listed in the code documentation. 76s 76s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 76s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 76s Northwest Division for the U.S. Department of Energy. 76s 76s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 76s Portions Copyright (c) 2002-2020, Nathan A. Baker. 76s Portions Copyright (c) 1999-2002, The Regents of the University of California. 76s Portions Copyright (c) 1995, Michael Holst. 76s All rights reserved. 76s 76s Redistribution and use in source and binary forms, with or without 76s modification, are permitted provided that the following conditions are met: 76s 76s * Redistributions of source code must retain the above copyright notice, this 76s list of conditions and the following disclaimer. 76s 76s * Redistributions in binary form must reproduce the above copyright notice, 76s this list of conditions and the following disclaimer in the documentation 76s and/or other materials provided with the distribution. 76s 76s * Neither the name of the developer nor the names of its contributors may be 76s used to endorse or promote products derived from this software without 76s specific prior written permission. 76s 76s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 76s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 76s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 76s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 76s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 76s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 76s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 76s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 76s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 76s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 76s ---------------------------------------------------------------------- 76s APBS uses FETK (the Finite Element ToolKit) to solve the 76s Poisson-Boltzmann equation numerically. FETK is a portable collection 76s of finite element modeling class libraries developed by the Michael Holst 76s research group and written in an object-oriented form of C. FEtk is 76s designed to solve general coupled systems of nonlinear partial differential 76s equations using adaptive finite element methods, inexact Newton methods, 76s and algebraic multilevel methods. More information about FEtk may be found 76s at . 76s ---------------------------------------------------------------------- 76s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 76s Aqua is a modified form of the Holst group PMG library 76s which has been modified by Patrice Koehl 76s for improved efficiency and 76s memory usage when solving the Poisson-Boltzmann equation. 76s ---------------------------------------------------------------------- 76s Please cite your use of APBS as: 76s 76s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 76s nanosystems: application to microtubules and the ribosome. Proc. 76s Natl. Acad. Sci. USA 98, 10037-10041 2001. 76s 76s 76s This executable compiled on Jan 3 2025 at 11:01:42 76s 76s Parsing input file apbs-mol-auto.in... 76s rank 0 size 1... 76s Parsed input file. 76s Got paths for 1 molecules 76s Reading PQR-format atom data from ion.pqr. 76s 1 atoms 76s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 76s Net charge 1.00e+00 e 76s Preparing to run 6 PBE calculations. 76s ---------------------------------------- 76s CALCULATION #1 (solvated): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.280 MB total, 61.280 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.781 x 0.781 x 0.781 76s Grid lengths: 50.000 x 50.000 x 50.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Multiple Debye-Huckel sphere boundary conditions 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 78.540 76s Using "molecular" surface definition; no smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 9.607073836227E+02 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s CALCULATION #2 (solvated): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.280 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.383 x 0.383 x 0.383 76s Grid lengths: 24.495 x 24.495 x 24.495 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 78.540 76s Using "molecular" surface definition; no smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 2.200266567971E+03 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s CALCULATION #3 (solvated): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.280 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.188 x 0.188 x 0.188 76s Grid lengths: 12.000 x 12.000 x 12.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 78.540 76s Using "molecular" surface definition; no smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Potential to be written to potential.dx.gz 76s Total electrostatic energy = 4.732245131587E+03 kJ/mol 76s Calculating forces... 76s Writing potential to potential-PE0.dx.gz 76s ---------------------------------------- 76s CALCULATION #4 (reference): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.207 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.781 x 0.781 x 0.781 76s Grid lengths: 50.000 x 50.000 x 50.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Multiple Debye-Huckel sphere boundary conditions 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 1.000 76s Using "molecular" surface definition; no smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 1.190871482831E+03 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s CALCULATION #5 (reference): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.207 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.383 x 0.383 x 0.383 76s Grid lengths: 24.495 x 24.495 x 24.495 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 1.000 76s Using "molecular" surface definition; no smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 2.430874049735E+03 kJ/mol 76s Calculating forces... 76s [focusFillBound()]: WARNING: 76s Unusually large potential values 76s detected on the focusing boundary! 76s Convergence not guaranteed for NPBE/NRPBE calculations! 76s 76s ---------------------------------------- 76s CALCULATION #6 (reference): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.207 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.188 x 0.188 x 0.188 76s Grid lengths: 12.000 x 12.000 x 12.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 1.000 76s Using "molecular" surface definition; no smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 4.962018684215E+03 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s PRINT STATEMENTS 76s 76s print energy 1 (solvated) - 2 (reference) end 76s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 76s Global net ELEC energy = -2.297735526282E+02 kJ/mol 76s ---------------------------------------- 76s CLEANING UP AND SHUTTING DOWN... 76s Destroying force arrays. 76s No energy arrays to destroy. 76s Destroying multigrid structures. 76s Destroying finite element structures. 76s Destroying 1 molecules 76s Final memory usage: 0.001 MB total, 122.102 MB high water 76s 76s 76s Thanks for using APBS! 76s 76s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 76s *** PASSED *** 76s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 76s *** PASSED *** 76s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 76s *** PASSED *** 76s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 76s *** PASSED *** 76s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 76s *** PASSED *** 76s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 76s *** PASSED *** 76s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 76s *** PASSED *** 76s Elapsed time: 0.711307 seconds 76s -------------------------------------------------------------------------------- 76s -------------------------------------------------------------------------------- 76s Testing input file apbs-smol-auto.in 76s 76s Checking for intermediate energies in input file apbs-mol-auto.out 76s EXPECTED COMPUTED: 7 76s EXPECTED EXPECTED: 7 76s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 76s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 76s COMPUTED RESULT 960.7073836227 76s COMPUTED RESULT 2200.266567971 76s COMPUTED RESULT 4732.245131587 76s COMPUTED RESULT 1190.871482831 76s COMPUTED RESULT 2430.874049735 76s COMPUTED RESULT 4962.018684215 76s COMPUTED RESULT -229.7735526282 76s BINARY: /usr/bin/apbs 76s INPUT: apbs-smol-auto.in 76s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 76s asc_getToken: Error occurred (bailing out). 76s Vio_scanf: Format problem with input. 76s 76s 76s ---------------------------------------------------------------------- 76s APBS -- Adaptive Poisson-Boltzmann Solver 76s Version APBS 3.4.1 76s 76s Nathan A. Baker (nathan.baker@pnnl.gov) 76s Pacific Northwest National Laboratory 76s 76s Additional contributing authors listed in the code documentation. 76s 76s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 76s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 76s Northwest Division for the U.S. Department of Energy. 76s 76s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 76s Portions Copyright (c) 2002-2020, Nathan A. Baker. 76s Portions Copyright (c) 1999-2002, The Regents of the University of California. 76s Portions Copyright (c) 1995, Michael Holst. 76s All rights reserved. 76s 76s Redistribution and use in source and binary forms, with or without 76s modification, are permitted provided that the following conditions are met: 76s 76s * Redistributions of source code must retain the above copyright notice, this 76s list of conditions and the following disclaimer. 76s 76s * Redistributions in binary form must reproduce the above copyright notice, 76s this list of conditions and the following disclaimer in the documentation 76s and/or other materials provided with the distribution. 76s 76s * Neither the name of the developer nor the names of its contributors may be 76s used to endorse or promote products derived from this software without 76s specific prior written permission. 76s 76s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 76s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 76s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 76s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 76s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 76s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 76s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 76s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 76s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 76s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 76s ---------------------------------------------------------------------- 76s APBS uses FETK (the Finite Element ToolKit) to solve the 76s Poisson-Boltzmann equation numerically. FETK is a portable collection 76s of finite element modeling class libraries developed by the Michael Holst 76s research group and written in an object-oriented form of C. FEtk is 76s designed to solve general coupled systems of nonlinear partial differential 76s equations using adaptive finite element methods, inexact Newton methods, 76s and algebraic multilevel methods. More information about FEtk may be found 76s at . 76s ---------------------------------------------------------------------- 76s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 76s Aqua is a modified form of the Holst group PMG library 76s which has been modified by Patrice Koehl 76s for improved efficiency and 76s memory usage when solving the Poisson-Boltzmann equation. 76s ---------------------------------------------------------------------- 76s Please cite your use of APBS as: 76s 76s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 76s nanosystems: application to microtubules and the ribosome. Proc. 76s Natl. Acad. Sci. USA 98, 10037-10041 2001. 76s 76s 76s This executable compiled on Jan 3 2025 at 11:01:42 76s 76s Parsing input file apbs-smol-auto.in... 76s rank 0 size 1... 76s Parsed input file. 76s Got paths for 1 molecules 76s Reading PQR-format atom data from ion.pqr. 76s 1 atoms 76s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 76s Net charge 1.00e+00 e 76s Preparing to run 6 PBE calculations. 76s ---------------------------------------- 76s CALCULATION #1 (solvated): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.280 MB total, 61.280 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.781 x 0.781 x 0.781 76s Grid lengths: 50.000 x 50.000 x 50.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Multiple Debye-Huckel sphere boundary conditions 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 78.540 76s Using "molecular" surface definition;harmonic average smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 9.532928767450E+02 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s CALCULATION #2 (solvated): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.280 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.383 x 0.383 x 0.383 76s Grid lengths: 24.495 x 24.495 x 24.495 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 78.540 76s Using "molecular" surface definition;harmonic average smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 2.201243880085E+03 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s CALCULATION #3 (solvated): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.280 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.188 x 0.188 x 0.188 76s Grid lengths: 12.000 x 12.000 x 12.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 78.540 76s Using "molecular" surface definition;harmonic average smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 4.733006258977E+03 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s CALCULATION #4 (reference): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.207 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.781 x 0.781 x 0.781 76s Grid lengths: 50.000 x 50.000 x 50.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Multiple Debye-Huckel sphere boundary conditions 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 1.000 76s Using "molecular" surface definition;harmonic average smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 1.190871482831E+03 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s CALCULATION #5 (reference): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.207 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.383 x 0.383 x 0.383 76s Grid lengths: 24.495 x 24.495 x 24.495 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 1.000 76s Using "molecular" surface definition;harmonic average smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 2.430874049735E+03 kJ/mol 76s Calculating forces... 76s [focusFillBound()]: WARNING: 76s Unusually large potential values 76s detected on the focusing boundary! 76s Convergence not guaranteed for NPBE/NRPBE calculations! 76s 76s ---------------------------------------- 76s CALCULATION #6 (reference): MULTIGRID 76s Setting up problem... 76s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 76s Debye length: 0 A 76s Current memory usage: 61.207 MB total, 122.102 MB high water 76s Using cubic spline charge discretization. 76s Grid dimensions: 65 x 65 x 65 76s Grid spacings: 0.188 x 0.188 x 0.188 76s Grid lengths: 12.000 x 12.000 x 12.000 76s Grid center: (0.000, 0.000, 0.000) 76s Multigrid levels: 5 76s Molecule ID: 1 76s Linearized traditional PBE 76s Boundary conditions from focusing 76s 0 ion species (0.000 M ionic strength): 76s Solute dielectric: 1.000 76s Solvent dielectric: 1.000 76s Using "molecular" surface definition;harmonic average smoothing 76s Solvent probe radius: 1.400 A 76s Temperature: 298.150 K 76s Electrostatic energies will be calculated 76s Total electrostatic energy = 4.962018684215E+03 kJ/mol 76s Calculating forces... 76s ---------------------------------------- 76s PRINT STATEMENTS 76s 76s print energy 1 (solvated) - 2 (reference) end 76s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 76s Global net ELEC energy = -2.290124252387E+02 kJ/mol 76s ---------------------------------------- 76s CLEANING UP AND SHUTTING DOWN... 76s Destroying force arrays. 76s No energy arrays to destroy. 76s Destroying multigrid structures. 76s Destroying finite element structures. 76s Destroying 1 molecules 76s Final memory usage: 0.001 MB total, 122.102 MB high water 76s 76s 76s Thanks for using APBS! 76s 76s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 76s *** PASSED *** 76s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 76s *** PASSED *** 76s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 76s *** PASSED *** 76s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 76s *** PASSED *** 76s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 76s *** PASSED *** 76s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 76s *** PASSED *** 76s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 76s *** PASSED *** 76s Elapsed time: 0.65983 seconds 76s -------------------------------------------------------------------------------- 76s -------------------------------------------------------------------------------- 76s Testing input file apbs-mol-parallel.in 76s 76s Splitting the input file into 4 separate files using the inputgen utility 76s 77s Checking for intermediate energies in input file apbs-smol-auto.out 77s EXPECTED COMPUTED: 7 77s EXPECTED EXPECTED: 7 77s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 77s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 77s COMPUTED RESULT 953.292876745 77s COMPUTED RESULT 2201.243880085 77s COMPUTED RESULT 4733.006258977 77s COMPUTED RESULT 1190.871482831 77s COMPUTED RESULT 2430.874049735 77s COMPUTED RESULT 4962.018684215 77s COMPUTED RESULT -229.0124252387 77s BINARY: /usr/bin/apbs 77s INPUT: apbs-mol-parallel-PE0.in 77s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 77s asc_getToken: Error occurred (bailing out). 77s Vio_scanf: Format problem with input. 77s 77s 77s ---------------------------------------------------------------------- 77s APBS -- Adaptive Poisson-Boltzmann Solver 77s Version APBS 3.4.1 77s 77s Nathan A. Baker (nathan.baker@pnnl.gov) 77s Pacific Northwest National Laboratory 77s 77s Additional contributing authors listed in the code documentation. 77s 77s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 77s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 77s Northwest Division for the U.S. Department of Energy. 77s 77s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 77s Portions Copyright (c) 2002-2020, Nathan A. Baker. 77s Portions Copyright (c) 1999-2002, The Regents of the University of California. 77s Portions Copyright (c) 1995, Michael Holst. 77s All rights reserved. 77s 77s Redistribution and use in source and binary forms, with or without 77s modification, are permitted provided that the following conditions are met: 77s 77s * Redistributions of source code must retain the above copyright notice, this 77s list of conditions and the following disclaimer. 77s 77s * Redistributions in binary form must reproduce the above copyright notice, 77s this list of conditions and the following disclaimer in the documentation 77s and/or other materials provided with the distribution. 77s 77s * Neither the name of the developer nor the names of its contributors may be 77s used to endorse or promote products derived from this software without 77s specific prior written permission. 77s 77s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 77s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 77s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 77s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 77s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 77s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 77s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 77s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 77s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 77s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 77s ---------------------------------------------------------------------- 77s APBS uses FETK (the Finite Element ToolKit) to solve the 77s Poisson-Boltzmann equation numerically. FETK is a portable collection 77s of finite element modeling class libraries developed by the Michael Holst 77s research group and written in an object-oriented form of C. FEtk is 77s designed to solve general coupled systems of nonlinear partial differential 77s equations using adaptive finite element methods, inexact Newton methods, 77s and algebraic multilevel methods. More information about FEtk may be found 77s at . 77s ---------------------------------------------------------------------- 77s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 77s Aqua is a modified form of the Holst group PMG library 77s which has been modified by Patrice Koehl 77s for improved efficiency and 77s memory usage when solving the Poisson-Boltzmann equation. 77s ---------------------------------------------------------------------- 77s Please cite your use of APBS as: 77s 77s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 77s nanosystems: application to microtubules and the ribosome. Proc. 77s Natl. Acad. Sci. USA 98, 10037-10041 2001. 77s 77s 77s This executable compiled on Jan 3 2025 at 11:01:42 77s 77s Parsing input file apbs-mol-parallel-PE0.in... 77s rank 0 size 1... 77s Parsed input file. 77s Got paths for 1 molecules 77s Reading PQR-format atom data from ion.pqr. 77s 1 atoms 77s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 77s Net charge 1.00e+00 e 77s Preparing to run 6 PBE calculations. 77s ---------------------------------------- 77s CALCULATION #1 (solvated): MULTIGRID 77s Setting up problem... 77s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 77s Debye length: 0 A 77s Current memory usage: 61.280 MB total, 61.280 MB high water 77s Using cubic spline charge discretization. 77s Partition overlap fraction = 0.1 77s Processor array = 2 x 2 x 1 77s Grid dimensions: 65 x 65 x 65 77s Grid spacings: 0.781 x 0.781 x 0.781 77s Grid lengths: 50.000 x 50.000 x 50.000 77s Grid center: (0.000, 0.000, 0.000) 77s Multigrid levels: 5 77s Molecule ID: 1 77s Linearized traditional PBE 77s Multiple Debye-Huckel sphere boundary conditions 77s 0 ion species (0.000 M ionic strength): 77s Solute dielectric: 1.000 77s Solvent dielectric: 78.540 77s Using "molecular" surface definition; no smoothing 77s Solvent probe radius: 1.400 A 77s Temperature: 298.150 K 77s Electrostatic energies will be calculated 77s Total electrostatic energy = 2.401768459022E+02 kJ/mol 77s Calculating forces... 77s ---------------------------------------- 77s CALCULATION #2 (solvated): MULTIGRID 77s Setting up problem... 77s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 77s Debye length: 0 A 77s Current memory usage: 61.280 MB total, 122.102 MB high water 77s Using cubic spline charge discretization. 77s Partition overlap fraction = 0.1 77s Processor array = 2 x 2 x 1 77s Grid dimensions: 65 x 65 x 65 77s Grid spacings: 0.296 x 0.296 x 0.383 77s Grid lengths: 18.944 x 18.944 x 24.495 77s Grid center: (-2.411, -2.411, 0.000) 77s Multigrid levels: 5 77s Molecule ID: 1 77s Linearized traditional PBE 77s Boundary conditions from focusing 77s 0 ion species (0.000 M ionic strength): 77s Solute dielectric: 1.000 77s Solvent dielectric: 78.540 77s Using "molecular" surface definition; no smoothing 77s Solvent probe radius: 1.400 A 77s Temperature: 298.150 K 77s Electrostatic energies will be calculated 77s Total electrostatic energy = 8.142935592471E+02 kJ/mol 77s Calculating forces... 77s [focusFillBound()]: WARNING: 77s Unusually large potential values 77s detected on the focusing boundary! 77s Convergence not guaranteed for NPBE/NRPBE calculations! 77s 77s ---------------------------------------- 77s CALCULATION #3 (solvated): MULTIGRID 77s Setting up problem... 77s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 77s Debye length: 0 A 77s Current memory usage: 61.280 MB total, 122.102 MB high water 77s Using cubic spline charge discretization. 77s Partition overlap fraction = 0.1 77s Processor array = 2 x 2 x 1 77s Grid dimensions: 65 x 65 x 65 77s Grid spacings: 0.112 x 0.112 x 0.188 77s Grid lengths: 7.178 x 7.178 x 12.000 77s Grid center: (-2.411, -2.411, 0.000) 77s Multigrid levels: 5 77s Molecule ID: 1 77s Linearized traditional PBE 77s Boundary conditions from focusing 77s 0 ion species (0.000 M ionic strength): 77s Solute dielectric: 1.000 77s Solvent dielectric: 78.540 77s Using "molecular" surface definition; no smoothing 77s Solvent probe radius: 1.400 A 77s Temperature: 298.150 K 77s Electrostatic energies will be calculated 77s Total electrostatic energy = 1.485255308186E+03 kJ/mol 77s Calculating forces... 77s ---------------------------------------- 77s CALCULATION #4 (reference): MULTIGRID 77s Setting up problem... 77s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 77s Debye length: 0 A 77s Current memory usage: 61.207 MB total, 122.102 MB high water 77s Using cubic spline charge discretization. 77s Partition overlap fraction = 0.1 77s Processor array = 2 x 2 x 1 77s Grid dimensions: 65 x 65 x 65 77s Grid spacings: 0.781 x 0.781 x 0.781 77s Grid lengths: 50.000 x 50.000 x 50.000 77s Grid center: (0.000, 0.000, 0.000) 77s Multigrid levels: 5 77s Molecule ID: 1 77s Linearized traditional PBE 77s Multiple Debye-Huckel sphere boundary conditions 77s 0 ion species (0.000 M ionic strength): 77s Solute dielectric: 1.000 77s Solvent dielectric: 1.000 77s Using "molecular" surface definition; no smoothing 77s Solvent probe radius: 1.400 A 77s Temperature: 298.150 K 77s Electrostatic energies will be calculated 77s Total electrostatic energy = 2.977178707009E+02 kJ/mol 77s Calculating forces... 77s ---------------------------------------- 77s CALCULATION #5 (reference): MULTIGRID 77s Setting up problem... 77s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 77s Debye length: 0 A 77s Current memory usage: 61.207 MB total, 122.102 MB high water 77s Using cubic spline charge discretization. 77s Partition overlap fraction = 0.1 77s Processor array = 2 x 2 x 1 77s Grid dimensions: 65 x 65 x 65 77s Grid spacings: 0.296 x 0.296 x 0.383 77s Grid lengths: 18.944 x 18.944 x 24.495 77s Grid center: (-2.411, -2.411, 0.000) 77s Multigrid levels: 5 77s Molecule ID: 1 77s Linearized traditional PBE 77s Boundary conditions from focusing 77s 0 ion species (0.000 M ionic strength): 77s Solute dielectric: 1.000 77s Solvent dielectric: 1.000 77s Using "molecular" surface definition; no smoothing 77s Solvent probe radius: 1.400 A 77s Temperature: 298.150 K 77s Electrostatic energies will be calculated 77s Total electrostatic energy = 8.799304557588E+02 kJ/mol 77s Calculating forces... 77s [focusFillBound()]: WARNING: 77s Unusually large potential values 77s detected on the focusing boundary! 77s Convergence not guaranteed for NPBE/NRPBE calculations! 77s 77s ---------------------------------------- 77s CALCULATION #6 (reference): MULTIGRID 77s Setting up problem... 77s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 77s Debye length: 0 A 77s Current memory usage: 61.207 MB total, 122.102 MB high water 77s Using cubic spline charge discretization. 77s Partition overlap fraction = 0.1 77s Processor array = 2 x 2 x 1 77s Grid dimensions: 65 x 65 x 65 77s Grid spacings: 0.112 x 0.112 x 0.188 77s Grid lengths: 7.178 x 7.178 x 12.000 77s Grid center: (-2.411, -2.411, 0.000) 77s Multigrid levels: 5 77s Molecule ID: 1 77s Linearized traditional PBE 77s Boundary conditions from focusing 77s 0 ion species (0.000 M ionic strength): 77s Solute dielectric: 1.000 77s Solvent dielectric: 1.000 77s Using "molecular" surface definition; no smoothing 77s Solvent probe radius: 1.400 A 77s Temperature: 298.150 K 77s Electrostatic energies will be calculated 77s Total electrostatic energy = 1.542873949131E+03 kJ/mol 77s Calculating forces... 77s ---------------------------------------- 77s PRINT STATEMENTS 77s 77s print energy 1 (solvated) - 2 (reference) end 77s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 77s Global net ELEC energy = -5.761864094552E+01 kJ/mol 77s ---------------------------------------- 77s CLEANING UP AND SHUTTING DOWN... 77s Destroying force arrays. 77s No energy arrays to destroy. 77s Destroying multigrid structures. 77s Destroying finite element structures. 77s Destroying 1 molecules 77s Final memory usage: 0.001 MB total, 122.102 MB high water 77s 77s 77s Thanks for using APBS! 77s 77s Processor 0 results: 77s 2.401768459022e+02 77s 8.142935592471e+02 77s 1.485255308186e+03 77s 2.977178707009e+02 77s 8.799304557588e+02 77s 1.542873949131e+03 77s -5.761864094552e+01 77s 78s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 78s BINARY: /usr/bin/apbs 78s INPUT: apbs-mol-parallel-PE1.in 78s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 78s asc_getToken: Error occurred (bailing out). 78s Vio_scanf: Format problem with input. 78s 78s 78s ---------------------------------------------------------------------- 78s APBS -- Adaptive Poisson-Boltzmann Solver 78s Version APBS 3.4.1 78s 78s Nathan A. Baker (nathan.baker@pnnl.gov) 78s Pacific Northwest National Laboratory 78s 78s Additional contributing authors listed in the code documentation. 78s 78s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 78s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 78s Northwest Division for the U.S. Department of Energy. 78s 78s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 78s Portions Copyright (c) 2002-2020, Nathan A. Baker. 78s Portions Copyright (c) 1999-2002, The Regents of the University of California. 78s Portions Copyright (c) 1995, Michael Holst. 78s All rights reserved. 78s 78s Redistribution and use in source and binary forms, with or without 78s modification, are permitted provided that the following conditions are met: 78s 78s * Redistributions of source code must retain the above copyright notice, this 78s list of conditions and the following disclaimer. 78s 78s * Redistributions in binary form must reproduce the above copyright notice, 78s this list of conditions and the following disclaimer in the documentation 78s and/or other materials provided with the distribution. 78s 78s * Neither the name of the developer nor the names of its contributors may be 78s used to endorse or promote products derived from this software without 78s specific prior written permission. 78s 78s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 78s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 78s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 78s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 78s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 78s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 78s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 78s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 78s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 78s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 78s ---------------------------------------------------------------------- 78s APBS uses FETK (the Finite Element ToolKit) to solve the 78s Poisson-Boltzmann equation numerically. FETK is a portable collection 78s of finite element modeling class libraries developed by the Michael Holst 78s research group and written in an object-oriented form of C. FEtk is 78s designed to solve general coupled systems of nonlinear partial differential 78s equations using adaptive finite element methods, inexact Newton methods, 78s and algebraic multilevel methods. More information about FEtk may be found 78s at . 78s ---------------------------------------------------------------------- 78s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 78s Aqua is a modified form of the Holst group PMG library 78s which has been modified by Patrice Koehl 78s for improved efficiency and 78s memory usage when solving the Poisson-Boltzmann equation. 78s ---------------------------------------------------------------------- 78s Please cite your use of APBS as: 78s 78s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 78s nanosystems: application to microtubules and the ribosome. Proc. 78s Natl. Acad. Sci. USA 98, 10037-10041 2001. 78s 78s 78s This executable compiled on Jan 3 2025 at 11:01:42 78s 78s Parsing input file apbs-mol-parallel-PE1.in... 78s rank 0 size 1... 78s Parsed input file. 78s Got paths for 1 molecules 78s Reading PQR-format atom data from ion.pqr. 78s 1 atoms 78s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 78s Net charge 1.00e+00 e 78s Preparing to run 6 PBE calculations. 78s ---------------------------------------- 78s CALCULATION #1 (solvated): MULTIGRID 78s Setting up problem... 78s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 78s Debye length: 0 A 78s Current memory usage: 61.280 MB total, 61.280 MB high water 78s Using cubic spline charge discretization. 78s Partition overlap fraction = 0.1 78s Processor array = 2 x 2 x 1 78s Grid dimensions: 65 x 65 x 65 78s Grid spacings: 0.781 x 0.781 x 0.781 78s Grid lengths: 50.000 x 50.000 x 50.000 78s Grid center: (0.000, 0.000, 0.000) 78s Multigrid levels: 5 78s Molecule ID: 1 78s Linearized traditional PBE 78s Multiple Debye-Huckel sphere boundary conditions 78s 0 ion species (0.000 M ionic strength): 78s Solute dielectric: 1.000 78s Solvent dielectric: 78.540 78s Using "molecular" surface definition; no smoothing 78s Solvent probe radius: 1.400 A 78s Temperature: 298.150 K 78s Electrostatic energies will be calculated 78s Total electrostatic energy = 2.401768459022E+02 kJ/mol 78s Calculating forces... 78s ---------------------------------------- 78s CALCULATION #2 (solvated): MULTIGRID 78s Setting up problem... 78s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 78s Debye length: 0 A 78s Current memory usage: 61.280 MB total, 122.102 MB high water 78s Using cubic spline charge discretization. 78s Partition overlap fraction = 0.1 78s Processor array = 2 x 2 x 1 78s Grid dimensions: 65 x 65 x 65 78s Grid spacings: 0.296 x 0.296 x 0.383 78s Grid lengths: 18.944 x 18.944 x 24.495 78s Grid center: (2.411, -2.411, 0.000) 78s Multigrid levels: 5 78s Molecule ID: 1 78s Linearized traditional PBE 78s Boundary conditions from focusing 78s 0 ion species (0.000 M ionic strength): 78s Solute dielectric: 1.000 78s Solvent dielectric: 78.540 78s Using "molecular" surface definition; no smoothing 78s Solvent probe radius: 1.400 A 78s Temperature: 298.150 K 78s Electrostatic energies will be calculated 78s Total electrostatic energy = 8.142778312125E+02 kJ/mol 78s Calculating forces... 78s [focusFillBound()]: WARNING: 78s Unusually large potential values 78s detected on the focusing boundary! 78s Convergence not guaranteed for NPBE/NRPBE calculations! 78s 78s ---------------------------------------- 78s CALCULATION #3 (solvated): MULTIGRID 78s Setting up problem... 78s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 78s Debye length: 0 A 78s Current memory usage: 61.280 MB total, 122.102 MB high water 78s Using cubic spline charge discretization. 78s Partition overlap fraction = 0.1 78s Processor array = 2 x 2 x 1 78s Grid dimensions: 65 x 65 x 65 78s Grid spacings: 0.112 x 0.112 x 0.188 78s Grid lengths: 7.178 x 7.178 x 12.000 78s Grid center: (2.411, -2.411, 0.000) 78s Multigrid levels: 5 78s Molecule ID: 1 78s Linearized traditional PBE 78s Boundary conditions from focusing 78s 0 ion species (0.000 M ionic strength): 78s Solute dielectric: 1.000 78s Solvent dielectric: 78.540 78s Using "molecular" surface definition; no smoothing 78s Solvent probe radius: 1.400 A 78s Temperature: 298.150 K 78s Electrostatic energies will be calculated 78s Total electrostatic energy = 1.485246667424E+03 kJ/mol 78s Calculating forces... 78s ---------------------------------------- 78s CALCULATION #4 (reference): MULTIGRID 78s Setting up problem... 78s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 78s Debye length: 0 A 78s Current memory usage: 61.207 MB total, 122.102 MB high water 78s Using cubic spline charge discretization. 78s Partition overlap fraction = 0.1 78s Processor array = 2 x 2 x 1 78s Grid dimensions: 65 x 65 x 65 78s Grid spacings: 0.781 x 0.781 x 0.781 78s Grid lengths: 50.000 x 50.000 x 50.000 78s Grid center: (0.000, 0.000, 0.000) 78s Multigrid levels: 5 78s Molecule ID: 1 78s Linearized traditional PBE 78s Multiple Debye-Huckel sphere boundary conditions 78s 0 ion species (0.000 M ionic strength): 78s Solute dielectric: 1.000 78s Solvent dielectric: 1.000 78s Using "molecular" surface definition; no smoothing 78s Solvent probe radius: 1.400 A 78s Temperature: 298.150 K 78s Electrostatic energies will be calculated 78s Total electrostatic energy = 2.977178707009E+02 kJ/mol 78s Calculating forces... 78s ---------------------------------------- 78s CALCULATION #5 (reference): MULTIGRID 78s Setting up problem... 78s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 78s Debye length: 0 A 78s Current memory usage: 61.207 MB total, 122.102 MB high water 78s Using cubic spline charge discretization. 78s Partition overlap fraction = 0.1 78s Processor array = 2 x 2 x 1 78s Grid dimensions: 65 x 65 x 65 78s Grid spacings: 0.296 x 0.296 x 0.383 78s Grid lengths: 18.944 x 18.944 x 24.495 78s Grid center: (2.411, -2.411, 0.000) 78s Multigrid levels: 5 78s Molecule ID: 1 78s Linearized traditional PBE 78s Boundary conditions from focusing 78s 0 ion species (0.000 M ionic strength): 78s Solute dielectric: 1.000 78s Solvent dielectric: 1.000 78s Using "molecular" surface definition; no smoothing 78s Solvent probe radius: 1.400 A 78s Temperature: 298.150 K 78s Electrostatic energies will be calculated 78s Total electrostatic energy = 8.799304557588E+02 kJ/mol 78s Calculating forces... 78s [focusFillBound()]: WARNING: 78s Unusually large potential values 78s detected on the focusing boundary! 78s Convergence not guaranteed for NPBE/NRPBE calculations! 78s 78s ---------------------------------------- 78s CALCULATION #6 (reference): MULTIGRID 78s Setting up problem... 78s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 78s Debye length: 0 A 78s Current memory usage: 61.207 MB total, 122.102 MB high water 78s Using cubic spline charge discretization. 78s Partition overlap fraction = 0.1 78s Processor array = 2 x 2 x 1 78s Grid dimensions: 65 x 65 x 65 78s Grid spacings: 0.112 x 0.112 x 0.188 78s Grid lengths: 7.178 x 7.178 x 12.000 78s Grid center: (2.411, -2.411, 0.000) 78s Multigrid levels: 5 78s Molecule ID: 1 78s Linearized traditional PBE 78s Boundary conditions from focusing 78s 0 ion species (0.000 M ionic strength): 78s Solute dielectric: 1.000 78s Solvent dielectric: 1.000 78s Using "molecular" surface definition; no smoothing 78s Solvent probe radius: 1.400 A 78s Temperature: 298.150 K 78s Electrostatic energies will be calculated 78s Total electrostatic energy = 1.542873949131E+03 kJ/mol 78s Calculating forces... 78s ---------------------------------------- 78s PRINT STATEMENTS 78s 78s print energy 1 (solvated) - 2 (reference) end 78s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 78s Global net ELEC energy = -5.762728170718E+01 kJ/mol 78s ---------------------------------------- 78s CLEANING UP AND SHUTTING DOWN... 78s Destroying force arrays. 78s No energy arrays to destroy. 78s Destroying multigrid structures. 78s Destroying finite element structures. 78s Destroying 1 molecules 78s Final memory usage: 0.001 MB total, 122.102 MB high water 78s 78s 78s Thanks for using APBS! 78s 78s Processor 1 results: 78s 2.401768459022e+02 78s 8.142778312125e+02 78s 1.485246667424e+03 78s 2.977178707009e+02 78s 8.799304557588e+02 78s 1.542873949131e+03 78s -5.762728170718e+01 78s 79s Processor 2 results: 79s 2.401768459091e+02 79s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 79s BINARY: /usr/bin/apbs 79s INPUT: apbs-mol-parallel-PE2.in 79s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 79s asc_getToken: Error occurred (bailing out). 79s Vio_scanf: Format problem with input. 79s 79s 79s ---------------------------------------------------------------------- 79s APBS -- Adaptive Poisson-Boltzmann Solver 79s Version APBS 3.4.1 79s 79s Nathan A. Baker (nathan.baker@pnnl.gov) 79s Pacific Northwest National Laboratory 79s 79s Additional contributing authors listed in the code documentation. 79s 79s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 79s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 79s Northwest Division for the U.S. Department of Energy. 79s 79s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 79s Portions Copyright (c) 2002-2020, Nathan A. Baker. 79s Portions Copyright (c) 1999-2002, The Regents of the University of California. 79s Portions Copyright (c) 1995, Michael Holst. 79s All rights reserved. 79s 79s Redistribution and use in source and binary forms, with or without 79s modification, are permitted provided that the following conditions are met: 79s 79s * Redistributions of source code must retain the above copyright notice, this 79s list of conditions and the following disclaimer. 79s 79s * Redistributions in binary form must reproduce the above copyright notice, 79s this list of conditions and the following disclaimer in the documentation 79s and/or other materials provided with the distribution. 79s 79s * Neither the name of the developer nor the names of its contributors may be 79s used to endorse or promote products derived from this software without 79s specific prior written permission. 79s 79s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 79s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 79s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 79s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 79s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 79s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 79s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 79s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 79s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 79s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 79s ---------------------------------------------------------------------- 79s APBS uses FETK (the Finite Element ToolKit) to solve the 79s Poisson-Boltzmann equation numerically. FETK is a portable collection 79s of finite element modeling class libraries developed by the Michael Holst 79s research group and written in an object-oriented form of C. FEtk is 79s designed to solve general coupled systems of nonlinear partial differential 79s equations using adaptive finite element methods, inexact Newton methods, 79s and algebraic multilevel methods. More information about FEtk may be found 79s at . 79s ---------------------------------------------------------------------- 79s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 79s Aqua is a modified form of the Holst group PMG library 79s which has been modified by Patrice Koehl 79s for improved efficiency and 79s memory usage when solving the Poisson-Boltzmann equation. 79s ---------------------------------------------------------------------- 79s Please cite your use of APBS as: 79s 79s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 79s nanosystems: application to microtubules and the ribosome. Proc. 79s Natl. Acad. Sci. USA 98, 10037-10041 2001. 79s 79s 79s This executable compiled on Jan 3 2025 at 11:01:42 79s 79s Parsing input file apbs-mol-parallel-PE2.in... 79s rank 0 size 1... 79s Parsed input file. 79s Got paths for 1 molecules 79s Reading PQR-format atom data from ion.pqr. 79s 1 atoms 79s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 79s Net charge 1.00e+00 e 79s Preparing to run 6 PBE calculations. 79s ---------------------------------------- 79s CALCULATION #1 (solvated): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.280 MB total, 61.280 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.781 x 0.781 x 0.781 79s Grid lengths: 50.000 x 50.000 x 50.000 79s Grid center: (0.000, 0.000, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Multiple Debye-Huckel sphere boundary conditions 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 78.540 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 2.401768459091E+02 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s CALCULATION #2 (solvated): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.280 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.296 x 0.296 x 0.383 79s Grid lengths: 18.944 x 18.944 x 24.495 79s Grid center: (-2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 78.540 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 8.142935605696E+02 kJ/mol 79s Calculating forces... 79s [focusFillBound()]: WARNING: 79s Unusually large potential values 79s detected on the focusing boundary! 79s Convergence not guaranteed for NPBE/NRPBE calculations! 79s 79s ---------------------------------------- 79s CALCULATION #3 (solvated): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.280 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.112 x 0.112 x 0.188 79s Grid lengths: 7.178 x 7.178 x 12.000 79s Grid center: (-2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 78.540 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 1.485255306569E+03 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s CALCULATION #4 (reference): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.207 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.781 x 0.781 x 0.781 79s Grid lengths: 50.000 x 50.000 x 50.000 79s Grid center: (0.000, 0.000, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Multiple Debye-Huckel sphere boundary conditions 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 1.000 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 2.977178707146E+02 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s CALCULATION #5 (reference): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.207 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.296 x 0.296 x 0.383 79s Grid lengths: 18.944 x 18.944 x 24.495 79s Grid center: (-2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 1.000 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 8.799304557596E+02 kJ/mol 79s Calculating forces... 79s [focusFillBound()]: WARNING: 79s Unusually large potential values 79s detected on the focusing boundary! 79s Convergence not guaranteed for NPBE/NRPBE calculations! 79s 79s ---------------------------------------- 79s CALCULATION #6 (reference): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.207 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.112 x 0.112 x 0.188 79s Grid lengths: 7.178 x 7.178 x 12.000 79s Grid center: (-2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 1.000 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 1.542873949141E+03 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s PRINT STATEMENTS 79s 79s print energy 1 (solvated) - 2 (reference) end 79s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 79s Global net ELEC energy = -5.761864257239E+01 kJ/mol 79s ---------------------------------------- 79s CLEANING UP AND SHUTTING DOWN... 79s Destroying force arrays. 79s No energy arrays to destroy. 79s Destroying multigrid structures. 79s Destroying finite element structures. 79s Destroying 1 molecules 79s Final memory usage: 0.001 MB total, 122.102 MB high water 79s 79s 79s Thanks for using APBS! 79s 79s 8.142935605696e+02 79s 1.485255306569e+03 79s 2.977178707146e+02 79s 8.799304557596e+02 79s 1.542873949141e+03 79s -5.761864257239e+01 79s 79s Processor 3 results: 79s 2.401768459091e+02 79s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 79s BINARY: /usr/bin/apbs 79s INPUT: apbs-mol-parallel-PE3.in 79s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 79s asc_getToken: Error occurred (bailing out). 79s Vio_scanf: Format problem with input. 79s 79s 79s ---------------------------------------------------------------------- 79s APBS -- Adaptive Poisson-Boltzmann Solver 79s Version APBS 3.4.1 79s 79s Nathan A. Baker (nathan.baker@pnnl.gov) 79s Pacific Northwest National Laboratory 79s 79s Additional contributing authors listed in the code documentation. 79s 79s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 79s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 79s Northwest Division for the U.S. Department of Energy. 79s 79s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 79s Portions Copyright (c) 2002-2020, Nathan A. Baker. 79s Portions Copyright (c) 1999-2002, The Regents of the University of California. 79s Portions Copyright (c) 1995, Michael Holst. 79s All rights reserved. 79s 79s Redistribution and use in source and binary forms, with or without 79s modification, are permitted provided that the following conditions are met: 79s 79s * Redistributions of source code must retain the above copyright notice, this 79s list of conditions and the following disclaimer. 79s 79s * Redistributions in binary form must reproduce the above copyright notice, 79s this list of conditions and the following disclaimer in the documentation 79s and/or other materials provided with the distribution. 79s 79s * Neither the name of the developer nor the names of its contributors may be 79s used to endorse or promote products derived from this software without 79s specific prior written permission. 79s 79s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 79s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 79s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 79s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 79s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 79s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 79s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 79s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 79s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 79s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 79s ---------------------------------------------------------------------- 79s APBS uses FETK (the Finite Element ToolKit) to solve the 79s Poisson-Boltzmann equation numerically. FETK is a portable collection 79s of finite element modeling class libraries developed by the Michael Holst 79s research group and written in an object-oriented form of C. FEtk is 79s designed to solve general coupled systems of nonlinear partial differential 79s equations using adaptive finite element methods, inexact Newton methods, 79s and algebraic multilevel methods. More information about FEtk may be found 79s at . 79s ---------------------------------------------------------------------- 79s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 79s Aqua is a modified form of the Holst group PMG library 79s which has been modified by Patrice Koehl 79s for improved efficiency and 79s memory usage when solving the Poisson-Boltzmann equation. 79s ---------------------------------------------------------------------- 79s Please cite your use of APBS as: 79s 79s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 79s nanosystems: application to microtubules and the ribosome. Proc. 79s Natl. Acad. Sci. USA 98, 10037-10041 2001. 79s 79s 79s This executable compiled on Jan 3 2025 at 11:01:42 79s 79s Parsing input file apbs-mol-parallel-PE3.in... 79s rank 0 size 1... 79s Parsed input file. 79s Got paths for 1 molecules 79s Reading PQR-format atom data from ion.pqr. 79s 1 atoms 79s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 79s Net charge 1.00e+00 e 79s Preparing to run 6 PBE calculations. 79s ---------------------------------------- 79s CALCULATION #1 (solvated): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.280 MB total, 61.280 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.781 x 0.781 x 0.781 79s Grid lengths: 50.000 x 50.000 x 50.000 79s Grid center: (0.000, 0.000, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Multiple Debye-Huckel sphere boundary conditions 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 78.540 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 2.401768459091E+02 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s CALCULATION #2 (solvated): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.280 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.296 x 0.296 x 0.383 79s Grid lengths: 18.944 x 18.944 x 24.495 79s Grid center: (2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 78.540 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 8.142778325440E+02 kJ/mol 79s Calculating forces... 79s [focusFillBound()]: WARNING: 79s Unusually large potential values 79s detected on the focusing boundary! 79s Convergence not guaranteed for NPBE/NRPBE calculations! 79s 79s ---------------------------------------- 79s CALCULATION #3 (solvated): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.280 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.112 x 0.112 x 0.188 79s Grid lengths: 7.178 x 7.178 x 12.000 79s Grid center: (2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 78.540 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 1.485246665692E+03 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s CALCULATION #4 (reference): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.207 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.781 x 0.781 x 0.781 79s Grid lengths: 50.000 x 50.000 x 50.000 79s Grid center: (0.000, 0.000, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Multiple Debye-Huckel sphere boundary conditions 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 1.000 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 2.977178707146E+02 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s CALCULATION #5 (reference): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.207 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.296 x 0.296 x 0.383 79s Grid lengths: 18.944 x 18.944 x 24.495 79s Grid center: (2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 1.000 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 8.799304557596E+02 kJ/mol 79s Calculating forces... 79s [focusFillBound()]: WARNING: 79s Unusually large potential values 79s detected on the focusing boundary! 79s Convergence not guaranteed for NPBE/NRPBE calculations! 79s 79s ---------------------------------------- 79s CALCULATION #6 (reference): MULTIGRID 79s Setting up problem... 79s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 79s Debye length: 0 A 79s Current memory usage: 61.207 MB total, 122.102 MB high water 79s Using cubic spline charge discretization. 79s Partition overlap fraction = 0.1 79s Processor array = 2 x 2 x 1 79s Grid dimensions: 65 x 65 x 65 79s Grid spacings: 0.112 x 0.112 x 0.188 79s Grid lengths: 7.178 x 7.178 x 12.000 79s Grid center: (2.411, 2.411, 0.000) 79s Multigrid levels: 5 79s Molecule ID: 1 79s Linearized traditional PBE 79s Boundary conditions from focusing 79s 0 ion species (0.000 M ionic strength): 79s Solute dielectric: 1.000 79s Solvent dielectric: 1.000 79s Using "molecular" surface definition; no smoothing 79s Solvent probe radius: 1.400 A 79s Temperature: 298.150 K 79s Electrostatic energies will be calculated 79s Total electrostatic energy = 1.542873949141E+03 kJ/mol 79s Calculating forces... 79s ---------------------------------------- 79s PRINT STATEMENTS 79s 79s print energy 1 (solvated) - 2 (reference) end 79s Local net energy (PE 0) = -5.762728344954E+01 kJ/mol 79s Global net ELEC energy = -5.762728344954E+01 kJ/mol 79s ---------------------------------------- 79s CLEANING UP AND SHUTTING DOWN... 79s Destroying force arrays. 79s No energy arrays to destroy. 79s Destroying multigrid structures. 79s Destroying finite element structures. 79s Destroying 1 molecules 79s Final memory usage: 0.001 MB total, 122.102 MB high water 79s 79s 79s Thanks for using APBS! 79s 79s 8.142778325440e+02 79s 1.485246665692e+03 79s 2.977178707146e+02 79s 8.799304557596e+02 79s 1.542873949141e+03 79s -5.762728344954e+01 79s 79s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 79s *** PASSED *** 79s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 79s *** PASSED *** 79s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 79s *** PASSED *** 79s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 79s *** PASSED *** 79s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 79s *** PASSED *** 79s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 79s *** PASSED *** 79s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 79s *** PASSED *** 79s Elapsed time: 2.968915 seconds 79s -------------------------------------------------------------------------------- 79s -------------------------------------------------------------------------------- 79s Testing input file apbs-smol-parallel.in 79s 79s Splitting the input file into 4 separate files using the inputgen utility 79s 80s Processor 0 results: 80s 2.383232191816e+02 80s 8.145369591602e+02 80s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 80s EXPECTED COMPUTED: 7 80s EXPECTED EXPECTED: 7 80s COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] 80s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 80s COMPUTED RESULT 960.7073836226 80s COMPUTED RESULT 3257.1427835731997 80s COMPUTED RESULT 5941.0039478710005 80s COMPUTED RESULT 1190.8714828309999 80s COMPUTED RESULT 3519.7218230368003 80s COMPUTED RESULT 6171.495796544 80s COMPUTED RESULT -230.49184867463003 80s BINARY: /usr/bin/apbs 80s INPUT: apbs-smol-parallel-PE0.in 80s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 80s asc_getToken: Error occurred (bailing out). 80s Vio_scanf: Format problem with input. 80s 80s 80s ---------------------------------------------------------------------- 80s APBS -- Adaptive Poisson-Boltzmann Solver 80s Version APBS 3.4.1 80s 80s Nathan A. Baker (nathan.baker@pnnl.gov) 80s Pacific Northwest National Laboratory 80s 80s Additional contributing authors listed in the code documentation. 80s 80s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 80s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 80s Northwest Division for the U.S. Department of Energy. 80s 80s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 80s Portions Copyright (c) 2002-2020, Nathan A. Baker. 80s Portions Copyright (c) 1999-2002, The Regents of the University of California. 80s Portions Copyright (c) 1995, Michael Holst. 80s All rights reserved. 80s 80s Redistribution and use in source and binary forms, with or without 80s modification, are permitted provided that the following conditions are met: 80s 80s * Redistributions of source code must retain the above copyright notice, this 80s list of conditions and the following disclaimer. 80s 80s * Redistributions in binary form must reproduce the above copyright notice, 80s this list of conditions and the following disclaimer in the documentation 80s and/or other materials provided with the distribution. 80s 80s * Neither the name of the developer nor the names of its contributors may be 80s used to endorse or promote products derived from this software without 80s specific prior written permission. 80s 80s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 80s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 80s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 80s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 80s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 80s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 80s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 80s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 80s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 80s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 80s ---------------------------------------------------------------------- 80s APBS uses FETK (the Finite Element ToolKit) to solve the 80s Poisson-Boltzmann equation numerically. FETK is a portable collection 80s of finite element modeling class libraries developed by the Michael Holst 80s research group and written in an object-oriented form of C. FEtk is 80s designed to solve general coupled systems of nonlinear partial differential 80s equations using adaptive finite element methods, inexact Newton methods, 80s and algebraic multilevel methods. More information about FEtk may be found 80s at . 80s ---------------------------------------------------------------------- 80s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 80s Aqua is a modified form of the Holst group PMG library 80s which has been modified by Patrice Koehl 80s for improved efficiency and 80s memory usage when solving the Poisson-Boltzmann equation. 80s ---------------------------------------------------------------------- 80s Please cite your use of APBS as: 80s 80s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 80s nanosystems: application to microtubules and the ribosome. Proc. 80s Natl. Acad. Sci. USA 98, 10037-10041 2001. 80s 80s 80s This executable compiled on Jan 3 2025 at 11:01:42 80s 80s Parsing input file apbs-smol-parallel-PE0.in... 80s rank 0 size 1... 80s Parsed input file. 80s Got paths for 1 molecules 80s Reading PQR-format atom data from ion.pqr. 80s 1 atoms 80s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 80s Net charge 1.00e+00 e 80s Preparing to run 6 PBE calculations. 80s ---------------------------------------- 80s CALCULATION #1 (solvated): MULTIGRID 80s Setting up problem... 80s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 80s Debye length: 0 A 80s Current memory usage: 61.280 MB total, 61.280 MB high water 80s Using cubic spline charge discretization. 80s Partition overlap fraction = 0.1 80s Processor array = 2 x 2 x 1 80s Grid dimensions: 65 x 65 x 65 80s Grid spacings: 0.781 x 0.781 x 0.781 80s Grid lengths: 50.000 x 50.000 x 50.000 80s Grid center: (0.000, 0.000, 0.000) 80s Multigrid levels: 5 80s Molecule ID: 1 80s Linearized traditional PBE 80s Multiple Debye-Huckel sphere boundary conditions 80s 0 ion species (0.000 M ionic strength): 80s Solute dielectric: 1.000 80s Solvent dielectric: 78.540 80s Using "molecular" surface definition;harmonic average smoothing 80s Solvent probe radius: 1.400 A 80s Temperature: 298.150 K 80s Electrostatic energies will be calculated 80s Total electrostatic energy = 2.383232191816E+02 kJ/mol 80s Calculating forces... 80s ---------------------------------------- 80s CALCULATION #2 (solvated): MULTIGRID 80s Setting up problem... 80s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 80s Debye length: 0 A 80s Current memory usage: 61.280 MB total, 122.102 MB high water 80s Using cubic spline charge discretization. 80s Partition overlap fraction = 0.1 80s Processor array = 2 x 2 x 1 80s Grid dimensions: 65 x 65 x 65 80s Grid spacings: 0.296 x 0.296 x 0.383 80s Grid lengths: 18.944 x 18.944 x 24.495 80s Grid center: (-2.411, -2.411, 0.000) 80s Multigrid levels: 5 80s Molecule ID: 1 80s Linearized traditional PBE 80s Boundary conditions from focusing 80s 0 ion species (0.000 M ionic strength): 80s Solute dielectric: 1.000 80s Solvent dielectric: 78.540 80s Using "molecular" surface definition;harmonic average smoothing 80s Solvent probe radius: 1.400 A 80s Temperature: 298.150 K 80s Electrostatic energies will be calculated 80s Total electrostatic energy = 8.145369591602E+02 kJ/mol 80s Calculating forces... 80s [focusFillBound()]: WARNING: 80s Unusually large potential values 80s detected on the focusing boundary! 80s Convergence not guaranteed for NPBE/NRPBE calculations! 80s 80s ---------------------------------------- 80s CALCULATION #3 (solvated): MULTIGRID 80s Setting up problem... 80s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 80s Debye length: 0 A 80s Current memory usage: 61.280 MB total, 122.102 MB high water 80s Using cubic spline charge discretization. 80s Partition overlap fraction = 0.1 80s Processor array = 2 x 2 x 1 80s Grid dimensions: 65 x 65 x 65 80s Grid spacings: 0.112 x 0.112 x 0.188 80s Grid lengths: 7.178 x 7.178 x 12.000 80s Grid center: (-2.411, -2.411, 0.000) 80s Multigrid levels: 5 80s Molecule ID: 1 80s Linearized traditional PBE 80s Boundary conditions from focusing 80s 0 ion species (0.000 M ionic strength): 80s Solute dielectric: 1.000 80s Solvent dielectric: 78.540 80s Using "molecular" surface definition;harmonic average smoothing 80s Solvent probe radius: 1.400 A 80s Temperature: 298.150 K 80s Electrostatic energies will be calculated 80s Total electrostatic energy = 1.485524998001E+03 kJ/mol 80s Calculating forces... 80s ---------------------------------------- 80s CALCULATION #4 (reference): MULTIGRID 80s Setting up problem... 80s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 80s Debye length: 0 A 80s Current memory usage: 61.207 MB total, 122.102 MB high water 80s Using cubic spline charge discretization. 80s Partition overlap fraction = 0.1 80s Processor array = 2 x 2 x 1 80s Grid dimensions: 65 x 65 x 65 80s Grid spacings: 0.781 x 0.781 x 0.781 80s Grid lengths: 50.000 x 50.000 x 50.000 80s Grid center: (0.000, 0.000, 0.000) 80s Multigrid levels: 5 80s Molecule ID: 1 80s Linearized traditional PBE 80s Multiple Debye-Huckel sphere boundary conditions 80s 0 ion species (0.000 M ionic strength): 80s Solute dielectric: 1.000 80s Solvent dielectric: 1.000 80s Using "molecular" surface definition;harmonic average smoothing 80s Solvent probe radius: 1.400 A 80s Temperature: 298.150 K 80s Electrostatic energies will be calculated 80s Total electrostatic energy = 2.977178707009E+02 kJ/mol 80s Calculating forces... 80s ---------------------------------------- 80s CALCULATION #5 (reference): MULTIGRID 80s Setting up problem... 80s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 80s Debye length: 0 A 80s Current memory usage: 61.207 MB total, 122.102 MB high water 80s Using cubic spline charge discretization. 80s Partition overlap fraction = 0.1 80s Processor array = 2 x 2 x 1 80s Grid dimensions: 65 x 65 x 65 80s Grid spacings: 0.296 x 0.296 x 0.383 80s Grid lengths: 18.944 x 18.944 x 24.495 80s Grid center: (-2.411, -2.411, 0.000) 80s Multigrid levels: 5 80s Molecule ID: 1 80s Linearized traditional PBE 80s Boundary conditions from focusing 80s 0 ion species (0.000 M ionic strength): 80s Solute dielectric: 1.000 80s Solvent dielectric: 1.000 80s Using "molecular" surface definition;harmonic average smoothing 80s Solvent probe radius: 1.400 A 80s Temperature: 298.150 K 80s Electrostatic energies will be calculated 80s Total electrostatic energy = 8.799304557588E+02 kJ/mol 80s Calculating forces... 80s [focusFillBound()]: WARNING: 80s Unusually large potential values 80s detected on the focusing boundary! 80s Convergence not guaranteed for NPBE/NRPBE calculations! 80s 80s ---------------------------------------- 80s CALCULATION #6 (reference): MULTIGRID 80s Setting up problem... 80s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 80s Debye length: 0 A 80s Current memory usage: 61.207 MB total, 122.102 MB high water 80s Using cubic spline charge discretization. 80s Partition overlap fraction = 0.1 80s Processor array = 2 x 2 x 1 80s Grid dimensions: 65 x 65 x 65 80s Grid spacings: 0.112 x 0.112 x 0.188 80s Grid lengths: 7.178 x 7.178 x 12.000 80s Grid center: (-2.411, -2.411, 0.000) 80s Multigrid levels: 5 80s Molecule ID: 1 80s Linearized traditional PBE 80s Boundary conditions from focusing 80s 0 ion species (0.000 M ionic strength): 80s Solute dielectric: 1.000 80s Solvent dielectric: 1.000 80s Using "molecular" surface definition;harmonic average smoothing 80s Solvent probe radius: 1.400 A 80s Temperature: 298.150 K 80s Electrostatic energies will be calculated 80s Total electrostatic energy = 1.542873949131E+03 kJ/mol 80s Calculating forces... 80s ---------------------------------------- 80s PRINT STATEMENTS 80s 80s print energy 1 (solvated) - 2 (reference) end 80s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 80s Global net ELEC energy = -5.734895113069E+01 kJ/mol 80s ---------------------------------------- 80s CLEANING UP AND SHUTTING DOWN... 80s Destroying force arrays. 80s No energy arrays to destroy. 80s Destroying multigrid structures. 80s Destroying finite element structures. 80s Destroying 1 molecules 80s Final memory usage: 0.001 MB total, 122.102 MB high water 80s 80s 80s Thanks for using APBS! 80s 80s 1.485524998001e+03 80s 2.977178707009e+02 80s 8.799304557588e+02 80s 1.542873949131e+03 80s -5.734895113069e+01 80s 81s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 81s BINARY: /usr/bin/apbs 81s INPUT: apbs-smol-parallel-PE1.in 81s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 81s asc_getToken: Error occurred (bailing out). 81s Vio_scanf: Format problem with input. 81s 81s 81s ---------------------------------------------------------------------- 81s APBS -- Adaptive Poisson-Boltzmann Solver 81s Version APBS 3.4.1 81s 81s Nathan A. Baker (nathan.baker@pnnl.gov) 81s Pacific Northwest National Laboratory 81s 81s Additional contributing authors listed in the code documentation. 81s 81s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 81s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 81s Northwest Division for the U.S. Department of Energy. 81s 81s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 81s Portions Copyright (c) 2002-2020, Nathan A. Baker. 81s Portions Copyright (c) 1999-2002, The Regents of the University of California. 81s Portions Copyright (c) 1995, Michael Holst. 81s All rights reserved. 81s 81s Redistribution and use in source and binary forms, with or without 81s modification, are permitted provided that the following conditions are met: 81s 81s * Redistributions of source code must retain the above copyright notice, this 81s list of conditions and the following disclaimer. 81s 81s * Redistributions in binary form must reproduce the above copyright notice, 81s this list of conditions and the following disclaimer in the documentation 81s and/or other materials provided with the distribution. 81s 81s * Neither the name of the developer nor the names of its contributors may be 81s used to endorse or promote products derived from this software without 81s specific prior written permission. 81s 81s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 81s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 81s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 81s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 81s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 81s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 81s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 81s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 81s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 81s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 81s ---------------------------------------------------------------------- 81s APBS uses FETK (the Finite Element ToolKit) to solve the 81s Poisson-Boltzmann equation numerically. FETK is a portable collection 81s of finite element modeling class libraries developed by the Michael Holst 81s research group and written in an object-oriented form of C. FEtk is 81s designed to solve general coupled systems of nonlinear partial differential 81s equations using adaptive finite element methods, inexact Newton methods, 81s and algebraic multilevel methods. More information about FEtk may be found 81s at . 81s ---------------------------------------------------------------------- 81s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 81s Aqua is a modified form of the Holst group PMG library 81s which has been modified by Patrice Koehl 81s for improved efficiency and 81s memory usage when solving the Poisson-Boltzmann equation. 81s ---------------------------------------------------------------------- 81s Please cite your use of APBS as: 81s 81s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 81s nanosystems: application to microtubules and the ribosome. Proc. 81s Natl. Acad. Sci. USA 98, 10037-10041 2001. 81s 81s 81s This executable compiled on Jan 3 2025 at 11:01:42 81s 81s Parsing input file apbs-smol-parallel-PE1.in... 81s rank 0 size 1... 81s Parsed input file. 81s Got paths for 1 molecules 81s Reading PQR-format atom data from ion.pqr. 81s 1 atoms 81s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 81s Net charge 1.00e+00 e 81s Preparing to run 6 PBE calculations. 81s ---------------------------------------- 81s CALCULATION #1 (solvated): MULTIGRID 81s Setting up problem... 81s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 81s Debye length: 0 A 81s Current memory usage: 61.280 MB total, 61.280 MB high water 81s Using cubic spline charge discretization. 81s Partition overlap fraction = 0.1 81s Processor array = 2 x 2 x 1 81s Grid dimensions: 65 x 65 x 65 81s Grid spacings: 0.781 x 0.781 x 0.781 81s Grid lengths: 50.000 x 50.000 x 50.000 81s Grid center: (0.000, 0.000, 0.000) 81s Multigrid levels: 5 81s Molecule ID: 1 81s Linearized traditional PBE 81s Multiple Debye-Huckel sphere boundary conditions 81s 0 ion species (0.000 M ionic strength): 81s Solute dielectric: 1.000 81s Solvent dielectric: 78.540 81s Using "molecular" surface definition;harmonic average smoothing 81s Solvent probe radius: 1.400 A 81s Temperature: 298.150 K 81s Electrostatic energies will be calculated 81s Total electrostatic energy = 2.383232191816E+02 kJ/mol 81s Calculating forces... 81s ---------------------------------------- 81s CALCULATION #2 (solvated): MULTIGRID 81s Setting up problem... 81s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 81s Debye length: 0 A 81s Current memory usage: 61.280 MB total, 122.102 MB high water 81s Using cubic spline charge discretization. 81s Partition overlap fraction = 0.1 81s Processor array = 2 x 2 x 1 81s Grid dimensions: 65 x 65 x 65 81s Grid spacings: 0.296 x 0.296 x 0.383 81s Grid lengths: 18.944 x 18.944 x 24.495 81s Grid center: (2.411, -2.411, 0.000) 81s Multigrid levels: 5 81s Molecule ID: 1 81s Linearized traditional PBE 81s Boundary conditions from focusing 81s 0 ion species (0.000 M ionic strength): 81s Solute dielectric: 1.000 81s Solvent dielectric: 78.540 81s Using "molecular" surface definition;harmonic average smoothing 81s Solvent probe radius: 1.400 A 81s Temperature: 298.150 K 81s Electrostatic energies will be calculated 81s Total electrostatic energy = 8.145419898332E+02 kJ/mol 81s Calculating forces... 81s [focusFillBound()]: WARNING: 81s Unusually large potential values 81s detected on the focusing boundary! 81s Convergence not guaranteed for NPBE/NRPBE calculations! 81s 81s ---------------------------------------- 81s CALCULATION #3 (solvated): MULTIGRID 81s Setting up problem... 81s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 81s Debye length: 0 A 81s Current memory usage: 61.280 MB total, 122.102 MB high water 81s Using cubic spline charge discretization. 81s Partition overlap fraction = 0.1 81s Processor array = 2 x 2 x 1 81s Grid dimensions: 65 x 65 x 65 81s Grid spacings: 0.112 x 0.112 x 0.188 81s Grid lengths: 7.178 x 7.178 x 12.000 81s Grid center: (2.411, -2.411, 0.000) 81s Multigrid levels: 5 81s Molecule ID: 1 81s Linearized traditional PBE 81s Boundary conditions from focusing 81s 0 ion species (0.000 M ionic strength): 81s Solute dielectric: 1.000 81s Solvent dielectric: 78.540 81s Using "molecular" surface definition;harmonic average smoothing 81s Solvent probe radius: 1.400 A 81s Temperature: 298.150 K 81s Electrostatic energies will be calculated 81s Total electrostatic energy = 1.485529328612E+03 kJ/mol 81s Calculating forces... 81s ---------------------------------------- 81s CALCULATION #4 (reference): MULTIGRID 81s Setting up problem... 81s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 81s Debye length: 0 A 81s Current memory usage: 61.207 MB total, 122.102 MB high water 81s Using cubic spline charge discretization. 81s Partition overlap fraction = 0.1 81s Processor array = 2 x 2 x 1 81s Grid dimensions: 65 x 65 x 65 81s Grid spacings: 0.781 x 0.781 x 0.781 81s Grid lengths: 50.000 x 50.000 x 50.000 81s Grid center: (0.000, 0.000, 0.000) 81s Multigrid levels: 5 81s Molecule ID: 1 81s Linearized traditional PBE 81s Multiple Debye-Huckel sphere boundary conditions 81s 0 ion species (0.000 M ionic strength): 81s Solute dielectric: 1.000 81s Solvent dielectric: 1.000 81s Using "molecular" surface definition;harmonic average smoothing 81s Solvent probe radius: 1.400 A 81s Temperature: 298.150 K 81s Electrostatic energies will be calculated 81s Total electrostatic energy = 2.977178707009E+02 kJ/mol 81s Calculating forces... 81s ---------------------------------------- 81s CALCULATION #5 (reference): MULTIGRID 81s Setting up problem... 81s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 81s Debye length: 0 A 81s Current memory usage: 61.207 MB total, 122.102 MB high water 81s Using cubic spline charge discretization. 81s Partition overlap fraction = 0.1 81s Processor array = 2 x 2 x 1 81s Grid dimensions: 65 x 65 x 65 81s Grid spacings: 0.296 x 0.296 x 0.383 81s Grid lengths: 18.944 x 18.944 x 24.495 81s Grid center: (2.411, -2.411, 0.000) 81s Multigrid levels: 5 81s Molecule ID: 1 81s Linearized traditional PBE 81s Boundary conditions from focusing 81s 0 ion species (0.000 M ionic strength): 81s Solute dielectric: 1.000 81s Solvent dielectric: 1.000 81s Using "molecular" surface definition;harmonic average smoothing 81s Solvent probe radius: 1.400 A 81s Temperature: 298.150 K 81s Electrostatic energies will be calculated 81s Total electrostatic energy = 8.799304557588E+02 kJ/mol 81s Calculating forces... 81s [focusFillBound()]: WARNING: 81s Unusually large potential values 81s detected on the focusing boundary! 81s Convergence not guaranteed for NPBE/NRPBE calculations! 81s 81s ---------------------------------------- 81s CALCULATION #6 (reference): MULTIGRID 81s Setting up problem... 81s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 81s Debye length: 0 A 81s Current memory usage: 61.207 MB total, 122.102 MB high water 81s Using cubic spline charge discretization. 81s Partition overlap fraction = 0.1 81s Processor array = 2 x 2 x 1 81s Grid dimensions: 65 x 65 x 65 81s Grid spacings: 0.112 x 0.112 x 0.188 81s Grid lengths: 7.178 x 7.178 x 12.000 81s Grid center: (2.411, -2.411, 0.000) 81s Multigrid levels: 5 81s Molecule ID: 1 81s Linearized traditional PBE 81s Boundary conditions from focusing 81s 0 ion species (0.000 M ionic strength): 81s Solute dielectric: 1.000 81s Solvent dielectric: 1.000 81s Using "molecular" surface definition;harmonic average smoothing 81s Solvent probe radius: 1.400 A 81s Temperature: 298.150 K 81s Electrostatic energies will be calculated 81s Total electrostatic energy = 1.542873949131E+03 kJ/mol 81s Calculating forces... 81s ---------------------------------------- 81s PRINT STATEMENTS 81s 81s print energy 1 (solvated) - 2 (reference) end 81s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 81s Global net ELEC energy = -5.734462051928E+01 kJ/mol 81s ---------------------------------------- 81s CLEANING UP AND SHUTTING DOWN... 81s Destroying force arrays. 81s No energy arrays to destroy. 81s Destroying multigrid structures. 81s Destroying finite element structures. 81s Destroying 1 molecules 81s Final memory usage: 0.001 MB total, 122.102 MB high water 81s 81s 81s Thanks for using APBS! 81s 81s Processor 1 results: 81s 2.383232191816e+02 81s 8.145419898332e+02 81s 1.485529328612e+03 81s 2.977178707009e+02 81s 8.799304557588e+02 81s 1.542873949131e+03 81s -5.734462051928e+01 81s 82s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 82s BINARY: /usr/bin/apbs 82s INPUT: apbs-smol-parallel-PE2.in 82s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 82s asc_getToken: Error occurred (bailing out). 82s Vio_scanf: Format problem with input. 82s 82s 82s ---------------------------------------------------------------------- 82s APBS -- Adaptive Poisson-Boltzmann Solver 82s Version APBS 3.4.1 82s 82s Nathan A. Baker (nathan.baker@pnnl.gov) 82s Pacific Northwest National Laboratory 82s 82s Additional contributing authors listed in the code documentation. 82s 82s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 82s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 82s Northwest Division for the U.S. Department of Energy. 82s 82s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 82s Portions Copyright (c) 2002-2020, Nathan A. Baker. 82s Portions Copyright (c) 1999-2002, The Regents of the University of California. 82s Portions Copyright (c) 1995, Michael Holst. 82s All rights reserved. 82s 82s Redistribution and use in source and binary forms, with or without 82s modification, are permitted provided that the following conditions are met: 82s 82s * Redistributions of source code must retain the above copyright notice, this 82s list of conditions and the following disclaimer. 82s 82s * Redistributions in binary form must reproduce the above copyright notice, 82s this list of conditions and the following disclaimer in the documentation 82s and/or other materials provided with the distribution. 82s 82s * Neither the name of the developer nor the names of its contributors may be 82s used to endorse or promote products derived from this software without 82s specific prior written permission. 82s 82s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 82s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 82s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 82s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 82s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 82s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 82s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 82s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 82s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 82s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 82s ---------------------------------------------------------------------- 82s APBS uses FETK (the Finite Element ToolKit) to solve the 82s Poisson-Boltzmann equation numerically. FETK is a portable collection 82s of finite element modeling class libraries developed by the Michael Holst 82s research group and written in an object-oriented form of C. FEtk is 82s designed to solve general coupled systems of nonlinear partial differential 82s equations using adaptive finite element methods, inexact Newton methods, 82s and algebraic multilevel methods. More information about FEtk may be found 82s at . 82s ---------------------------------------------------------------------- 82s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 82s Aqua is a modified form of the Holst group PMG library 82s which has been modified by Patrice Koehl 82s for improved efficiency and 82s memory usage when solving the Poisson-Boltzmann equation. 82s ---------------------------------------------------------------------- 82s Please cite your use of APBS as: 82s 82s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 82s nanosystems: application to microtubules and the ribosome. Proc. 82s Natl. Acad. Sci. USA 98, 10037-10041 2001. 82s 82s 82s This executable compiled on Jan 3 2025 at 11:01:42 82s 82s Parsing input file apbs-smol-parallel-PE2.in... 82s rank 0 size 1... 82s Parsed input file. 82s Got paths for 1 molecules 82s Reading PQR-format atom data from ion.pqr. 82s 1 atoms 82s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 82s Net charge 1.00e+00 e 82s Preparing to run 6 PBE calculations. 82s ---------------------------------------- 82s CALCULATION #1 (solvated): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.280 MB total, 61.280 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.781 x 0.781 x 0.781 82s Grid lengths: 50.000 x 50.000 x 50.000 82s Grid center: (0.000, 0.000, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Multiple Debye-Huckel sphere boundary conditions 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 78.540 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 2.383232191909E+02 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s CALCULATION #2 (solvated): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.280 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.296 x 0.296 x 0.383 82s Grid lengths: 18.944 x 18.944 x 24.495 82s Grid center: (-2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 78.540 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 8.145369593489E+02 kJ/mol 82s Calculating forces... 82s [focusFillBound()]: WARNING: 82s Unusually large potential values 82s detected on the focusing boundary! 82s Convergence not guaranteed for NPBE/NRPBE calculations! 82s 82s ---------------------------------------- 82s CALCULATION #3 (solvated): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.280 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.112 x 0.112 x 0.188 82s Grid lengths: 7.178 x 7.178 x 12.000 82s Grid center: (-2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 78.540 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 1.485524997676E+03 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s CALCULATION #4 (reference): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.207 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.781 x 0.781 x 0.781 82s Grid lengths: 50.000 x 50.000 x 50.000 82s Grid center: (0.000, 0.000, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Multiple Debye-Huckel sphere boundary conditions 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 1.000 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s TemperatureProcessor 2 results: 82s : 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 2.977178707146E+02 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s CALCULATION #5 (reference): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.207 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.296 x 0.296 x 0.383 82s Grid lengths: 18.944 x 18.944 x 24.495 82s Grid center: (-2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 1.000 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 8.799304557596E+02 kJ/mol 82s Calculating forces... 82s [focusFillBound()]: WARNING: 82s Unusually large potential values 82s detected on the focusing boundary! 82s Convergence not guaranteed for NPBE/NRPBE calculations! 82s 82s ---------------------------------------- 82s CALCULATION #6 (reference): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.207 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.112 x 0.112 x 0.188 82s Grid lengths: 7.178 x 7.178 x 12.000 82s Grid center: (-2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 1.000 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 1.542873949141E+03 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s PRINT STATEMENTS 82s 82s print energy 1 (solvated) - 2 (reference) end 82s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 82s Global net ELEC energy = -5.734895146550E+01 kJ/mol 82s ---------------------------------------- 82s CLEANING UP AND SHUTTING DOWN... 82s Destroying force arrays. 82s No energy arrays to destroy. 82s Destroying multigrid structures. 82s Destroying finite element structures. 82s Destroying 1 molecules 82s Final memory usage: 0.001 MB total, 122.102 MB high water 82s 82s 82s Thanks for using APBS! 82s 82s 2.383232191909e+02 82s 8.145369593489e+02 82s 1.485524997676e+03 82s 2.977178707146e+02 82s 8.799304557596e+02 82s 1.542873949141e+03 82s -5.734895146550e+01 82s 82s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 82s BINARY: /usr/bin/apbs 82s INPUT: apbs-smol-parallel-PE3.in 82s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 82s asc_getToken: Error occurred (bailing out). 82s Vio_scanf: Format problem with input. 82s 82s 82s ---------------------------------------------------------------------- 82s APBS -- Adaptive Poisson-Boltzmann Solver 82s Version APBS 3.4.1 82s 82s Nathan A. Baker (nathan.baker@pnnl.gov) 82s Pacific Northwest National Laboratory 82s 82s Additional contributing authors listed in the code documentation. 82s 82s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 82s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 82s Northwest Division for the U.S. Department of Energy. 82s 82s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 82s Portions Copyright (c) 2002-2020, Nathan A. Baker. 82s Portions Copyright (c) 1999-2002, The Regents of the University of California. 82s Portions Copyright (c) 1995, Michael Holst. 82s All rights reserved. 82s 82s Redistribution and use in source and binary forms, with or without 82s modification, are permitted provided that the following conditions are met: 82s 82s * Redistributions of source code must retain the above copyright notice, this 82s list of conditions and the following disclaimer. 82s 82s * Redistributions in binary form must reproduce the above copyright notice, 82s this list of conditions and the following disclaimer in the documentation 82s and/or other materials provided with the distribution. 82s 82s * Neither the name of the developer nor the names of its contributors may be 82s used to endorse or promote products derived from this software without 82s specific prior written permission. 82s 82s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 82s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 82s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 82s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 82s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 82s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 82s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 82s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 82s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 82s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 82s ---------------------------------------------------------------------- 82s APBS uses FETK (the Finite Element ToolKit) to solve the 82s Poisson-Boltzmann equation numerically. FETK is a portable collection 82s of finite element modeling class libraries developed by the Michael Holst 82s research group and written in an object-oriented form of C. FEtk is 82s designed to solve general coupled systems of nonlinear partial differential 82s equations using adaptive finite element methods, inexact Newton methods, 82s and algebraic multilevel methods. More information about FEtk may be found 82s at . 82s ---------------------------------------------------------------------- 82s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 82s Aqua is a modified form of the Holst group PMG library 82s which has been modified by Patrice Koehl 82s for improved efficiency and 82s memory usage when solving the Poisson-Boltzmann equation. 82s ---------------------------------------------------------------------- 82s Please cite your use of APBS as: 82s 82s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 82s nanosystems: application to microtubules and the ribosome. Proc. 82s Natl. Acad. Sci. USA 98, 10037-10041 2001. 82s 82s 82s This executable compiled on Jan 3 2025 at 11:01:42 82s 82s Parsing input file apbs-smol-parallel-PE3.in... 82s rank 0 size 1... 82s Parsed input file. 82s Got paths for 1 molecules 82s Reading PQR-format atom data from ion.pqr. 82s 1 atoms 82s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 82s Net charge 1.00e+00 e 82s Preparing to run 6 PBE calculations. 82s ---------------------------------------- 82s CALCULATION #1 (solvated): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.280 MB total, 61.280 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.781 x 0.781 x 0.781 82s Grid lengths: 50.000 x 50.000 x 50.000 82s Grid center: (0.000, 0.000, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Multiple Debye-Huckel sphere boundary conditions 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 78.540 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 2.383232191909E+02 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s CALCULATION #2 (solvated): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.280 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.296 x 0.296 x 0.383 82s Grid lengths: 18.944 x 18.944 x 24.495 82s Grid center: (2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 78.540 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 8.145419900310E+02 kJ/mol 82s Calculating forces... 82s [focusFillBound()]: WARNING: 82s Unusually large potential values 82s detected on the focusing boundary! 82s Convergence not guaranteed for NPBE/NRPBE calculations! 82s 82s ---------------------------------------- 82s CALCULATION #3 (solvated): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.280 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.112 x 0.112 x 0.188 82s Grid lengths: 7.178 x 7.178 x 12.000 82s Grid center: (2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 78.540 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 1.485529328301E+03 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s CALCULATION #4 (reference): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.207 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.781 x 0.781 x 0.781 82s Grid lengths: 50.000 x 50.000 x 50.000 82s Grid center: (0.000, 0.000, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Multiple Debye-Huckel sphere boundary conditions 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 1.000 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 2.977178707146E+02 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s CALCULATION #5 (reference): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.207 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.296 x 0.296 x 0.383 82s Grid lengths: 18.944 x 18.944 x 24.495 82s Grid center: (2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 1.000 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 8.799304557596E+02 kJ/mol 82s Calculating forces... 82s [focusFillBound()]: WARNING: 82s Unusually large potential values 82s detected on the focusing boundary! 82s Convergence not guaranteed for NPBE/NRPBE calculations! 82s 82s ---------------------------------------- 82s CALCULATION #6 (reference): MULTIGRID 82s Setting up problem... 82s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 82s Debye length: 0 A 82s Current memory usage: 61.207 MB total, 122.102 MB high water 82s Using cubic spline charge discretization. 82s Partition overlap fraction = 0.1 82s Processor array = 2 x 2 x 1 82s Grid dimensions: 65 x 65 x 65 82s Grid spacings: 0.112 x 0.112 x 0.188 82s Grid lengths: 7.178 x 7.178 x 12.000 82s Grid center: (2.411, 2.411, 0.000) 82s Multigrid levels: 5 82s Molecule ID: 1 82s Linearized traditional PBE 82s Boundary conditions from focusing 82s 0 ion species (0.000 M ionic strength): 82s Solute dielectric: 1.000 82s Solvent dielectric: 1.000 82s Using "molecular" surface definition;harmonic average smoothing 82s Solvent probe radius: 1.400 A 82s Temperature: 298.150 K 82s Electrostatic energies will be calculated 82s Total electrostatic energy = 1.542873949141E+03 kJ/mol 82s Calculating forces... 82s ---------------------------------------- 82s PRINT STATEMENTS 82s 82s print energy 1 (solvated) - 2 (reference) end 82s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 82s Global net ELEC energy = -5.734462084052E+01 kJ/mol 82s ---------------------------------------- 82s CLEANING UP AND SHUTTING DOWN... 82s Destroying force arrays. 82s No energy arrays to destroy. 82s Destroying multigrid structures. 82s Destroying finite element structures. 82s Destroying 1 molecules 82s Final memory usage: 0.001 MB total, 122.102 MB high water 82s 82s 82s Thanks for using APBS! 82s 82s Processor 3 results: 82s 2.383232191909e+02 82s 8.145419900310e+02 82s 1.485529328301e+03 82s 2.977178707146e+02 82s 8.799304557596e+02 82s 1.542873949141e+03 82s -5.734462084052e+01 82s 82s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 82s *** PASSED *** 82s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 82s *** PASSED *** 82s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 82s *** PASSED *** 82s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 82s *** PASSED *** 82s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 82s *** PASSED *** 82s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 82s *** PASSED *** 82s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 82s *** PASSED *** 82s Elapsed time: 2.981883 seconds 82s -------------------------------------------------------------------------------- 82s Total elapsed time: 7.322521 seconds 82s Test results have been logged 82s -------------------------------------------------------------------------------- 82s -------------------------------------------------------------------------------- 82s Testing input file apbs-mol-auto.in 82s 119s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 119s EXPECTED COMPUTED: 7 119s EXPECTED EXPECTED: 7 119s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 119s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 119s COMPUTED RESULT 953.292876745 119s COMPUTED RESULT 3258.1578983732998 119s COMPUTED RESULT 5942.108652589999 119s COMPUTED RESULT 1190.8714828309999 119s COMPUTED RESULT 3519.7218230368003 119s COMPUTED RESULT 6171.495796544 119s COMPUTED RESULT -229.38714395599 119s Running tests for actin-dimer-auto section 119s BINARY: /usr/bin/apbs 119s INPUT: apbs-mol-auto.in 119s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 119s asc_getToken: Error occurred (bailing out). 119s Vio_scanf: Format problem with input. 119s 119s 119s ---------------------------------------------------------------------- 119s APBS -- Adaptive Poisson-Boltzmann Solver 119s Version APBS 3.4.1 119s 119s Nathan A. Baker (nathan.baker@pnnl.gov) 119s Pacific Northwest National Laboratory 119s 119s Additional contributing authors listed in the code documentation. 119s 119s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 119s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 119s Northwest Division for the U.S. Department of Energy. 119s 119s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 119s Portions Copyright (c) 2002-2020, Nathan A. Baker. 119s Portions Copyright (c) 1999-2002, The Regents of the University of California. 119s Portions Copyright (c) 1995, Michael Holst. 119s All rights reserved. 119s 119s Redistribution and use in source and binary forms, with or without 119s modification, are permitted provided that the following conditions are met: 119s 119s * Redistributions of source code must retain the above copyright notice, this 119s list of conditions and the following disclaimer. 119s 119s * Redistributions in binary form must reproduce the above copyright notice, 119s this list of conditions and the following disclaimer in the documentation 119s and/or other materials provided with the distribution. 119s 119s * Neither the name of the developer nor the names of its contributors may be 119s used to endorse or promote products derived from this software without 119s specific prior written permission. 119s 119s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 119s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 119s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 119s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 119s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 119s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 119s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 119s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 119s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 119s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 119s ---------------------------------------------------------------------- 119s APBS uses FETK (the Finite Element ToolKit) to solve the 119s Poisson-Boltzmann equation numerically. FETK is a portable collection 119s of finite element modeling class libraries developed by the Michael Holst 119s research group and written in an object-oriented form of C. FEtk is 119s designed to solve general coupled systems of nonlinear partial differential 119s equations using adaptive finite element methods, inexact Newton methods, 119s and algebraic multilevel methods. More information about FEtk may be found 119s at . 119s ---------------------------------------------------------------------- 119s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 119s Aqua is a modified form of the Holst group PMG library 119s which has been modified by Patrice Koehl 119s for improved efficiency and 119s memory usage when solving the Poisson-Boltzmann equation. 119s ---------------------------------------------------------------------- 119s Please cite your use of APBS as: 119s 119s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 119s nanosystems: application to microtubules and the ribosome. Proc. 119s Natl. Acad. Sci. USA 98, 10037-10041 2001. 119s 119s 119s This executable compiled on Jan 3 2025 at 11:01:42 119s 119s Parsing input file apbs-mol-auto.in... 119s rank 0 size 1... 119s Parsed input file. 119s Got paths for 3 molecules 119s Reading PQR-format atom data from mol1.pqr. 119s asc_getToken: Error occurred (bailing out). 119s Vio_scanf: Format problem with input. 119s 5877 atoms 119s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 119s Net charge -1.20e+01 e 119s Reading PQR-format atom data from mol2.pqr. 119s asc_getToken: Error occurred (bailing out). 119s Vio_scanf: Format problem with input. 119s 5877 atoms 119s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 119s Net charge -1.20e+01 e 119s Reading PQR-format atom data from complex.pqr. 119s 11754 atoms 119s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 119s Net charge -2.40e+01 e 119s Preparing to run 6 PBE calculations. 119s ---------------------------------------- 119s CALCULATION #1 (mol1): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 119s Debye length: 13.5959 A 119s Current memory usage: 1028.322 MB total, 1028.322 MB high water 119s Using linear spline charge discretization. 119s Grid dimensions: 161 x 161 x 161 119s Grid spacings: 0.975 x 0.756 x 1.012 119s Grid lengths: 156.000 x 121.000 x 162.000 119s Grid center: (2.518, -2.465, 16.742) 119s Multigrid levels: 4 119s Molecule ID: 1 119s Nonlinear traditional PBE 119s Single Debye-Huckel sphere boundary conditions 119s 2 ion species (0.050 M ionic strength): 119s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 119s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 119s Solute dielectric: 2.000 119s Solvent dielectric: 78.400 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 1.527617850342E+05 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #2 (mol1): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 119s Debye length: 13.5959 A 119s Current memory usage: 1028.322 MB total, 2042.113 MB high water 119s Using linear spline charge discretization. 119s Grid dimensions: 161 x 161 x 161 119s Grid spacings: 0.700 x 0.569 x 0.725 119s Grid lengths: 112.000 x 91.000 x 116.000 119s Grid center: (2.518, -2.465, 16.742) 119s Multigrid levels: 4 119s Molecule ID: 1 119s Nonlinear traditional PBE 119s Boundary conditions from focusing 119s 2 ion species (0.050 M ionic strength): 119s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 119s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 119s Solute dielectric: 2.000 119s Solvent dielectric: 78.400 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 2.919510754196E+05 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #3 (mol2): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 119s Debye length: 13.5959 A 119s Current memory usage: 1030.291 MB total, 2042.113 MB high water 119s Using linear spline charge discretization. 119s Grid dimensions: 161 x 161 x 161 119s Grid spacings: 0.975 x 0.756 x 1.012 119s Grid lengths: 156.000 x 121.000 x 162.000 119s Grid center: (2.518, -2.465, 16.742) 119s Multigrid levels: 4 119s Molecule ID: 2 119s Nonlinear traditional PBE 119s Single Debye-Huckel sphere boundary conditions 119s 2 ion species (0.050 M ionic strength): 119s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 119s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 119s Solute dielectric: 2.000 119s Solvent dielectric: 78.400 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 1.527671844880E+05 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #4 (mol2): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 119s Debye length: 13.5959 A 119s Current memory usage: 1030.291 MB total, 2046.048 MB high water 119s Using linear spline charge discretization. 119s Grid dimensions: 161 x 161 x 161 119s Grid spacings: 0.700 x 0.569 x 0.725 119s Grid lengths: 112.000 x 91.000 x 116.000 119s Grid center: (2.518, -2.465, 16.742) 119s Multigrid levels: 4 119s Molecule ID: 2 119s Nonlinear traditional PBE 119s Boundary conditions from focusing 119s 2 ion species (0.050 M ionic strength): 119s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 119s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 119s Solute dielectric: 2.000 119s Solvent dielectric: 78.400 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 2.915468859278E+05 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #5 (complex): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 119s Debye length: 13.5959 A 119s Current memory usage: 1046.446 MB total, 2046.048 MB high water 119s Using linear spline charge discretization. 119s Grid dimensions: 161 x 161 x 161 119s Grid spacings: 0.975 x 0.756 x 1.012 119s Grid lengths: 156.000 x 121.000 x 162.000 119s Grid center: (2.518, -2.465, 16.742) 119s Multigrid levels: 4 119s Molecule ID: 3 119s Nonlinear traditional PBE 119s Single Debye-Huckel sphere boundary conditions 119s 2 ion species (0.050 M ionic strength): 119s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 119s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 119s Solute dielectric: 2.000 119s Solvent dielectric: 78.400 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 3.056317807611E+05 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #6 (complex): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 119s Debye length: 13.5959 A 119s Current memory usage: 1046.446 MB total, 2069.492 MB high water 119s Using linear spline charge discretization. 119s Grid dimensions: 161 x 161 x 161 119s Grid spacings: 0.700 x 0.569 x 0.725 119s Grid lengths: 112.000 x 91.000 x 116.000 119s Grid center: (2.518, -2.465, 16.742) 119s Multigrid levels: 4 119s Molecule ID: 3 119s Nonlinear traditional PBE 119s Boundary conditions from focusing 119s 2 ion species (0.050 M ionic strength): 119s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 119s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 119s Solute dielectric: 2.000 119s Solvent dielectric: 78.400 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 5.836028296532E+05 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s PRINT STATEMENTS 119s 119s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 119s Local net energy (PE 0) = 1.048683058625E+02 kJ/mol 119s Global net ELEC energy = 1.048683058625E+02 kJ/mol 119s ---------------------------------------- 119s CLEANING UP AND SHUTTING DOWN... 119s Destroying force arrays. 119s No energy arrays to destroy. 119s Destroying multigrid structures. 119s Destroying finite element structures. 119s Destroying 3 molecules 119s Final memory usage: 0.001 MB total, 2069.492 MB high water 119s 119s 119s Thanks for using APBS! 119s 119s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 119s *** PASSED *** 119s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 119s *** PASSED *** 119s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 119s *** PASSED *** 119s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 119s *** PASSED *** 119s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 119s *** PASSED *** 119s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 120s *** PASSED *** 120s Testing computed result against expected result (1.048683058625e+02, 1.048683060915e+02) 120s *** PASSED *** 120s Elapsed time: 37.136323 seconds 120s -------------------------------------------------------------------------------- 120s -------------------------------------------------------------------------------- 120s Testing input file apbs-smol-auto.in 120s 149s Checking for intermediate energies in input file apbs-mol-auto.out 149s EXPECTED COMPUTED: 7 149s EXPECTED EXPECTED: 7 149s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058625] 149s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 149s COMPUTED RESULT 152761.7850342 149s COMPUTED RESULT 291951.0754196 149s COMPUTED RESULT 152767.184488 149s COMPUTED RESULT 291546.8859278 149s COMPUTED RESULT 305631.7807611 149s COMPUTED RESULT 583602.8296532 149s COMPUTED RESULT 104.8683058625 149s BINARY: /usr/bin/apbs 149s INPUT: apbs-smol-auto.in 149s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 149s asc_getToken: Error occurred (bailing out). 149s Vio_scanf: Format problem with input. 149s 149s 149s ---------------------------------------------------------------------- 149s APBS -- Adaptive Poisson-Boltzmann Solver 149s Version APBS 3.4.1 149s 149s Nathan A. Baker (nathan.baker@pnnl.gov) 149s Pacific Northwest National Laboratory 149s 149s Additional contributing authors listed in the code documentation. 149s 149s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 149s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 149s Northwest Division for the U.S. Department of Energy. 149s 149s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 149s Portions Copyright (c) 2002-2020, Nathan A. Baker. 149s Portions Copyright (c) 1999-2002, The Regents of the University of California. 149s Portions Copyright (c) 1995, Michael Holst. 149s All rights reserved. 149s 149s Redistribution and use in source and binary forms, with or without 149s modification, are permitted provided that the following conditions are met: 149s 149s * Redistributions of source code must retain the above copyright notice, this 149s list of conditions and the following disclaimer. 149s 149s * Redistributions in binary form must reproduce the above copyright notice, 149s this list of conditions and the following disclaimer in the documentation 149s and/or other materials provided with the distribution. 149s 149s * Neither the name of the developer nor the names of its contributors may be 149s used to endorse or promote products derived from this software without 149s specific prior written permission. 149s 149s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 149s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 149s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 149s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 149s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 149s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 149s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 149s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 149s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 149s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 149s ---------------------------------------------------------------------- 149s APBS uses FETK (the Finite Element ToolKit) to solve the 149s Poisson-Boltzmann equation numerically. FETK is a portable collection 149s of finite element modeling class libraries developed by the Michael Holst 149s research group and written in an object-oriented form of C. FEtk is 149s designed to solve general coupled systems of nonlinear partial differential 149s equations using adaptive finite element methods, inexact Newton methods, 149s and algebraic multilevel methods. More information about FEtk may be found 149s at . 149s ---------------------------------------------------------------------- 149s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 149s Aqua is a modified form of the Holst group PMG library 149s which has been modified by Patrice Koehl 149s for improved efficiency and 149s memory usage when solving the Poisson-Boltzmann equation. 149s ---------------------------------------------------------------------- 149s Please cite your use of APBS as: 149s 149s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 149s nanosystems: application to microtubules and the ribosome. Proc. 149s Natl. Acad. Sci. USA 98, 10037-10041 2001. 149s 149s 149s This executable compiled on Jan 3 2025 at 11:01:42 149s 149s Parsing input file apbs-smol-auto.in... 149s rank 0 size 1... 149s Parsed input file. 149s Got paths for 3 molecules 149s Reading PQR-format atom data from mol1.pqr. 149s asc_getToken: Error occurred (bailing out). 149s Vio_scanf: Format problem with input. 149s 5877 atoms 149s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 149s Net charge -1.20e+01 e 149s Reading PQR-format atom data from mol2.pqr. 149s asc_getToken: Error occurred (bailing out). 149s Vio_scanf: Format problem with input. 149s 5877 atoms 149s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 149s Net charge -1.20e+01 e 149s Reading PQR-format atom data from complex.pqr. 149s 11754 atoms 149s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 149s Net charge -2.40e+01 e 149s Preparing to run 6 PBE calculations. 149s ---------------------------------------- 149s CALCULATION #1 (mol1): MULTIGRID 149s Setting up problem... 149s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 149s Debye length: 13.5959 A 149s Current memory usage: 1028.322 MB total, 1028.322 MB high water 149s Using linear spline charge discretization. 149s Grid dimensions: 161 x 161 x 161 149s Grid spacings: 0.975 x 0.756 x 1.012 149s Grid lengths: 156.000 x 121.000 x 162.000 149s Grid center: (2.518, -2.465, 16.742) 149s Multigrid levels: 4 149s Molecule ID: 1 149s Nonlinear traditional PBE 149s Single Debye-Huckel sphere boundary conditions 149s 2 ion species (0.050 M ionic strength): 149s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 149s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 149s Solute dielectric: 2.000 149s Solvent dielectric: 78.400 149s Using "molecular" surface definition;harmonic average smoothing 149s Solvent probe radius: 1.400 A 149s Temperature: 298.150 K 149s Electrostatic energies will be calculated 149s Total electrostatic energy = 1.528632421825E+05 kJ/mol 149s Calculating forces... 149s ---------------------------------------- 149s CALCULATION #2 (mol1): MULTIGRID 149s Setting up problem... 149s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 149s Debye length: 13.5959 A 149s Current memory usage: 1028.322 MB total, 2042.113 MB high water 149s Using linear spline charge discretization. 149s Grid dimensions: 161 x 161 x 161 149s Grid spacings: 0.700 x 0.569 x 0.725 149s Grid lengths: 112.000 x 91.000 x 116.000 149s Grid center: (2.518, -2.465, 16.742) 149s Multigrid levels: 4 149s Molecule ID: 1 149s Nonlinear traditional PBE 149s Boundary conditions from focusing 149s 2 ion species (0.050 M ionic strength): 149s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 149s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 149s Solute dielectric: 2.000 149s Solvent dielectric: 78.400 149s Using "molecular" surface definition;harmonic average smoothing 149s Solvent probe radius: 1.400 A 149s Temperature: 298.150 K 149s Electrostatic energies will be calculated 149s Total electrostatic energy = 2.920618662320E+05 kJ/mol 149s Calculating forces... 149s ---------------------------------------- 149s CALCULATION #3 (mol2): MULTIGRID 149s Setting up problem... 149s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 149s Debye length: 13.5959 A 149s Current memory usage: 1030.291 MB total, 2042.113 MB high water 149s Using linear spline charge discretization. 149s Grid dimensions: 161 x 161 x 161 149s Grid spacings: 0.975 x 0.756 x 1.012 149s Grid lengths: 156.000 x 121.000 x 162.000 149s Grid center: (2.518, -2.465, 16.742) 149s Multigrid levels: 4 149s Molecule ID: 2 149s Nonlinear traditional PBE 149s Single Debye-Huckel sphere boundary conditions 149s 2 ion species (0.050 M ionic strength): 149s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 149s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 149s Solute dielectric: 2.000 149s Solvent dielectric: 78.400 149s Using "molecular" surface definition;harmonic average smoothing 149s Solvent probe radius: 1.400 A 149s Temperature: 298.150 K 149s Electrostatic energies will be calculated 149s Total electrostatic energy = 1.529297900572E+05 kJ/mol 149s Calculating forces... 149s ---------------------------------------- 149s CALCULATION #4 (mol2): MULTIGRID 149s Setting up problem... 149s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 149s Debye length: 13.5959 A 149s Current memory usage: 1030.291 MB total, 2046.048 MB high water 149s Using linear spline charge discretization. 149s Grid dimensions: 161 x 161 x 161 149s Grid spacings: 0.700 x 0.569 x 0.725 149s Grid lengths: 112.000 x 91.000 x 116.000 149s Grid center: (2.518, -2.465, 16.742) 149s Multigrid levels: 4 149s Molecule ID: 2 149s Nonlinear traditional PBE 149s Boundary conditions from focusing 149s 2 ion species (0.050 M ionic strength): 149s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 149s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 149s Solute dielectric: 2.000 149s Solvent dielectric: 78.400 149s Using "molecular" surface definition;harmonic average smoothing 149s Solvent probe radius: 1.400 A 149s Temperature: 298.150 K 149s Electrostatic energies will be calculated 149s Total electrostatic energy = 2.916592202835E+05 kJ/mol 149s Calculating forces... 149s ---------------------------------------- 149s CALCULATION #5 (complex): MULTIGRID 149s Setting up problem... 149s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 149s Debye length: 13.5959 A 149s Current memory usage: 1046.446 MB total, 2046.048 MB high water 149s Using linear spline charge discretization. 149s Grid dimensions: 161 x 161 x 161 149s Grid spacings: 0.975 x 0.756 x 1.012 149s Grid lengths: 156.000 x 121.000 x 162.000 149s Grid center: (2.518, -2.465, 16.742) 149s Multigrid levels: 4 149s Molecule ID: 3 149s Nonlinear traditional PBE 149s Single Debye-Huckel sphere boundary conditions 149s 2 ion species (0.050 M ionic strength): 149s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 149s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 149s Solute dielectric: 2.000 149s Solvent dielectric: 78.400 149s Using "molecular" surface definition;harmonic average smoothing 149s Solvent probe radius: 1.400 A 149s Temperature: 298.150 K 149s Electrostatic energies will be calculated 149s Total electrostatic energy = 3.059244262535E+05 kJ/mol 149s Calculating forces... 149s ---------------------------------------- 149s CALCULATION #6 (complex): MULTIGRID 149s Setting up problem... 149s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 149s Debye length: 13.5959 A 149s Current memory usage: 1046.446 MB total, 2069.492 MB high water 149s Using linear spline charge discretization. 149s Grid dimensions: 161 x 161 x 161 149s Grid spacings: 0.700 x 0.569 x 0.725 149s Grid lengths: 112.000 x 91.000 x 116.000 149s Grid center: (2.518, -2.465, 16.742) 149s Multigrid levels: 4 149s Molecule ID: 3 149s Nonlinear traditional PBE 149s Boundary conditions from focusing 149s 2 ion species (0.050 M ionic strength): 149s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 149s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 149s Solute dielectric: 2.000 149s Solvent dielectric: 78.400 149s Using "molecular" surface definition;harmonic average smoothing 149s Solvent probe radius: 1.400 A 149s Temperature: 298.150 K 149s Electrostatic energies will be calculated 149s Total electrostatic energy = 5.838306706232E+05 kJ/mol 149s Calculating forces... 149s ---------------------------------------- 149s PRINT STATEMENTS 149s 149s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 149s Local net energy (PE 0) = 1.095841077691E+02 kJ/mol 149s Global net ELEC energy = 1.095841077691E+02 kJ/mol 149s ---------------------------------------- 149s CLEANING UP AND SHUTTING DOWN... 149s Destroying force arrays. 149s No energy arrays to destroy. 149s Destroying multigrid structures. 149s Destroying finite element structures. 149s Destroying 3 molecules 149s Final memory usage: 0.001 MB total, 2069.492 MB high water 149s 149s 149s Thanks for using APBS! 149s 149s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 149s *** PASSED *** 149s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 149s *** PASSED *** 149s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 149s *** PASSED *** 149s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 149s *** PASSED *** 149s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 149s *** PASSED *** 149s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 149s *** PASSED *** 149s Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) 149s *** PASSED *** 149s Elapsed time: 29.339402 seconds 149s -------------------------------------------------------------------------------- 149s Total elapsed time: 66.475725 seconds 149s Test results have been logged 149s -------------------------------------------------------------------------------- 149s -------------------------------------------------------------------------------- 149s Testing input file alkanes.in 149s 154s Checking for intermediate energies in input file apbs-smol-auto.out 154s EXPECTED COMPUTED: 7 154s EXPECTED EXPECTED: 7 154s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] 154s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 154s COMPUTED RESULT 152863.2421825 154s COMPUTED RESULT 292061.866232 154s COMPUTED RESULT 152929.7900572 154s COMPUTED RESULT 291659.2202835 154s COMPUTED RESULT 305924.4262535 154s COMPUTED RESULT 583830.6706232 154s COMPUTED RESULT 109.5841077691 154s Running tests for alkanes section 154s BINARY: /usr/bin/apbs 154s INPUT: alkanes.in 154s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 154s 154s ---------------------------------------------------------------------- 154s APBS -- Adaptive Poisson-Boltzmann Solver 154s Version APBS 3.4.1 154s 154s Nathan A. Baker (nathan.baker@pnnl.gov) 154s Pacific Northwest National Laboratory 154s 154s Additional contributing authors listed in the code documentation. 154s 154s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 154s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 154s Northwest Division for the U.S. Department of Energy. 154s 154s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 154s Portions Copyright (c) 2002-2020, Nathan A. Baker. 154s Portions Copyright (c) 1999-2002, The Regents of the University of California. 154s Portions Copyright (c) 1995, Michael Holst. 154s All rights reserved. 154s 154s Redistribution and use in source and binary forms, with or without 154s modification, are permitted provided that the following conditions are met: 154s 154s * Redistributions of source code must retain the above copyright notice, this 154s list of conditions and the following disclaimer. 154s 154s * Redistributions in binary form must reproduce the above copyright notice, 154s this list of conditions and the following disclaimer in the documentation 154s and/or other materials provided with the distribution. 154s 154s * Neither the name of the developer nor the names of its contributors may be 154s used to endorse or promote products derived from this software without 154s specific prior written permission. 154s 154s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 154s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 154s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 154s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 154s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 154s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 154s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 154s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 154s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 154s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 154s ---------------------------------------------------------------------- 154s APBS uses FETK (the Finite Element ToolKit) to solve the 154s Poisson-Boltzmann equation numerically. FETK is a portable collection 154s of finite element modeling class libraries developed by the Michael Holst 154s research group and written in an object-oriented form of C. FEtk is 154s designed to solve general coupled systems of nonlinear partial differential 154s equations using adaptive finite element methods, inexact Newton methods, 154s and algebraic multilevel methods. More information about FEtk may be found 154s at . 154s ---------------------------------------------------------------------- 154s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 154s Aqua is a modified form of the Holst group PMG library 154s which has been modified by Patrice Koehl 154s for improved efficiency and 154s memory usage when solving the Poisson-Boltzmann equation. 154s ---------------------------------------------------------------------- 154s Please cite your use of APBS as: 154s 154s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 154s nanosystems: application to microtubules and the ribosome. Proc. 154s Natl. Acad. Sci. USA 98, 10037-10041 2001. 154s 154s 154s This executable compiled on Jan 3 2025 at 11:01:42 154s 154s Parsing input file alkanes.in... 154s rank 0 size 1... 154s Parsed input file. 154s Reading parameter data from parm.dat. 154s Got paths for 11 molecules 154s Reading PDB-format atom data from 2-methylbutane.pdb. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 17 atoms 154s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 154s Net charge 4.33e+00 e 154s Reading PDB-format atom data from butane.pdb. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 14 atoms 154s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 154s Net charge 3.51e+00 e 154s Reading PDB-format atom data from cyclohexane.pdb. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 18 atoms 154s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 154s Net charge 4.93e+00 e 154s Reading PDB-format atom data from cyclopentane.pdb. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 13 atoms 154s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 154s Net charge 3.88e+00 e 154s Reading PDB-format atom data from ethane.pdb. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 8 atoms 154s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 154s Net charge 1.87e+00 e 154s Reading PDB-format atom data from hexane.pdb. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 20 atoms 154s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 154s Net charge 5.16e+00 e 154s Reading PDB-format atom data from isobutane.pdb. 154s asc_getToken: Error occurred (bailing out). 154s Vio_scanf: Format problem with input. 154s 14 atoms 154s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 155s Net charge 3.51e+00 e 155s Reading PDB-format atom data from methane.pdb. 155s asc_getToken: Error occurred (bailing out). 155s Vio_scanf: Format problem with input. 155s 5 atoms 155s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 155s Net charge 1.05e+00 e 155s Reading PDB-format atom data from neopentane.pdb. 155s asc_getToken: Error occurred (bailing out). 155s Vio_scanf: Format problem with input. 155s 17 atoms 155s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 155s Net charge 4.33e+00 e 155s Reading PDB-format atom data from pentane.pdb. 155s asc_getToken: Error occurred (bailing out). 155s Vio_scanf: Format problem with input. 155s 17 atoms 155s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 155s Net charge 4.33e+00 e 155s Reading PDB-format atom data from propane.pdb. 155s 11 atoms 155s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 155s Net charge 2.69e+00 e 155s Preparing to run 11 PBE calculations. 155s ---------------------------------------- 155s CALCULATION #1 (solvated-2-methylbutane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 3.815624614267E+00 155s SASA for atom 1: 0.000000000000E+00 155s SASA for atom 2: 6.122920124655E-01 155s SASA for atom 3: 3.957497153740E+00 155s SASA for atom 4: 4.308445014544E+00 155s SASA for atom 5: 1.843264951960E+01 155s SASA for atom 6: 1.837011296483E+01 155s SASA for atom 7: 1.666599184724E+01 155s SASA for atom 8: 1.480031796315E+01 155s SASA for atom 9: 1.603020354037E+01 155s SASA for atom 10: 1.473778140838E+01 155s SASA for atom 11: 1.611879699297E+01 155s SASA for atom 12: 1.810954398660E+01 155s SASA for atom 13: 1.420100931324E+01 155s SASA for atom 14: 1.437298483886E+01 155s SASA for atom 15: 1.814081226399E+01 155s SASA for atom 16: 2.152820898091E+01 155s 155s Total solvent accessible surface area: 214.202 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 3.243280922127E-02 155s Surface tension*area energy for atom 1: 0.000000000000E+00 155s Surface tension*area energy for atom 2: 5.204482105957E-03 155s Surface tension*area energy for atom 3: 3.363872580679E-02 155s Surface tension*area energy for atom 4: 3.662178262362E-02 155s Surface tension*area energy for atom 5: 1.566775209166E-01 155s Surface tension*area energy for atom 6: 1.561459602010E-01 155s Surface tension*area energy for atom 7: 1.416609307015E-01 155s Surface tension*area energy for atom 8: 1.258027026868E-01 155s Surface tension*area energy for atom 9: 1.362567300932E-01 155s Surface tension*area energy for atom 10: 1.252711419712E-01 155s Surface tension*area energy for atom 11: 1.370097744402E-01 155s Surface tension*area energy for atom 12: 1.539311238861E-01 155s Surface tension*area energy for atom 13: 1.207085791625E-01 155s Surface tension*area energy for atom 14: 1.221703711303E-01 155s Surface tension*area energy for atom 15: 1.541969042439E-01 155s Surface tension*area energy for atom 16: 1.829897763377E-01 155s 155s Total surface tension energy: 1.82072 kJ/mol 155s 155s Total solvent accessible volume: 253.665 A^3 155s 155s Total pressure*volume energy: 60.7274 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.271287875274E+00 155s WCA energy for atom 1: -5.600872869478E+00 155s WCA energy for atom 2: -5.773775123943E+00 155s WCA energy for atom 3: -6.072801488986E+00 155s WCA energy for atom 4: -6.378470721845E+00 155s WCA energy for atom 5: -1.573474558351E+00 155s WCA energy for atom 6: -1.582338715648E+00 155s WCA energy for atom 7: -1.504044838266E+00 155s WCA energy for atom 8: -1.351002262819E+00 155s WCA energy for atom 9: -1.437367175239E+00 155s WCA energy for atom 10: -1.384626257493E+00 155s WCA energy for atom 11: -1.468867560891E+00 155s WCA energy for atom 12: -1.557005662832E+00 155s WCA energy for atom 13: -1.473759654043E+00 155s WCA energy for atom 14: -1.502261431335E+00 155s WCA energy for atom 15: -1.550940901474E+00 155s WCA energy for atom 16: -1.667828659696E+00 155s 155s Total WCA energy: -48.1507 kJ/mol 155s 155s Total non-polar energy = 1.439739455792E+01 kJ/mol 155s ---------------------------------------- 155s CALCULATION #2 (solvated-butane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 4.405515699447E+00 155s SASA for atom 1: 8.213673337951E-01 155s SASA for atom 2: 8.064333822716E-01 155s SASA for atom 3: 4.375647796400E+00 155s SASA for atom 4: 1.855251124959E+01 155s SASA for atom 5: 2.147609518526E+01 155s SASA for atom 6: 1.852645435176E+01 155s SASA for atom 7: 1.660345529247E+01 155s SASA for atom 8: 1.658782115377E+01 155s SASA for atom 9: 1.658260977421E+01 155s SASA for atom 10: 1.658260977421E+01 155s SASA for atom 11: 2.145003828744E+01 155s SASA for atom 12: 1.852124297220E+01 155s SASA for atom 13: 1.856293400871E+01 155s 155s Total solvent accessible surface area: 193.855 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 3.744688344530E-02 155s Surface tension*area energy for atom 1: 6.981622337259E-03 155s Surface tension*area energy for atom 2: 6.854683749309E-03 155s Surface tension*area energy for atom 3: 3.719300626940E-02 155s Surface tension*area energy for atom 4: 1.576963456215E-01 155s Surface tension*area energy for atom 5: 1.825468090747E-01 155s Surface tension*area energy for atom 6: 1.574748619900E-01 155s Surface tension*area energy for atom 7: 1.411293699860E-01 155s Surface tension*area energy for atom 8: 1.409964798071E-01 155s Surface tension*area energy for atom 9: 1.409521830808E-01 155s Surface tension*area energy for atom 10: 1.409521830808E-01 155s Surface tension*area energy for atom 11: 1.823253254433E-01 155s Surface tension*area energy for atom 12: 1.574305652637E-01 155s Surface tension*area energy for atom 13: 1.577849390741E-01 155s 155s Total surface tension energy: 1.64777 kJ/mol 155s 155s Total solvent accessible volume: 217.863 A^3 155s 155s Total pressure*volume energy: 52.1564 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.728858147814E+00 155s WCA energy for atom 1: -6.204037472587E+00 155s WCA energy for atom 2: -6.202937735018E+00 155s WCA energy for atom 3: -6.728762249931E+00 155s WCA energy for atom 4: -1.623549989062E+00 155s WCA energy for atom 5: -1.709092300778E+00 155s WCA energy for atom 6: -1.625196457114E+00 155s WCA energy for atom 7: -1.484289341167E+00 155s WCA energy for atom 8: -1.485410538626E+00 155s WCA energy for atom 9: -1.485593139015E+00 155s WCA energy for atom 10: -1.484878734279E+00 155s WCA energy for atom 11: -1.708585062695E+00 155s WCA energy for atom 12: -1.625094916482E+00 155s WCA energy for atom 13: -1.624416805392E+00 155s 155s Total WCA energy: -41.7207 kJ/mol 155s 155s Total non-polar energy = 1.208346456826E+01 kJ/mol 155s ---------------------------------------- 155s CALCULATION #3 (solvated-cyclohexane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 7.840324549863E-01 155s SASA for atom 1: 8.064333822716E-01 155s SASA for atom 2: 8.288343095569E-01 155s SASA for atom 3: 7.840324549863E-01 155s SASA for atom 4: 7.989664065098E-01 155s SASA for atom 5: 8.363012853187E-01 155s SASA for atom 6: 2.001169752764E+01 155s SASA for atom 7: 1.616048802948E+01 155s SASA for atom 8: 2.001169752764E+01 155s SASA for atom 9: 1.619175630687E+01 155s SASA for atom 10: 1.616048802948E+01 155s SASA for atom 11: 1.993352683418E+01 155s SASA for atom 12: 2.001169752764E+01 155s SASA for atom 13: 1.618133354774E+01 155s SASA for atom 14: 1.617091078861E+01 155s SASA for atom 15: 2.001690890721E+01 155s SASA for atom 16: 1.993873821374E+01 155s SASA for atom 17: 1.617091078861E+01 155s 155s Total solvent accessible surface area: 221.799 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 6.664275867383E-03 155s Surface tension*area energy for atom 1: 6.854683749309E-03 155s Surface tension*area energy for atom 2: 7.045091631234E-03 155s Surface tension*area energy for atom 3: 6.664275867383E-03 155s Surface tension*area energy for atom 4: 6.791214455333E-03 155s Surface tension*area energy for atom 5: 7.108560925209E-03 155s Surface tension*area energy for atom 6: 1.700994289850E-01 155s Surface tension*area energy for atom 7: 1.373641482506E-01 155s Surface tension*area energy for atom 8: 1.700994289850E-01 155s Surface tension*area energy for atom 9: 1.376299286084E-01 155s Surface tension*area energy for atom 10: 1.373641482506E-01 155s Surface tension*area energy for atom 11: 1.694349780905E-01 155s Surface tension*area energy for atom 12: 1.700994289850E-01 155s Surface tension*area energy for atom 13: 1.375413351558E-01 155s Surface tension*area energy for atom 14: 1.374527417032E-01 155s Surface tension*area energy for atom 15: 1.701437257113E-01 155s Surface tension*area energy for atom 16: 1.694792748168E-01 155s Surface tension*area energy for atom 17: 1.374527417032E-01 155s 155s Total surface tension energy: 1.88529 kJ/mol 155s 155s Total solvent accessible volume: 267.435 A^3 155s 155s Total pressure*volume energy: 64.0239 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -5.793234697241E+00 155s WCA energy for atom 1: -5.784370526583E+00 155s WCA energy for atom 2: -5.791799130412E+00 155s WCA energy for atom 3: -5.788504399087E+00 155s WCA energy for atom 4: -5.797319672490E+00 155s WCA energy for atom 5: -5.787358035342E+00 155s WCA energy for atom 6: -1.523887929614E+00 155s WCA energy for atom 7: -1.413678912317E+00 155s WCA energy for atom 8: -1.521751604392E+00 155s WCA energy for atom 9: -1.414741802525E+00 155s WCA energy for atom 10: -1.413367854344E+00 155s WCA energy for atom 11: -1.523407238081E+00 155s WCA energy for atom 12: -1.523000623583E+00 155s WCA energy for atom 13: -1.413922068538E+00 155s WCA energy for atom 14: -1.416316744211E+00 155s WCA energy for atom 15: -1.524577474659E+00 155s WCA energy for atom 16: -1.523300410052E+00 155s WCA energy for atom 17: -1.414522566061E+00 155s 155s Total WCA energy: -52.3691 kJ/mol 155s 155s Total non-polar energy = 1.354016672221E+01 kJ/mol 155s ---------------------------------------- 155s CALCULATION #4 (solvated-cyclopentane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 9.490526193215E+00 155s SASA for atom 1: 9.512927120500E+00 155s SASA for atom 2: 2.299828534626E+00 155s SASA for atom 3: 1.919012770776E+00 155s SASA for atom 4: 2.307295510388E+00 155s SASA for atom 5: 2.325838699632E+01 155s SASA for atom 6: 2.325838699632E+01 155s SASA for atom 7: 2.045987617019E+01 155s SASA for atom 8: 2.067875411190E+01 155s SASA for atom 9: 2.028790064456E+01 155s SASA for atom 10: 1.897463299431E+01 155s SASA for atom 11: 2.048593306801E+01 155s SASA for atom 12: 2.070481100972E+01 155s 155s Total solvent accessible surface area: 193.638 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 8.066947264233E-02 155s Surface tension*area energy for atom 1: 8.085988052425E-02 155s Surface tension*area energy for atom 2: 1.954854254432E-02 155s Surface tension*area energy for atom 3: 1.631160855160E-02 155s Surface tension*area energy for atom 4: 1.961201183830E-02 155s Surface tension*area energy for atom 5: 1.976962894687E-01 155s Surface tension*area energy for atom 6: 1.976962894687E-01 155s Surface tension*area energy for atom 7: 1.739089474466E-01 155s Surface tension*area energy for atom 8: 1.757694099511E-01 155s Surface tension*area energy for atom 9: 1.724471554788E-01 155s Surface tension*area energy for atom 10: 1.612843804516E-01 155s Surface tension*area energy for atom 11: 1.741304310781E-01 155s Surface tension*area energy for atom 12: 1.759908935826E-01 155s 155s Total surface tension energy: 1.64593 kJ/mol 155s 155s Total solvent accessible volume: 217.998 A^3 155s 155s Total pressure*volume energy: 52.1887 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.343496616804E+00 155s WCA energy for atom 1: -6.327869601807E+00 155s WCA energy for atom 2: -6.334858040579E+00 155s WCA energy for atom 3: -6.296075406417E+00 155s WCA energy for atom 4: -6.345600816761E+00 155s WCA energy for atom 5: -1.663697465126E+00 155s WCA energy for atom 6: -1.662444032853E+00 155s WCA energy for atom 7: -1.572325104493E+00 155s WCA energy for atom 8: -1.604626551065E+00 155s WCA energy for atom 9: -1.586431484963E+00 155s WCA energy for atom 10: -1.554291291374E+00 155s WCA energy for atom 11: -1.574315220751E+00 155s WCA energy for atom 12: -1.604941679892E+00 155s 155s Total WCA energy: -44.471 kJ/mol 155s 155s Total non-polar energy = 9.363673200142E+00 kJ/mol 155s ---------------------------------------- 155s CALCULATION #5 (solvated-ethane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 5.995981536705E+00 155s SASA for atom 1: 5.966113633657E+00 155s SASA for atom 2: 2.121552620704E+01 155s SASA for atom 3: 2.124158310486E+01 155s SASA for atom 4: 2.125200586399E+01 155s SASA for atom 5: 2.123116034573E+01 155s SASA for atom 6: 2.125200586399E+01 155s SASA for atom 7: 2.127285138225E+01 155s 155s Total solvent accessible surface area: 139.427 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 5.096584306199E-02 155s Surface tension*area energy for atom 1: 5.071196588609E-02 155s Surface tension*area energy for atom 2: 1.803319727598E-01 155s Surface tension*area energy for atom 3: 1.805534563913E-01 155s Surface tension*area energy for atom 4: 1.806420498439E-01 155s Surface tension*area energy for atom 5: 1.804648629387E-01 155s Surface tension*area energy for atom 6: 1.806420498439E-01 155s Surface tension*area energy for atom 7: 1.808192367491E-01 155s 155s Total surface tension energy: 1.18513 kJ/mol 155s 155s Total solvent accessible volume: 140.346 A^3 155s 155s Total pressure*volume energy: 33.5988 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -7.360066353115E+00 155s WCA energy for atom 1: -7.355483516201E+00 155s WCA energy for atom 2: -1.776106201066E+00 155s WCA energy for atom 3: -1.773973940651E+00 155s WCA energy for atom 4: -1.775401936843E+00 155s WCA energy for atom 5: -1.773464835521E+00 155s WCA energy for atom 6: -1.774382856097E+00 155s WCA energy for atom 7: -1.772366599434E+00 155s 155s Total WCA energy: -25.3612 kJ/mol 155s 155s Total non-polar energy = 9.422717598546E+00 kJ/mol 155s ---------------------------------------- 155s CALCULATION #6 (solvated-hexane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 4.405515699447E+00 155s SASA for atom 1: 8.213673337951E-01 155s SASA for atom 2: 3.285469335181E-01 155s SASA for atom 3: 2.986790304710E-01 155s SASA for atom 4: 1.855251124959E+01 155s SASA for atom 5: 2.147609518526E+01 155s SASA for atom 6: 1.852645435176E+01 155s SASA for atom 7: 1.655655287639E+01 155s SASA for atom 8: 1.655134149682E+01 155s SASA for atom 9: 1.360170066332E+01 155s SASA for atom 10: 1.357043238593E+01 155s SASA for atom 11: 1.381536722546E+01 155s SASA for atom 12: 1.384142412329E+01 155s SASA for atom 13: 7.765654792245E-01 155s SASA for atom 14: 1.684839013200E+01 155s SASA for atom 15: 1.682233323417E+01 155s SASA for atom 16: 4.166572475070E+00 155s SASA for atom 17: 2.179398933870E+01 155s SASA for atom 18: 1.877660057086E+01 155s SASA for atom 19: 1.876096643216E+01 155s 155s Total solvent accessible surface area: 250.291 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 3.744688344530E-02 155s Surface tension*area energy for atom 1: 6.981622337259E-03 155s Surface tension*area energy for atom 2: 2.792648934903E-03 155s Surface tension*area energy for atom 3: 2.538771759003E-03 155s Surface tension*area energy for atom 4: 1.576963456215E-01 155s Surface tension*area energy for atom 5: 1.825468090747E-01 155s Surface tension*area energy for atom 6: 1.574748619900E-01 155s Surface tension*area energy for atom 7: 1.407306994493E-01 155s Surface tension*area energy for atom 8: 1.406864027230E-01 155s Surface tension*area energy for atom 9: 1.156144556382E-01 155s Surface tension*area energy for atom 10: 1.153486752804E-01 155s Surface tension*area energy for atom 11: 1.174306214164E-01 155s Surface tension*area energy for atom 12: 1.176521050479E-01 155s Surface tension*area energy for atom 13: 6.600806573408E-03 155s Surface tension*area energy for atom 14: 1.432113161220E-01 155s Surface tension*area energy for atom 15: 1.429898324905E-01 155s Surface tension*area energy for atom 16: 3.541586603809E-02 155s Surface tension*area energy for atom 17: 1.852489093789E-01 155s Surface tension*area energy for atom 18: 1.596011048523E-01 155s Surface tension*area energy for atom 19: 1.594682146734E-01 155s 155s Total surface tension energy: 2.12748 kJ/mol 155s 155s Total solvent accessible volume: 298.053 A^3 155s 155s Total pressure*volume energy: 71.3539 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.635406071935E+00 155s WCA energy for atom 1: -5.957247427848E+00 155s WCA energy for atom 2: -5.524801144538E+00 155s WCA energy for atom 3: -5.522294168859E+00 155s WCA energy for atom 4: -1.605314409440E+00 155s WCA energy for atom 5: -1.701051761776E+00 155s WCA energy for atom 6: -1.606669162773E+00 155s WCA energy for atom 7: -1.442505934938E+00 155s WCA energy for atom 8: -1.443059002759E+00 155s WCA energy for atom 9: -1.328947132810E+00 155s WCA energy for atom 10: -1.328906972440E+00 155s WCA energy for atom 11: -1.331566344214E+00 155s WCA energy for atom 12: -1.328041776815E+00 155s WCA energy for atom 13: -5.937562025661E+00 155s WCA energy for atom 14: -1.442277774427E+00 155s WCA energy for atom 15: -1.442777091510E+00 155s WCA energy for atom 16: -6.602262542378E+00 155s WCA energy for atom 17: -1.698172146664E+00 155s WCA energy for atom 18: -1.600970858835E+00 155s WCA energy for atom 19: -1.600841970217E+00 155s 155s Total WCA energy: -57.0807 kJ/mol 155s 155s Total non-polar energy = 1.640068943201E+01 kJ/mol 155s ---------------------------------------- 155s CALCULATION #7 (solvated-isobutane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 3.464676753463E+00 155s SASA for atom 1: 1.984493338158E+01 155s SASA for atom 2: 1.778643845361E+01 155s SASA for atom 3: 1.671289426332E+01 155s SASA for atom 4: 0.000000000000E+00 155s SASA for atom 5: 3.531879535319E+00 155s SASA for atom 6: 1.673895116114E+01 155s SASA for atom 7: 1.793756846098E+01 155s SASA for atom 8: 1.973549441072E+01 155s SASA for atom 9: 1.710895911022E+01 155s SASA for atom 10: 4.599657069253E+00 155s SASA for atom 11: 1.937069784121E+01 155s SASA for atom 12: 1.654613011726E+01 155s SASA for atom 13: 1.936548646165E+01 155s 155s Total solvent accessible surface area: 192.744 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 2.944975240444E-02 155s Surface tension*area energy for atom 1: 1.686819337434E-01 155s Surface tension*area energy for atom 2: 1.511847268556E-01 155s Surface tension*area energy for atom 3: 1.420596012382E-01 155s Surface tension*area energy for atom 4: 0.000000000000E+00 155s Surface tension*area energy for atom 5: 3.002097605021E-02 155s Surface tension*area energy for atom 6: 1.422810848697E-01 155s Surface tension*area energy for atom 7: 1.524693319183E-01 155s Surface tension*area energy for atom 8: 1.677517024912E-01 155s Surface tension*area energy for atom 9: 1.454261524369E-01 155s Surface tension*area energy for atom 10: 3.909708508865E-02 155s Surface tension*area energy for atom 11: 1.646509316503E-01 155s Surface tension*area energy for atom 12: 1.406421059967E-01 155s Surface tension*area energy for atom 13: 1.646066349240E-01 155s 155s Total surface tension energy: 1.63832 kJ/mol 155s 155s Total solvent accessible volume: 218.943 A^3 155s 155s Total pressure*volume energy: 52.415 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.381016335247E+00 155s WCA energy for atom 1: -1.612317964554E+00 155s WCA energy for atom 2: -1.588013719598E+00 155s WCA energy for atom 3: -1.532162371190E+00 155s WCA energy for atom 4: -5.987950445279E+00 155s WCA energy for atom 5: -6.393089030861E+00 155s WCA energy for atom 6: -1.533454887042E+00 155s WCA energy for atom 7: -1.587650918485E+00 155s WCA energy for atom 8: -1.614083521570E+00 155s WCA energy for atom 9: -1.442402031577E+00 155s WCA energy for atom 10: -6.408813541353E+00 155s WCA energy for atom 11: -1.605830214390E+00 155s WCA energy for atom 12: -1.529385873788E+00 155s WCA energy for atom 13: -1.605662490385E+00 155s 155s Total WCA energy: -40.8218 kJ/mol 155s 155s Total non-polar energy = 1.323144287435E+01 kJ/mol 155s ---------------------------------------- 155s CALCULATION #8 (solvated-methane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 1.231304303117E+01 155s SASA for atom 1: 2.323233009850E+01 155s SASA for atom 2: 2.345641941977E+01 155s SASA for atom 3: 2.377431357320E+01 155s SASA for atom 4: 2.264344420771E+01 155s 155s Total solvent accessible surface area: 105.42 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 1.046608657649E-01 155s Surface tension*area energy for atom 1: 1.974748058372E-01 155s Surface tension*area energy for atom 2: 1.993795650680E-01 155s Surface tension*area energy for atom 3: 2.020816653722E-01 155s Surface tension*area energy for atom 4: 1.924692757655E-01 155s 155s Total surface tension energy: 0.896066 kJ/mol 155s 155s Total solvent accessible volume: 95.985 A^3 155s 155s Total pressure*volume energy: 22.9788 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -8.133807570805E+00 155s WCA energy for atom 1: -1.962181541765E+00 155s WCA energy for atom 2: -1.964078319162E+00 155s WCA energy for atom 3: -1.963015006647E+00 155s WCA energy for atom 4: -1.957425549100E+00 155s 155s Total WCA energy: -15.9805 kJ/mol 155s 155s Total non-polar energy = 7.894367190329E+00 kJ/mol 155s ---------------------------------------- 155s CALCULATION #9 (solvated-neopentane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 2.441701074100E+00 155s SASA for atom 1: 1.663993494942E+01 155s SASA for atom 2: 1.715586152630E+01 155s SASA for atom 3: 1.645753666466E+01 155s SASA for atom 4: 0.000000000000E+00 155s SASA for atom 5: 2.389432243768E+00 155s SASA for atom 6: 1.638457735076E+01 155s SASA for atom 7: 1.667641460637E+01 155s SASA for atom 8: 1.721839808108E+01 155s SASA for atom 9: 2.419300146815E+00 155s SASA for atom 10: 1.640021148945E+01 155s SASA for atom 11: 1.666599184724E+01 155s SASA for atom 12: 1.719234118325E+01 155s SASA for atom 13: 2.449168049862E+00 155s SASA for atom 14: 1.723403221977E+01 155s SASA for atom 15: 1.639500010989E+01 155s SASA for atom 16: 1.663472356985E+01 155s 155s Total solvent accessible surface area: 210.755 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 2.075445912985E-02 155s Surface tension*area energy for atom 1: 1.414394470700E-01 155s Surface tension*area energy for atom 2: 1.458248229736E-01 155s Surface tension*area energy for atom 3: 1.398890616496E-01 155s Surface tension*area energy for atom 4: 0.000000000000E+00 155s Surface tension*area energy for atom 5: 2.031017407203E-02 155s Surface tension*area energy for atom 6: 1.392689074814E-01 155s Surface tension*area energy for atom 7: 1.417495241541E-01 155s Surface tension*area energy for atom 8: 1.463563836891E-01 155s Surface tension*area energy for atom 9: 2.056405124793E-02 155s Surface tension*area energy for atom 10: 1.394017976603E-01 155s Surface tension*area energy for atom 11: 1.416609307015E-01 155s Surface tension*area energy for atom 12: 1.461349000577E-01 155s Surface tension*area energy for atom 13: 2.081792842383E-02 155s Surface tension*area energy for atom 14: 1.464892738680E-01 155s Surface tension*area energy for atom 15: 1.393575009340E-01 155s Surface tension*area energy for atom 16: 1.413951503437E-01 155s 155s Total surface tension energy: 1.79141 kJ/mol 155s 155s Total solvent accessible volume: 251.127 A^3 155s 155s Total pressure*volume energy: 60.1198 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.011082520236E+00 155s WCA energy for atom 1: -1.497367782613E+00 155s WCA energy for atom 2: -1.498546483218E+00 155s WCA energy for atom 3: -1.492562171495E+00 155s WCA energy for atom 4: -5.447325863939E+00 155s WCA energy for atom 5: -6.004516149175E+00 155s WCA energy for atom 6: -1.492776531092E+00 155s WCA energy for atom 7: -1.496078170066E+00 155s WCA energy for atom 8: -1.501529655270E+00 155s WCA energy for atom 9: -5.996267554365E+00 155s WCA energy for atom 10: -1.492194267752E+00 155s WCA energy for atom 11: -1.496027211216E+00 155s WCA energy for atom 12: -1.500561393960E+00 155s WCA energy for atom 13: -6.000218612907E+00 155s WCA energy for atom 14: -1.500859921426E+00 155s WCA energy for atom 15: -1.492908499790E+00 155s WCA energy for atom 16: -1.494057174414E+00 155s 155s Total WCA energy: -47.4149 kJ/mol 155s 155s Total non-polar energy = 1.449633815052E+01 kJ/mol 155s ---------------------------------------- 155s CALCULATION #10 (solvated-pentane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 4.405515699447E+00 155s SASA for atom 1: 8.213673337951E-01 155s SASA for atom 2: 3.285469335181E-01 155s SASA for atom 3: 7.466975761774E-01 155s SASA for atom 4: 1.855251124959E+01 155s SASA for atom 5: 2.147609518526E+01 155s SASA for atom 6: 1.852645435176E+01 155s SASA for atom 7: 1.655655287639E+01 155s SASA for atom 8: 1.655134149682E+01 155s SASA for atom 9: 1.360170066332E+01 155s SASA for atom 10: 1.357043238593E+01 155s SASA for atom 11: 1.685881289113E+01 155s SASA for atom 12: 1.687444702982E+01 155s SASA for atom 13: 4.196440378117E+00 155s SASA for atom 14: 1.881308022781E+01 155s SASA for atom 15: 1.882350298694E+01 155s SASA for atom 16: 2.182004623652E+01 155s 155s Total solvent accessible surface area: 222.524 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 3.744688344530E-02 155s Surface tension*area energy for atom 1: 6.981622337259E-03 155s Surface tension*area energy for atom 2: 2.792648934903E-03 155s Surface tension*area energy for atom 3: 6.346929397508E-03 155s Surface tension*area energy for atom 4: 1.576963456215E-01 155s Surface tension*area energy for atom 5: 1.825468090747E-01 155s Surface tension*area energy for atom 6: 1.574748619900E-01 155s Surface tension*area energy for atom 7: 1.407306994493E-01 155s Surface tension*area energy for atom 8: 1.406864027230E-01 155s Surface tension*area energy for atom 9: 1.156144556382E-01 155s Surface tension*area energy for atom 10: 1.153486752804E-01 155s Surface tension*area energy for atom 11: 1.432999095746E-01 155s Surface tension*area energy for atom 12: 1.434327997535E-01 155s Surface tension*area energy for atom 13: 3.566974321399E-02 155s Surface tension*area energy for atom 14: 1.599111819364E-01 155s Surface tension*area energy for atom 15: 1.599997753890E-01 155s Surface tension*area energy for atom 16: 1.854703930104E-01 155s 155s Total surface tension energy: 1.89145 kJ/mol 155s 155s Total solvent accessible volume: 258.93 A^3 155s 155s Total pressure*volume energy: 61.9878 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.655804319869E+00 155s WCA energy for atom 1: -6.027315962813E+00 155s WCA energy for atom 2: -5.696430965386E+00 155s WCA energy for atom 3: -6.016749084714E+00 155s WCA energy for atom 4: -1.608595384643E+00 155s WCA energy for atom 5: -1.703300955380E+00 155s WCA energy for atom 6: -1.609931495887E+00 155s WCA energy for atom 7: -1.457107525189E+00 155s WCA energy for atom 8: -1.457741620594E+00 155s WCA energy for atom 9: -1.354235498709E+00 155s WCA energy for atom 10: -1.354106470090E+00 155s WCA energy for atom 11: -1.456736412636E+00 155s WCA energy for atom 12: -1.455995435596E+00 155s WCA energy for atom 13: -6.633650611186E+00 155s WCA energy for atom 14: -1.605996088477E+00 155s WCA energy for atom 15: -1.606549890103E+00 155s WCA energy for atom 16: -1.700042300035E+00 155s 155s Total WCA energy: -49.4003 kJ/mol 155s 155s Total non-polar energy = 1.447900211546E+01 kJ/mol 155s ---------------------------------------- 155s CALCULATION #11 (solvated-propane): APOLAR 155s 155s Solvent Accessible Surface Area (SASA) for each atom: 155s SASA for atom 0: 3.173464698754E+00 155s SASA for atom 1: 1.931858404557E+01 155s SASA for atom 2: 2.014198201675E+01 155s SASA for atom 3: 2.149694070352E+01 155s SASA for atom 4: 1.904078819252E+00 155s SASA for atom 5: 2.067354273233E+01 155s SASA for atom 6: 1.937590922077E+01 155s SASA for atom 7: 3.098794941136E+00 155s SASA for atom 8: 1.942802301642E+01 155s SASA for atom 9: 1.973028303116E+01 155s SASA for atom 10: 2.204934693736E+01 155s 155s Total solvent accessible surface area: 170.391 A^2 155s 155s Surface tension*area energies (gamma * SASA) for each atom: 155s Surface tension*area energy for atom 0: 2.697444993941E-02 155s Surface tension*area energy for atom 1: 1.642079643873E-01 155s Surface tension*area energy for atom 2: 1.712068471424E-01 155s Surface tension*area energy for atom 3: 1.827239959799E-01 155s Surface tension*area energy for atom 4: 1.618466996365E-02 155s Surface tension*area energy for atom 5: 1.757251132248E-01 155s Surface tension*area energy for atom 6: 1.646952283766E-01 155s Surface tension*area energy for atom 7: 2.633975699966E-02 155s Surface tension*area energy for atom 8: 1.651381956396E-01 155s Surface tension*area energy for atom 9: 1.677074057649E-01 155s Surface tension*area energy for atom 10: 1.874194489675E-01 155s 155s Total surface tension energy: 1.44832 kJ/mol 155s 155s Total solvent accessible volume: 183.573 A^3 155s 155s Total pressure*volume energy: 43.9474 kJ/mol 155s 155s WCA dispersion Energies for each atom: 155s WCA energy for atom 0: -6.818670105515E+00 155s WCA energy for atom 1: -1.641297645338E+00 155s WCA energy for atom 2: -1.649584120441E+00 155s WCA energy for atom 3: -1.711408141255E+00 155s WCA energy for atom 4: -6.624720142882E+00 155s WCA energy for atom 5: -1.610117050515E+00 155s WCA energy for atom 6: -1.596858009746E+00 155s WCA energy for atom 7: -6.816460624835E+00 155s WCA energy for atom 8: -1.642782751806E+00 155s WCA energy for atom 9: -1.645779566650E+00 155s WCA energy for atom 10: -1.714436154542E+00 155s 155s Total WCA energy: -33.4721 kJ/mol 155s 155s Total non-polar energy = 1.192358496286E+01 kJ/mol 155s ---------------------------------------- 155s PRINT STATEMENTS 155s 155s print APOL energy 1 (solvated-2-methylbutane) end 155s Global net APOL energy = 1.439739455792E+01 kJ/mol 155s 155s print APOL energy 2 (solvated-butane) end 155s Global net APOL energy = 1.208346456826E+01 kJ/mol 155s 155s print APOL energy 3 (solvated-cyclohexane) end 155s Global net APOL energy = 1.354016672221E+01 kJ/mol 155s 155s print APOL energy 4 (solvated-cyclopentane) end 155s Global net APOL energy = 9.363673200142E+00 kJ/mol 155s 155s print APOL energy 5 (solvated-ethane) end 155s Global net APOL energy = 9.422717598546E+00 kJ/mol 155s 155s print APOL energy 6 (solvated-hexane) end 155s Global net APOL energy = 1.640068943201E+01 kJ/mol 155s 155s print APOL energy 7 (solvated-isobutane) end 155s Global net APOL energy = 1.323144287435E+01 kJ/mol 155s 155s print APOL energy 8 (solvated-methane) end 155s Global net APOL energy = 7.894367190329E+00 kJ/mol 155s 155s print APOL energy 9 (solvated-neopentane) end 155s Global net APOL energy = 1.449633815052E+01 kJ/mol 155s 155s print APOL energy 10 (solvated-pentane) end 155s Global net APOL energy = 1.447900211546E+01 kJ/mol 155s 155s print APOL energy 11 (solvated-propane) end 155s Global net APOL energy = 1.192358496286E+01 kJ/mol 155s ---------------------------------------- 155s CLEANING UP AND SHUTTING DOWN... 155s Destroying force arrays. 155s No energy arrays to destroy. 155s Destroying multigrid structures. 155s Destroying finite element structures. 155s Destroying 11 molecules 155s Final memory usage: 0.001 MB total, 2.267 MB high water 155s 155s 155s Thanks for using APBS! 155s 155s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 155s *** PASSED *** 155s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 155s *** PASSED *** 155s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 155s *** PASSED *** 155s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 155s *** PASSED *** 155s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 155s *** PASSED *** 155s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 155s *** PASSED *** 155s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 155s *** PASSED *** 155s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 155s *** PASSED *** 155s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 155s *** PASSED *** 155s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 155s *** PASSED *** 155s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 155s *** PASSED *** 155s Elapsed time: 5.675006 seconds 155s -------------------------------------------------------------------------------- 155s Total elapsed time: 5.675006 seconds 155s Test results have been logged 155s -------------------------------------------------------------------------------- 155s -------------------------------------------------------------------------------- 155s Testing input file 1d7h-dmso-mol.in 155s 159s Checking for intermediate energies in input file alkanes.out 159s EXPECTED COMPUTED: 11 159s EXPECTED EXPECTED: 11 159s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 159s 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'] 159s COMPUTED RESULT 14.39739455792 159s COMPUTED RESULT 12.08346456826 159s COMPUTED RESULT 13.54016672221 159s COMPUTED RESULT 9.363673200142 159s COMPUTED RESULT 9.422717598546 159s COMPUTED RESULT 16.40068943201 159s COMPUTED RESULT 13.23144287435 159s COMPUTED RESULT 7.894367190329 159s COMPUTED RESULT 14.49633815052 159s COMPUTED RESULT 14.47900211546 159s COMPUTED RESULT 11.92358496286 159s Running tests for FKBP section 159s BINARY: /usr/bin/apbs 159s INPUT: 1d7h-dmso-mol.in 159s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 159s asc_getToken: Error occurred (bailing out). 159s Vio_scanf: Format problem with input. 159s 159s 159s ---------------------------------------------------------------------- 159s APBS -- Adaptive Poisson-Boltzmann Solver 159s Version APBS 3.4.1 159s 159s Nathan A. Baker (nathan.baker@pnnl.gov) 159s Pacific Northwest National Laboratory 159s 159s Additional contributing authors listed in the code documentation. 159s 159s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 159s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 159s Northwest Division for the U.S. Department of Energy. 159s 159s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 159s Portions Copyright (c) 2002-2020, Nathan A. Baker. 159s Portions Copyright (c) 1999-2002, The Regents of the University of California. 159s Portions Copyright (c) 1995, Michael Holst. 159s All rights reserved. 159s 159s Redistribution and use in source and binary forms, with or without 159s modification, are permitted provided that the following conditions are met: 159s 159s * Redistributions of source code must retain the above copyright notice, this 159s list of conditions and the following disclaimer. 159s 159s * Redistributions in binary form must reproduce the above copyright notice, 159s this list of conditions and the following disclaimer in the documentation 159s and/or other materials provided with the distribution. 159s 159s * Neither the name of the developer nor the names of its contributors may be 159s used to endorse or promote products derived from this software without 159s specific prior written permission. 159s 159s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 159s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 159s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 159s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 159s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 159s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 159s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 159s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 159s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 159s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 159s ---------------------------------------------------------------------- 159s APBS uses FETK (the Finite Element ToolKit) to solve the 159s Poisson-Boltzmann equation numerically. FETK is a portable collection 159s of finite element modeling class libraries developed by the Michael Holst 159s research group and written in an object-oriented form of C. FEtk is 159s designed to solve general coupled systems of nonlinear partial differential 159s equations using adaptive finite element methods, inexact Newton methods, 159s and algebraic multilevel methods. More information about FEtk may be found 159s at . 159s ---------------------------------------------------------------------- 159s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 159s Aqua is a modified form of the Holst group PMG library 159s which has been modified by Patrice Koehl 159s for improved efficiency and 159s memory usage when solving the Poisson-Boltzmann equation. 159s ---------------------------------------------------------------------- 159s Please cite your use of APBS as: 159s 159s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 159s nanosystems: application to microtubules and the ribosome. Proc. 159s Natl. Acad. Sci. USA 98, 10037-10041 2001. 159s 159s 159s This executable compiled on Jan 3 2025 at 11:01:42 159s 159s Parsing input file 1d7h-dmso-mol.in... 159s rank 0 size 1... 159s Parsed input file. 159s Got paths for 3 molecules 159s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 159s asc_getToken: Error occurred (bailing out). 159s Vio_scanf: Format problem with input. 159s 1673 atoms 159s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 159s Net charge 9.91e-01 e 159s Reading PQR-format atom data from dmso-min.pqr. 159s asc_getToken: Error occurred (bailing out). 159s Vio_scanf: Format problem with input. 159s 10 atoms 159s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 159s Net charge 2.78e-17 e 159s Reading PQR-format atom data from 1d7h-min.pqr. 159s 1663 atoms 159s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 159s Net charge 9.91e-01 e 159s Preparing to run 12 PBE calculations. 159s ---------------------------------------- 159s CALCULATION #1 (complex-solv-coarse): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 30.4176 A 159s Current memory usage: 122.059 MB total, 122.059 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 1.500 x 1.500 x 1.500 159s Grid lengths: 96.000 x 96.000 x 96.000 159s Grid center: (25.875, 18.349, 19.112) 159s Multigrid levels: 5 159s Molecule ID: 1 159s Linearized traditional PBE 159s Multiple Debye-Huckel sphere boundary conditions 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 78.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 1.060899690259E+04 kJ/mol 159s Calculating forces... 159s [focusFillBound()]: WARNING: 159s Unusually large potential values 159s detected on the focusing boundary! 159s Convergence not guaranteed for NPBE/NRPBE calculations! 159s 159s ---------------------------------------- 159s CALCULATION #2 (complex-solv-fine): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 30.4176 A 159s Current memory usage: 122.059 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 0.225 x 0.225 x 0.225 159s Grid lengths: 14.400 x 14.400 x 14.400 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 1 159s Linearized traditional PBE 159s Boundary conditions from focusing 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 78.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 4.276523673491E+04 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s CALCULATION #3 (complex-ref-coarse): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 4.87072 A 159s Current memory usage: 122.059 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 1.500 x 1.500 x 1.500 159s Grid lengths: 96.000 x 96.000 x 96.000 159s Grid center: (25.875, 18.349, 19.112) 159s Multigrid levels: 5 159s Molecule ID: 1 159s Linearized traditional PBE 159s Multiple Debye-Huckel sphere boundary conditions 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 2.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 1.399234956777E+04 kJ/mol 159s Calculating forces... 159s [focusFillBound()]: WARNING: 159s Unusually large potential values 159s detected on the focusing boundary! 159s Convergence not guaranteed for NPBE/NRPBE calculations! 159s 159s ---------------------------------------- 159s CALCULATION #4 (complex-ref-fine): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 4.87072 A 159s Current memory usage: 122.059 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 0.225 x 0.225 x 0.225 159s Grid lengths: 14.400 x 14.400 x 14.400 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 1 159s Linearized traditional PBE 159s Boundary conditions from focusing 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 2.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 4.610066575192E+04 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 30.4176 A 159s Current memory usage: 62.428 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 1.500 x 1.500 x 1.500 159s Grid lengths: 96.000 x 96.000 x 96.000 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 2 159s Linearized traditional PBE 159s Multiple Debye-Huckel sphere boundary conditions 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 78.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 3.961107503213E+01 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s CALCULATION #6 (dmso-solv-fine): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 30.4176 A 159s Current memory usage: 62.428 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 0.225 x 0.225 x 0.225 159s Grid lengths: 14.400 x 14.400 x 14.400 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 2 159s Linearized traditional PBE 159s Boundary conditions from focusing 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 78.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 7.121048606059E+02 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 4.87072 A 159s Current memory usage: 62.428 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 1.500 x 1.500 x 1.500 159s Grid lengths: 96.000 x 96.000 x 96.000 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 2 159s Linearized traditional PBE 159s Multiple Debye-Huckel sphere boundary conditions 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 2.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 6.751571424823E+01 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s CALCULATION #8 (dmso-ref-fine): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 4.87072 A 159s Current memory usage: 62.428 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 0.225 x 0.225 x 0.225 159s Grid lengths: 14.400 x 14.400 x 14.400 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 2 159s Linearized traditional PBE 159s Boundary conditions from focusing 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 2.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 7.339101343121E+02 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 30.4176 A 159s Current memory usage: 121.736 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 1.500 x 1.500 x 1.500 159s Grid lengths: 96.000 x 96.000 x 96.000 159s Grid center: (25.875, 18.349, 19.112) 159s Multigrid levels: 5 159s Molecule ID: 3 159s Linearized traditional PBE 159s Multiple Debye-Huckel sphere boundary conditions 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 78.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 1.058410584089E+04 kJ/mol 159s Calculating forces... 159s [focusFillBound()]: WARNING: 159s Unusually large potential values 159s detected on the focusing boundary! 159s Convergence not guaranteed for NPBE/NRPBE calculations! 159s 159s ---------------------------------------- 159s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 30.4176 A 159s Current memory usage: 121.736 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 0.225 x 0.225 x 0.225 159s Grid lengths: 14.400 x 14.400 x 14.400 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 3 159s Linearized traditional PBE 159s Boundary conditions from focusing 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 78.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 4.205385249581E+04 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 4.87072 A 159s Current memory usage: 121.736 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 1.500 x 1.500 x 1.500 159s Grid lengths: 96.000 x 96.000 x 96.000 159s Grid center: (25.875, 18.349, 19.112) 159s Multigrid levels: 5 159s Molecule ID: 3 159s Linearized traditional PBE 159s Multiple Debye-Huckel sphere boundary conditions 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 2.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 1.395961902233E+04 kJ/mol 159s Calculating forces... 159s [focusFillBound()]: WARNING: 159s Unusually large potential values 159s detected on the focusing boundary! 159s Convergence not guaranteed for NPBE/NRPBE calculations! 159s 159s ---------------------------------------- 159s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 159s Setting up problem... 159s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 159s Debye length: 4.87072 A 159s Current memory usage: 121.736 MB total, 221.696 MB high water 159s Using linear spline charge discretization. 159s Grid dimensions: 65 x 65 x 65 159s Grid spacings: 0.225 x 0.225 x 0.225 159s Grid lengths: 14.400 x 14.400 x 14.400 159s Grid center: (17.751, 17.770, 20.492) 159s Multigrid levels: 5 159s Molecule ID: 3 159s Linearized traditional PBE 159s Boundary conditions from focusing 159s 2 ion species (0.010 M ionic strength): 159s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 159s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 159s Solute dielectric: 2.000 159s Solvent dielectric: 2.000 159s Using "molecular" surface definition; no smoothing 159s Solvent probe radius: 0.000 A 159s Temperature: 300.000 K 159s Electrostatic energies will be calculated 159s Total electrostatic energy = 4.538248433997E+04 kJ/mol 159s Calculating forces... 159s ---------------------------------------- 159s PRINT STATEMENTS 159s 159s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 159s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 159s Global net ELEC energy = -3.335429017008E+03 kJ/mol 159s 159s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 159s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 159s Global net ELEC energy = -2.180527370616E+01 kJ/mol 159s 159s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 159s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 159s Global net ELEC energy = -3.328631844166E+03 kJ/mol 159s 159s 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 159s Local net energy (PE 0) = 1.500810086371E+01 kJ/mol 159s Global net ELEC energy = 1.500810086371E+01 kJ/mol 159s ---------------------------------------- 159s CLEANING UP AND SHUTTING DOWN... 159s Destroying force arrays. 159s No energy arrays to destroy. 159s Destroying multigrid structures. 159s Destroying finite element structures. 159s Destroying 3 molecules 159s Final memory usage: 0.001 MB total, 221.696 MB high water 159s 159s 159s Thanks for using APBS! 159s 159s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 159s *** PASSED *** 159s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 159s *** PASSED *** 159s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 159s *** PASSED *** 159s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 159s *** PASSED *** 159s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 159s *** PASSED *** 159s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 159s *** PASSED *** 159s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 159s *** PASSED *** 159s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 159s *** PASSED *** 159s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 159s *** PASSED *** 159s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 159s *** PASSED *** 159s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 159s *** PASSED *** 159s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 159s *** PASSED *** 159s Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) 159s *** PASSED *** 159s Elapsed time: 4.756686 seconds 159s -------------------------------------------------------------------------------- 159s -------------------------------------------------------------------------------- 159s Testing input file 1d7h-dmso-smol.in 159s 164s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 164s *** PASSED *** 164s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 164s *** PASSED *** 164s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 164s *** PASSED *** 164s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 164s *** PASSED *** 164s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 164s *** PASSED *** 164s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 164s *** PASSED *** 164s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 164s *** PASSED *** 164s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 164s *** PASSED *** 164s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 164s *** PASSED *** 164s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 164s *** PASSED *** 164s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 164s *** PASSED *** 164s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 164s *** PASSED *** 164s Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) 164s *** PASSED *** 164s Elapsed time: 4.664175 seconds 164s -------------------------------------------------------------------------------- 164s -------------------------------------------------------------------------------- 164s Testing input file 1d7i-dss-mol.in 164s 164s Checking for intermediate energies in input file 1d7h-dmso-mol.out 164s EXPECTED COMPUTED: 16 164s EXPECTED EXPECTED: 16 164s 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] 164s 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'] 164s COMPUTED RESULT 10608.99690259 164s COMPUTED RESULT 42765.23673491 164s COMPUTED RESULT 13992.34956777 164s COMPUTED RESULT 46100.66575192 164s COMPUTED RESULT 39.61107503213 164s COMPUTED RESULT 712.1048606059 164s COMPUTED RESULT 67.51571424823 164s COMPUTED RESULT 733.9101343121 164s COMPUTED RESULT 10584.10584089 164s COMPUTED RESULT 42053.85249581 164s COMPUTED RESULT 13959.61902233 164s COMPUTED RESULT 45382.48433997 164s COMPUTED RESULT -3335.429017008 164s COMPUTED RESULT -21.80527370616 164s COMPUTED RESULT -3328.631844166 164s COMPUTED RESULT 15.00810086371 164s BINARY: /usr/bin/apbs 164s INPUT: 1d7h-dmso-smol.in 164s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 164s asc_getToken: Error occurred (bailing out). 164s Vio_scanf: Format problem with input. 164s 164s 164s ---------------------------------------------------------------------- 164s APBS -- Adaptive Poisson-Boltzmann Solver 164s Version APBS 3.4.1 164s 164s Nathan A. Baker (nathan.baker@pnnl.gov) 164s Pacific Northwest National Laboratory 164s 164s Additional contributing authors listed in the code documentation. 164s 164s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 164s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 164s Northwest Division for the U.S. Department of Energy. 164s 164s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 164s Portions Copyright (c) 2002-2020, Nathan A. Baker. 164s Portions Copyright (c) 1999-2002, The Regents of the University of California. 164s Portions Copyright (c) 1995, Michael Holst. 164s All rights reserved. 164s 164s Redistribution and use in source and binary forms, with or without 164s modification, are permitted provided that the following conditions are met: 164s 164s * Redistributions of source code must retain the above copyright notice, this 164s list of conditions and the following disclaimer. 164s 164s * Redistributions in binary form must reproduce the above copyright notice, 164s this list of conditions and the following disclaimer in the documentation 164s and/or other materials provided with the distribution. 164s 164s * Neither the name of the developer nor the names of its contributors may be 164s used to endorse or promote products derived from this software without 164s specific prior written permission. 164s 164s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 164s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 164s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 164s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 164s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 164s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 164s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 164s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 164s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 164s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 164s ---------------------------------------------------------------------- 164s APBS uses FETK (the Finite Element ToolKit) to solve the 164s Poisson-Boltzmann equation numerically. FETK is a portable collection 164s of finite element modeling class libraries developed by the Michael Holst 164s research group and written in an object-oriented form of C. FEtk is 164s designed to solve general coupled systems of nonlinear partial differential 164s equations using adaptive finite element methods, inexact Newton methods, 164s and algebraic multilevel methods. More information about FEtk may be found 164s at . 164s ---------------------------------------------------------------------- 164s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 164s Aqua is a modified form of the Holst group PMG library 164s which has been modified by Patrice Koehl 164s for improved efficiency and 164s memory usage when solving the Poisson-Boltzmann equation. 164s ---------------------------------------------------------------------- 164s Please cite your use of APBS as: 164s 164s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 164s nanosystems: application to microtubules and the ribosome. Proc. 164s Natl. Acad. Sci. USA 98, 10037-10041 2001. 164s 164s 164s This executable compiled on Jan 3 2025 at 11:01:42 164s 164s Parsing input file 1d7h-dmso-smol.in... 164s rank 0 size 1... 164s Parsed input file. 164s Got paths for 3 molecules 164s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 164s asc_getToken: Error occurred (bailing out). 164s Vio_scanf: Format problem with input. 164s 1673 atoms 164s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 164s Net charge 9.91e-01 e 164s Reading PQR-format atom data from dmso-min.pqr. 164s asc_getToken: Error occurred (bailing out). 164s Vio_scanf: Format problem with input. 164s 10 atoms 164s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 164s Net charge 2.78e-17 e 164s Reading PQR-format atom data from 1d7h-min.pqr. 164s 1663 atoms 164s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 164s Net charge 9.91e-01 e 164s Preparing to run 12 PBE calculations. 164s ---------------------------------------- 164s CALCULATION #1 (complex-solv-coarse): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 30.4176 A 164s Current memory usage: 122.059 MB total, 122.059 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 1.500 x 1.500 x 1.500 164s Grid lengths: 96.000 x 96.000 x 96.000 164s Grid center: (25.875, 18.349, 19.112) 164s Multigrid levels: 5 164s Molecule ID: 1 164s Linearized traditional PBE 164s Multiple Debye-Huckel sphere boundary conditions 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 78.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 1.074948704824E+04 kJ/mol 164s Calculating forces... 164s [focusFillBound()]: WARNING: 164s Unusually large potential values 164s detected on the focusing boundary! 164s Convergence not guaranteed for NPBE/NRPBE calculations! 164s 164s ---------------------------------------- 164s CALCULATION #2 (complex-solv-fine): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 30.4176 A 164s Current memory usage: 122.059 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 0.225 x 0.225 x 0.225 164s Grid lengths: 14.400 x 14.400 x 14.400 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 1 164s Linearized traditional PBE 164s Boundary conditions from focusing 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 78.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 4.289487256481E+04 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s CALCULATION #3 (complex-ref-coarse): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 4.87072 A 164s Current memory usage: 122.059 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 1.500 x 1.500 x 1.500 164s Grid lengths: 96.000 x 96.000 x 96.000 164s Grid center: (25.875, 18.349, 19.112) 164s Multigrid levels: 5 164s Molecule ID: 1 164s Linearized traditional PBE 164s Multiple Debye-Huckel sphere boundary conditions 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 2.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 1.399234956777E+04 kJ/mol 164s Calculating forces... 164s [focusFillBound()]: WARNING: 164s Unusually large potential values 164s detected on the focusing boundary! 164s Convergence not guaranteed for NPBE/NRPBE calculations! 164s 164s ---------------------------------------- 164s CALCULATION #4 (complex-ref-fine): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 4.87072 A 164s Current memory usage: 122.059 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 0.225 x 0.225 x 0.225 164s Grid lengths: 14.400 x 14.400 x 14.400 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 1 164s Linearized traditional PBE 164s Boundary conditions from focusing 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 2.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 4.610066575192E+04 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 30.4176 A 164s Current memory usage: 62.428 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 1.500 x 1.500 x 1.500 164s Grid lengths: 96.000 x 96.000 x 96.000 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 2 164s Linearized traditional PBE 164s Multiple Debye-Huckel sphere boundary conditions 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 78.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 3.719709905887E+01 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s CALCULATION #6 (dmso-solv-fine): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 30.4176 A 164s Current memory usage: 62.428 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 0.225 x 0.225 x 0.225 164s Grid lengths: 14.400 x 14.400 x 14.400 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 2 164s Linearized traditional PBE 164s Boundary conditions from focusing 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 78.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 7.125747080979E+02 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 4.87072 A 164s Current memory usage: 62.428 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 1.500 x 1.500 x 1.500 164s Grid lengths: 96.000 x 96.000 x 96.000 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 2 164s Linearized traditional PBE 164s Multiple Debye-Huckel sphere boundary conditions 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 2.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 6.751571424823E+01 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s CALCULATION #8 (dmso-ref-fine): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 4.87072 A 164s Current memory usage: 62.428 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 0.225 x 0.225 x 0.225 164s Grid lengths: 14.400 x 14.400 x 14.400 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 2 164s Linearized traditional PBE 164s Boundary conditions from focusing 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 2.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 7.339101343121E+02 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 30.4176 A 164s Current memory usage: 121.736 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 1.500 x 1.500 x 1.500 164s Grid lengths: 96.000 x 96.000 x 96.000 164s Grid center: (25.875, 18.349, 19.112) 164s Multigrid levels: 5 164s Molecule ID: 3 164s Linearized traditional PBE 164s Multiple Debye-Huckel sphere boundary conditions 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 78.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 1.071654753674E+04 kJ/mol 164s Calculating forces... 164s [focusFillBound()]: WARNING: 164s Unusually large potential values 164s detected on the focusing boundary! 164s Convergence not guaranteed for NPBE/NRPBE calculations! 164s 164s ---------------------------------------- 164s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 30.4176 A 164s Current memory usage: 121.736 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 0.225 x 0.225 x 0.225 164s Grid lengths: 14.400 x 14.400 x 14.400 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 3 164s Linearized traditional PBE 164s Boundary conditions from focusing 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 78.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 4.218178203716E+04 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 4.87072 A 164s Current memory usage: 121.736 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 1.500 x 1.500 x 1.500 164s Grid lengths: 96.000 x 96.000 x 96.000 164s Grid center: (25.875, 18.349, 19.112) 164s Multigrid levels: 5 164s Molecule ID: 3 164s Linearized traditional PBE 164s Multiple Debye-Huckel sphere boundary conditions 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 2.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 1.395961902233E+04 kJ/mol 164s Calculating forces... 164s [focusFillBound()]: WARNING: 164s Unusually large potential values 164s detected on the focusing boundary! 164s Convergence not guaranteed for NPBE/NRPBE calculations! 164s 164s ---------------------------------------- 164s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 164s Setting up problem... 164s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 164s Debye length: 4.87072 A 164s Current memory usage: 121.736 MB total, 221.696 MB high water 164s Using linear spline charge discretization. 164s Grid dimensions: 65 x 65 x 65 164s Grid spacings: 0.225 x 0.225 x 0.225 164s Grid lengths: 14.400 x 14.400 x 14.400 164s Grid center: (17.751, 17.770, 20.492) 164s Multigrid levels: 5 164s Molecule ID: 3 164s Linearized traditional PBE 164s Boundary conditions from focusing 164s 2 ion species (0.010 M ionic strength): 164s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 164s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 164s Solute dielectric: 2.000 164s Solvent dielectric: 2.000 164s Using "molecular" surface definition;harmonic average smoothing 164s Solvent probe radius: 0.000 A 164s Temperature: 300.000 K 164s Electrostatic energies will be calculated 164s Total electrostatic energy = 4.538248433997E+04 kJ/mol 164s Calculating forces... 164s ---------------------------------------- 164s PRINT STATEMENTS 164s 164s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 164s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 164s Global net ELEC energy = -3.205793187109E+03 kJ/mol 164s 164s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 164s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 164s Global net ELEC energy = -2.133542621421E+01 kJ/mol 164s 164s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 164s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 164s Global net ELEC energy = -3.200702302816E+03 kJ/mol 164s 164s 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 164s Local net energy (PE 0) = 1.624454192073E+01 kJ/mol 164s Global net ELEC energy = 1.624454192073E+01 kJ/mol 164s ---------------------------------------- 164s CLEANING UP AND SHUTTING DOWN... 164s Destroying force arrays. 164s No energy arrays to destroy. 164s Destroying multigrid structures. 164s Destroying finite element structures. 164s Destroying 3 molecules 164s Final memory usage: 0.001 MB total, 221.696 MB high water 164s 164s 164s Thanks for using APBS! 164s 169s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 169s *** PASSED *** 169s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 169s *** PASSED *** 169s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 169s *** PASSED *** 169s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 169s *** PASSED *** 169s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 169s *** PASSED *** 169s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 169s *** PASSED *** 169s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 169s *** PASSED *** 169s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 169s *** PASSED *** 169s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 169s *** PASSED *** 169s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 169s *** PASSED *** 169s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 169s *** PASSED *** 169s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 169s *** PASSED *** 169s Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) 169s *** PASSED *** 169s Elapsed time: 4.773111 seconds 169s -------------------------------------------------------------------------------- 169s -------------------------------------------------------------------------------- 169s Testing input file 1d7i-dss-smol.in 169s 169s Checking for intermediate energies in input file 1d7h-dmso-smol.out 169s EXPECTED COMPUTED: 16 169s EXPECTED EXPECTED: 16 169s 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] 169s 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'] 169s COMPUTED RESULT 10749.48704824 169s COMPUTED RESULT 42894.87256481 169s COMPUTED RESULT 13992.34956777 169s COMPUTED RESULT 46100.66575192 169s COMPUTED RESULT 37.19709905887 169s COMPUTED RESULT 712.5747080979 169s COMPUTED RESULT 67.51571424823 169s COMPUTED RESULT 733.9101343121 169s COMPUTED RESULT 10716.54753674 169s COMPUTED RESULT 42181.78203716 169s COMPUTED RESULT 13959.61902233 169s COMPUTED RESULT 45382.48433997 169s COMPUTED RESULT -3205.793187109 169s COMPUTED RESULT -21.33542621421 169s COMPUTED RESULT -3200.702302816 169s COMPUTED RESULT 16.24454192073 169s BINARY: /usr/bin/apbs 169s INPUT: 1d7i-dss-mol.in 169s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 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 1d7i-dss-mol.in... 169s rank 0 size 1... 169s Parsed input file. 169s Got paths for 3 molecules 169s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 1677 atoms 169s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 169s Net charge 9.91e-01 e 169s Reading PQR-format atom data from dss-min.pqr. 169s asc_getToken: Error occurred (bailing out). 169s Vio_scanf: Format problem with input. 169s 14 atoms 169s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 169s Net charge -8.33e-17 e 169s Reading PQR-format atom data from 1d7i-min.pqr. 169s 1663 atoms 169s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 169s Net charge 9.91e-01 e 169s Preparing to run 12 PBE calculations. 169s ---------------------------------------- 169s CALCULATION #1 (complex-solv-coarse): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 30.4176 A 169s Current memory usage: 122.425 MB total, 122.425 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 1.500 x 1.500 x 1.500 169s Grid lengths: 96.000 x 96.000 x 96.000 169s Grid center: (25.264, 18.988, 19.122) 169s Multigrid levels: 5 169s Molecule ID: 1 169s Linearized traditional PBE 169s Multiple Debye-Huckel sphere boundary conditions 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 78.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 9.160578033846E+03 kJ/mol 169s Calculating forces... 169s [focusFillBound()]: WARNING: 169s Unusually large potential values 169s detected on the focusing boundary! 169s Convergence not guaranteed for NPBE/NRPBE calculations! 169s 169s ---------------------------------------- 169s CALCULATION #2 (complex-solv-fine): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 30.4176 A 169s Current memory usage: 122.425 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 0.225 x 0.225 x 0.225 169s Grid lengths: 14.400 x 14.400 x 14.400 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 1 169s Linearized traditional PBE 169s Boundary conditions from focusing 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 78.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 3.955701871716E+04 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s CALCULATION #3 (complex-ref-coarse): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 4.87072 A 169s Current memory usage: 122.425 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 1.500 x 1.500 x 1.500 169s Grid lengths: 96.000 x 96.000 x 96.000 169s Grid center: (25.264, 18.988, 19.122) 169s Multigrid levels: 5 169s Molecule ID: 1 169s Linearized traditional PBE 169s Multiple Debye-Huckel sphere boundary conditions 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 2.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 1.264965939588E+04 kJ/mol 169s Calculating forces... 169s [focusFillBound()]: WARNING: 169s Unusually large potential values 169s detected on the focusing boundary! 169s Convergence not guaranteed for NPBE/NRPBE calculations! 169s 169s ---------------------------------------- 169s CALCULATION #4 (complex-ref-fine): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 4.87072 A 169s Current memory usage: 122.425 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 0.225 x 0.225 x 0.225 169s Grid lengths: 14.400 x 14.400 x 14.400 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 1 169s Linearized traditional PBE 169s Boundary conditions from focusing 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 2.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 4.301801664829E+04 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s CALCULATION #5 (dss-solv-coarse): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 30.4176 A 169s Current memory usage: 62.528 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 1.500 x 1.500 x 1.500 169s Grid lengths: 96.000 x 96.000 x 96.000 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 2 169s Linearized traditional PBE 169s Multiple Debye-Huckel sphere boundary conditions 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 78.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 9.431133325426E+01 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s CALCULATION #6 (dss-solv-fine): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 30.4176 A 169s Current memory usage: 62.528 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 0.225 x 0.225 x 0.225 169s Grid lengths: 14.400 x 14.400 x 14.400 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 2 169s Linearized traditional PBE 169s Boundary conditions from focusing 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 78.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 1.677348113184E+03 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s CALCULATION #7 (dss-ref-coarse): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 4.87072 A 169s Current memory usage: 62.528 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 1.500 x 1.500 x 1.500 169s Grid lengths: 96.000 x 96.000 x 96.000 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 2 169s Linearized traditional PBE 169s Multiple Debye-Huckel sphere boundary conditions 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 2.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 1.171079106781E+02 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s CALCULATION #8 (dss-ref-fine): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 4.87072 A 169s Current memory usage: 62.528 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 0.225 x 0.225 x 0.225 169s Grid lengths: 14.400 x 14.400 x 14.400 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 2 169s Linearized traditional PBE 169s Boundary conditions from focusing 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 2.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 1.697869784185E+03 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 30.4176 A 169s Current memory usage: 121.977 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 1.500 x 1.500 x 1.500 169s Grid lengths: 96.000 x 96.000 x 96.000 169s Grid center: (25.264, 18.988, 19.122) 169s Multigrid levels: 5 169s Molecule ID: 3 169s Linearized traditional PBE 169s Multiple Debye-Huckel sphere boundary conditions 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 78.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 9.040108332204E+03 kJ/mol 169s Calculating forces... 169s [focusFillBound()]: WARNING: 169s Unusually large potential values 169s detected on the focusing boundary! 169s Convergence not guaranteed for NPBE/NRPBE calculations! 169s 169s ---------------------------------------- 169s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 30.4176 A 169s Current memory usage: 121.977 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 0.225 x 0.225 x 0.225 169s Grid lengths: 14.400 x 14.400 x 14.400 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 3 169s Linearized traditional PBE 169s Boundary conditions from focusing 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 78.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 3.787747796627E+04 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 4.87072 A 169s Current memory usage: 121.977 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 1.500 x 1.500 x 1.500 169s Grid lengths: 96.000 x 96.000 x 96.000 169s Grid center: (25.264, 18.988, 19.122) 169s Multigrid levels: 5 169s Molecule ID: 3 169s Linearized traditional PBE 169s Multiple Debye-Huckel sphere boundary conditions 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 2.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 1.252495566243E+04 kJ/mol 169s Calculating forces... 169s [focusFillBound()]: WARNING: 169s Unusually large potential values 169s detected on the focusing boundary! 169s Convergence not guaranteed for NPBE/NRPBE calculations! 169s 169s ---------------------------------------- 169s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 169s Setting up problem... 169s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 169s Debye length: 4.87072 A 169s Current memory usage: 121.977 MB total, 222.305 MB high water 169s Using linear spline charge discretization. 169s Grid dimensions: 65 x 65 x 65 169s Grid spacings: 0.225 x 0.225 x 0.225 169s Grid lengths: 14.400 x 14.400 x 14.400 169s Grid center: (17.340, 19.211, 20.503) 169s Multigrid levels: 5 169s Molecule ID: 3 169s Linearized traditional PBE 169s Boundary conditions from focusing 169s 2 ion species (0.010 M ionic strength): 169s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 169s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 169s Solute dielectric: 2.000 169s Solvent dielectric: 2.000 169s Using "molecular" surface definition; no smoothing 169s Solvent probe radius: 0.000 A 169s Temperature: 300.000 K 169s Electrostatic energies will be calculated 169s Total electrostatic energy = 4.133237922574E+04 kJ/mol 169s Calculating forces... 169s ---------------------------------------- 169s PRINT STATEMENTS 169s 169s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 169s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 169s Global net ELEC energy = -3.460997931137E+03 kJ/mol 169s 169s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 169s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 169s Global net ELEC energy = -2.052167100108E+01 kJ/mol 169s 169s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 169s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 169s Global net ELEC energy = -3.454901259473E+03 kJ/mol 169s 169s 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 169s Local net energy (PE 0) = 1.442499933668E+01 kJ/mol 169s Global net ELEC energy = 1.442499933668E+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 3 molecules 169s Final memory usage: 0.001 MB total, 222.305 MB high water 169s 169s 169s Thanks for using APBS! 169s 173s Checking for intermediate energies in input file 1d7i-dss-mol.out 173s EXPECTED COMPUTED: 16 173s EXPECTED EXPECTED: 16 173s 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] 173s 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'] 173s COMPUTED RESULT 9160.578033846 173s COMPUTED RESULT 39557.01871716 173s COMPUTED RESULT 12649.65939588 173s COMPUTED RESULT 43018.01664829 173s COMPUTED RESULT 94.31133325426 173s COMPUTED RESULT 1677.348113184 173s COMPUTED RESULT 117.1079106781 173s COMPUTED RESULT 1697.869784185 173s COMPUTED RESULT 9040.108332204 173s COMPUTED RESULT 37877.47796627 173s COMPUTED RESULT 12524.95566243 173s COMPUTED RESULT 41332.37922574 173s COMPUTED RESULT -3460.997931137 173s COMPUTED RESULT -20.52167100108 173s COMPUTED RESULT -3454.901259473 173s COMPUTED RESULT 14.42499933668 173s BINARY: /usr/bin/apbs 173s INPUT: 1d7i-dss-smol.in 173s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 173s asc_getToken: Error occurred (bailing out). 173s Vio_scanf: Format problem with input. 173s 173s 173s ---------------------------------------------------------------------- 173s APBS -- Adaptive Poisson-Boltzmann Solver 173s Version APBS 3.4.1 173s 173s Nathan A. Baker (nathan.baker@pnnl.gov) 173s Pacific Northwest National Laboratory 173s 173s Additional contributing authors listed in the code documentation. 173s 173s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 173s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 173s Northwest Division for the U.S. Department of Energy. 173s 173s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 173s Portions Copyright (c) 2002-2020, Nathan A. Baker. 173s Portions Copyright (c) 1999-2002, The Regents of the University of California. 173s Portions Copyright (c) 1995, Michael Holst. 173s All rights reserved. 173s 173s Redistribution and use in source and binary forms, with or without 173s modification, are permitted provided that the following conditions are met: 173s 173s * Redistributions of source code must retain the above copyright notice, this 173s list of conditions and the following disclaimer. 173s 173s * Redistributions in binary form must reproduce the above copyright notice, 173s this list of conditions and the following disclaimer in the documentation 173s and/or other materials provided with the distribution. 173s 173s * Neither the name of the developer nor the names of its contributors may be 173s used to endorse or promote products derived from this software without 173s specific prior written permission. 173s 173s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 173s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 173s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 173s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 173s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 173s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 173s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 173s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 173s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 173s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 173s ---------------------------------------------------------------------- 173s APBS uses FETK (the Finite Element ToolKit) to solve the 173s Poisson-Boltzmann equation numerically. FETK is a portable collection 173s of finite element modeling class libraries developed by the Michael Holst 173s research group and written in an object-oriented form of C. FEtk is 173s designed to solve general coupled systems of nonlinear partial differential 173s equations using adaptive finite element methods, inexact Newton methods, 173s and algebraic multilevel methods. More information about FEtk may be found 173s at . 173s ---------------------------------------------------------------------- 173s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 173s Aqua is a modified form of the Holst group PMG library 173s which has been modified by Patrice Koehl 173s for improved efficiency and 173s memory usage when solving the Poisson-Boltzmann equation. 173s ---------------------------------------------------------------------- 173s Please cite your use of APBS as: 173s 173s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 173s nanosystems: application to microtubules and the ribosome. Proc. 173s Natl. Acad. Sci. USA 98, 10037-10041 2001. 173s 173s 173s This executable compiled on Jan 3 2025 at 11:01:42 173s 173s Parsing input file 1d7i-dss-smol.in... 173s rank 0 size 1... 173s Parsed input file. 173s Got paths for 3 molecules 173s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 173s asc_getToken: Error occurred (bailing out). 173s Vio_scanf: Format problem with input. 173s 1677 atoms 173s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 173s Net charge 9.91e-01 e 173s Reading PQR-format atom data from dss-min.pqr. 173s asc_getToken: Error occurred (bailing out). 173s Vio_scanf: Format problem with input. 173s 14 atoms 173s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 173s Net charge -8.33e-17 e 173s Reading PQR-format atom data from 1d7i-min.pqr. 173s 1663 atoms 173s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 173s Net charge 9.91e-01 e 173s Preparing to run 12 PBE calculations. 173s ---------------------------------------- 173s CALCULATION #1 (complex-solv-coarse): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 30.4176 A 173s Current memory usage: 122.425 MB total, 122.425 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 1.500 x 1.500 x 1.500 173s Grid lengths: 96.000 x 96.000 x 96.000 173s Grid center: (25.264, 18.988, 19.122) 173s Multigrid levels: 5 173s Molecule ID: 1 173s Linearized traditional PBE 173s Multiple Debye-Huckel sphere boundary conditions 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 78.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 9.634884642408E+03 kJ/mol 173s Calculating forces... 173s [focusFillBound()]: WARNING: 173s Unusually large potential values 173s detected on the focusing boundary! 173s Convergence not guaranteed for NPBE/NRPBE calculations! 173s 173s ---------------------------------------- 173s CALCULATION #2 (complex-solv-fine): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 30.4176 A 173s Current memory usage: 122.425 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 0.225 x 0.225 x 0.225 173s Grid lengths: 14.400 x 14.400 x 14.400 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 1 173s Linearized traditional PBE 173s Boundary conditions from focusing 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 78.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 4.003177540425E+04 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s CALCULATION #3 (complex-ref-coarse): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 4.87072 A 173s Current memory usage: 122.425 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 1.500 x 1.500 x 1.500 173s Grid lengths: 96.000 x 96.000 x 96.000 173s Grid center: (25.264, 18.988, 19.122) 173s Multigrid levels: 5 173s Molecule ID: 1 173s Linearized traditional PBE 173s Multiple Debye-Huckel sphere boundary conditions 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 2.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 1.264965939588E+04 kJ/mol 173s Calculating forces... 173s [focusFillBound()]: WARNING: 173s Unusually large potential values 173s detected on the focusing boundary! 173s Convergence not guaranteed for NPBE/NRPBE calculations! 173s 173s ---------------------------------------- 173s CALCULATION #4 (complex-ref-fine): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 4.87072 A 173s Current memory usage: 122.425 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 0.225 x 0.225 x 0.225 173s Grid lengths: 14.400 x 14.400 x 14.400 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 1 173s Linearized traditional PBE 173s Boundary conditions from focusing 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 2.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 4.301801664829E+04 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s CALCULATION #5 (dss-solv-coarse): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 30.4176 A 173s Current memory usage: 62.528 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 1.500 x 1.500 x 1.500 173s Grid lengths: 96.000 x 96.000 x 96.000 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 2 173s Linearized traditional PBE 173s Multiple Debye-Huckel sphere boundary conditions 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 78.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 7.942232645345E+01 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s CALCULATION #6 (dss-solv-fine): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 30.4176 A 173s Current memory usage: 62.528 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 0.225 x 0.225 x 0.225 173s Grid lengths: 14.400 x 14.400 x 14.400 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 2 173s Linearized traditional PBE 173s Boundary conditions from focusing 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 78.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 1.677798535473E+03 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s CALCULATION #7 (dss-ref-coarse): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 4.87072 A 173s Current memory usage: 62.528 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 1.500 x 1.500 x 1.500 173s Grid lengths: 96.000 x 96.000 x 96.000 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 2 173s Linearized traditional PBE 173s Multiple Debye-Huckel sphere boundary conditions 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 2.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 1.171079106781E+02 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s CALCULATION #8 (dss-ref-fine): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 4.87072 A 173s Current memory usage: 62.528 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 0.225 x 0.225 x 0.225 173s Grid lengths: 14.400 x 14.400 x 14.400 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 2 173s Linearized traditional PBE 173s Boundary conditions from focusing 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 2.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 1.697869784185E+03 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 30.4176 A 173s Current memory usage: 121.977 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 1.500 x 1.500 x 1.500 173s Grid lengths: 96.000 x 96.000 x 96.000 173s Grid center: (25.264, 18.988, 19.122) 173s Multigrid levels: 5 173s Molecule ID: 3 173s Linearized traditional PBE 173s Multiple Debye-Huckel sphere boundary conditions 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 78.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 9.507068451372E+03 kJ/mol 173s Calculating forces... 173s [focusFillBound()]: WARNING: 173s Unusually large potential values 173s detected on the focusing boundary! 173s Convergence not guaranteed for NPBE/NRPBE calculations! 173s 173s ---------------------------------------- 173s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 30.4176 A 173s Current memory usage: 121.977 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 0.225 x 0.225 x 0.225 173s Grid lengths: 14.400 x 14.400 x 14.400 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 3 173s Linearized traditional PBE 173s Boundary conditions from focusing 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 78.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 3.835075772299E+04 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 4.87072 A 173s Current memory usage: 121.977 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 1.500 x 1.500 x 1.500 173s Grid lengths: 96.000 x 96.000 x 96.000 173s Grid center: (25.264, 18.988, 19.122) 173s Multigrid levels: 5 173s Molecule ID: 3 173s Linearized traditional PBE 173s Multiple Debye-Huckel sphere boundary conditions 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 2.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 1.252495566243E+04 kJ/mol 173s Calculating forces... 173s [focusFillBound()]: WARNING: 173s Unusually large potential values 173s detected on the focusing boundary! 173s Convergence not guaranteed for NPBE/NRPBE calculations! 173s 173s ---------------------------------------- 173s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 173s Setting up problem... 173s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 173s Debye length: 4.87072 A 173s Current memory usage: 121.977 MB total, 222.305 MB high water 173s Using linear spline charge discretization. 173s Grid dimensions: 65 x 65 x 65 173s Grid spacings: 0.225 x 0.225 x 0.225 173s Grid lengths: 14.400 x 14.400 x 14.400 173s Grid center: (17.340, 19.211, 20.503) 173s Multigrid levels: 5 173s Molecule ID: 3 173s Linearized traditional PBE 173s Boundary conditions from focusing 173s 2 ion species (0.010 M ionic strength): 173s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 173s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 173s Solute dielectric: 2.000 173s Solvent dielectric: 2.000 173s Using "molecular" surface definition;harmonic average smoothing 173s Solvent probe radius: 0.000 A 173s Temperature: 300.000 K 173s Electrostatic energies will be calculated 173s Total electrostatic energy = 4.133237922574E+04 kJ/mol 173s Calculating forces... 173s ---------------------------------------- 173s PRINT STATEMENTS 173s 173s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 173s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 173s Global net ELEC energy = -2.986241244040E+03 kJ/mol 173s 173s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 173s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 173s Global net ELEC energy = -2.007124871262E+01 kJ/mol 173s 173s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 173s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 173s Global net ELEC energy = -2.981621502756E+03 kJ/mol 173s 173s 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 173s Local net energy (PE 0) = 1.545150742844E+01 kJ/mol 173s Global net ELEC energy = 1.545150742844E+01 kJ/mol 173s ---------------------------------------- 173s CLEANING UP AND SHUTTING DOWN... 173s Destroying force arrays. 173s No energy arrays to destroy. 173s Destroying multigrid structures. 173s Destroying finite element structures. 173s Destroying 3 molecules 173s Final memory usage: 0.001 MB total, 222.305 MB high water 173s 173s 173s Thanks for using APBS! 173s 173s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 173s *** PASSED *** 173s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 173s *** PASSED *** 173s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 173s *** PASSED *** 173s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 173s *** PASSED *** 173s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 173s *** PASSED *** 173s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 173s *** PASSED *** 173s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 173s *** PASSED *** 173s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 173s *** PASSED *** 173s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 173s *** PASSED *** 173s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 173s *** PASSED *** 173s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 173s *** PASSED *** 173s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 173s *** PASSED *** 173s Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) 173s *** PASSED *** 173s Elapsed time: 4.620825 seconds 173s -------------------------------------------------------------------------------- 173s Total elapsed time: 18.814797 seconds 173s Test results have been logged 173s -------------------------------------------------------------------------------- 173s -------------------------------------------------------------------------------- 173s Testing input file apbs-mol.in 173s 178s Checking for intermediate energies in input file 1d7i-dss-smol.out 178s EXPECTED COMPUTED: 16 178s EXPECTED EXPECTED: 16 178s 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] 178s 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'] 178s COMPUTED RESULT 9634.884642408 178s COMPUTED RESULT 40031.77540425 178s COMPUTED RESULT 12649.65939588 178s COMPUTED RESULT 43018.01664829 178s COMPUTED RESULT 79.42232645345 178s COMPUTED RESULT 1677.798535473 178s COMPUTED RESULT 117.1079106781 178s COMPUTED RESULT 1697.869784185 178s COMPUTED RESULT 9507.068451372 178s COMPUTED RESULT 38350.75772299 178s COMPUTED RESULT 12524.95566243 178s COMPUTED RESULT 41332.37922574 178s COMPUTED RESULT -2986.24124404 178s COMPUTED RESULT -20.07124871262 178s COMPUTED RESULT -2981.621502756 178s COMPUTED RESULT 15.45150742844 178s Running tests for hca-bind section 178s BINARY: /usr/bin/apbs 178s INPUT: apbs-mol.in 178s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 178s asc_getToken: Error occurred (bailing out). 178s Vio_scanf: Format problem with input. 178s 178s 178s ---------------------------------------------------------------------- 178s APBS -- Adaptive Poisson-Boltzmann Solver 178s Version APBS 3.4.1 178s 178s Nathan A. Baker (nathan.baker@pnnl.gov) 178s Pacific Northwest National Laboratory 178s 178s Additional contributing authors listed in the code documentation. 178s 178s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 178s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 178s Northwest Division for the U.S. Department of Energy. 178s 178s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 178s Portions Copyright (c) 2002-2020, Nathan A. Baker. 178s Portions Copyright (c) 1999-2002, The Regents of the University of California. 178s Portions Copyright (c) 1995, Michael Holst. 178s All rights reserved. 178s 178s Redistribution and use in source and binary forms, with or without 178s modification, are permitted provided that the following conditions are met: 178s 178s * Redistributions of source code must retain the above copyright notice, this 178s list of conditions and the following disclaimer. 178s 178s * Redistributions in binary form must reproduce the above copyright notice, 178s this list of conditions and the following disclaimer in the documentation 178s and/or other materials provided with the distribution. 178s 178s * Neither the name of the developer nor the names of its contributors may be 178s used to endorse or promote products derived from this software without 178s specific prior written permission. 178s 178s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 178s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 178s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 178s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 178s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 178s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 178s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 178s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 178s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 178s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 178s ---------------------------------------------------------------------- 178s APBS uses FETK (the Finite Element ToolKit) to solve the 178s Poisson-Boltzmann equation numerically. FETK is a portable collection 178s of finite element modeling class libraries developed by the Michael Holst 178s research group and written in an object-oriented form of C. FEtk is 178s designed to solve general coupled systems of nonlinear partial differential 178s equations using adaptive finite element methods, inexact Newton methods, 178s and algebraic multilevel methods. More information about FEtk may be found 178s at . 178s ---------------------------------------------------------------------- 178s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 178s Aqua is a modified form of the Holst group PMG library 178s which has been modified by Patrice Koehl 178s for improved efficiency and 178s memory usage when solving the Poisson-Boltzmann equation. 178s ---------------------------------------------------------------------- 178s Please cite your use of APBS as: 178s 178s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 178s nanosystems: application to microtubules and the ribosome. Proc. 178s Natl. Acad. Sci. USA 98, 10037-10041 2001. 178s 178s 178s This executable compiled on Jan 3 2025 at 11:01:42 178s 178s Parsing input file apbs-mol.in... 178s rank 0 size 1... 178s Parsed input file. 178s Got paths for 3 molecules 178s Reading PQR-format atom data from acet.pqr. 178s asc_getToken: Error occurred (bailing out). 178s Vio_scanf: Format problem with input. 178s 18 atoms 178s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 178s Net charge -1.00e+00 e 178s Reading PQR-format atom data from hca.pqr. 178s asc_getToken: Error occurred (bailing out). 178s Vio_scanf: Format problem with input. 178s 2482 atoms 178s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 178s Net charge 1.00e+00 e 178s Reading PQR-format atom data from complex.pqr. 178s 2500 atoms 178s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 178s Net charge -1.02e-14 e 178s Preparing to run 9 PBE calculations. 178s ---------------------------------------- 178s CALCULATION #1 (acet): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 62.727 MB total, 62.727 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: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Single Debye-Huckel sphere boundary conditions 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 2.213600726771E+02 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #2 (acet): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 62.727 MB total, 123.701 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.581 x 0.581 x 0.581 178s Grid lengths: 37.181 x 37.181 x 37.181 178s Grid center: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.825764811255E+03 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #3 (acet): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 62.727 MB total, 123.701 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 178s *** PASSED *** 178s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 178s *** PASSED *** 178s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 178s *** PASSED *** 178s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 178s *** PASSED *** 178s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 178s *** PASSED *** 178s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 178s *** PASSED *** 178s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 178s *** PASSED *** 178s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 178s *** PASSED *** 178s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 178s *** PASSED *** 178s Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) 178s *** PASSED *** 178s Elapsed time: 4.264104 seconds 178s -------------------------------------------------------------------------------- 178s -------------------------------------------------------------------------------- 178s Testing input file apbs-smol.in 178s 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: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 1 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 6.458471211905E+03 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #4 (hca): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 146.516 MB total, 146.516 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: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 2 178s Linearized traditional PBE 178s Single Debye-Huckel sphere boundary conditions 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 2.093606095527E+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 #5 (hca): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 146.516 MB total, 245.092 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.581 x 0.581 x 0.581 178s Grid lengths: 37.181 x 37.181 x 37.181 178s Grid center: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 2 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.515433544464E+05 kJ/mol 178s Calculating forces... 178s [focusFillBound()]: WARNING: 178s Unusually large potential values 178s detected on the focusing boundary! 178s Convergence not guaranteed for NPBE/NRPBE calculations! 178s 178s ---------------------------------------- 178s CALCULATION #6 (hca): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 146.516 MB total, 245.092 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: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 2 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.786369323561E+05 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s CALCULATION #7 (complex): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 146.926 MB total, 245.092 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: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 3 178s Linearized traditional PBE 178s Single Debye-Huckel sphere boundary conditions 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 2.105322784838E+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 #8 (complex): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 146.926 MB total, 245.725 MB high water 178s Using linear spline charge discretization. 178s Grid dimensions: 65 x 65 x 65 178s Grid spacings: 0.581 x 0.581 x 0.581 178s Grid lengths: 37.181 x 37.181 x 37.181 178s Grid center: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 3 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.533304996252E+05 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 #9 (complex): MULTIGRID 178s Setting up problem... 178s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 178s Debye length: 0 A 178s Current memory usage: 146.926 MB total, 245.725 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: (-6.028, 3.898, 15.179) 178s Multigrid levels: 5 178s Molecule ID: 3 178s Linearized traditional PBE 178s Boundary conditions from focusing 178s 2 ion species (0.000 M ionic strength): 178s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 178s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 178s Solute dielectric: 2.000 178s Solvent dielectric: 78.540 178s Using "molecular" surface definition; no smoothing 178s Solvent probe radius: 0.000 A 178s Temperature: 298.150 K 178s Electrostatic energies will be calculated 178s Total electrostatic energy = 1.850429388099E+05 kJ/mol 178s Calculating forces... 178s ---------------------------------------- 178s PRINT STATEMENTS 178s 178s print energy 3 (complex) - 1 (acet) - 2 (hca) end 178s Local net energy (PE 0) = -5.246475812665E+01 kJ/mol 178s Global net ELEC energy = -5.246475812665E+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, 245.725 MB high water 178s 178s 178s Thanks for using APBS! 178s 182s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 182s *** PASSED *** 182s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 182s *** PASSED *** 182s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 182s *** PASSED *** 182s Checking for intermediate energies in input file apbs-mol.out 182s EXPECTED COMPUTED: 10 182s EXPECTED EXPECTED: 10 182s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] 182s 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'] 182s COMPUTED RESULT 221.3600726771 182s COMPUTED RESULT 1825.764811255 182s COMPUTED RESULT 6458.471211905 182s COMPUTED RESULT 20936.06095527 182s COMPUTED RESULT 151543.3544464 182s COMPUTED RESULT 178636.9323561 182s COMPUTED RESULT 21053.22784838 182s COMPUTED RESULT 153330.4996252 182s COMPUTED RESULT 185042.9388099 182s COMPUTED RESULT -52.46475812665 182s BINARY: /usr/bin/apbs 182s INPUT: apbs-smol.in 182s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 182s asc_getToken: Error occurred (bailing out). 182s Vio_scanf: Format problem with input. 182s 182s 182s ---------------------------------------------------------------------- 182s APBS -- Adaptive Poisson-Boltzmann Solver 182s Version APBS 3.4.1 182s 182s Nathan A. Baker (nathan.baker@pnnl.gov) 182s Pacific Northwest National Laboratory 182s 182s Additional contributing authors listed in the code documentation. 182s 182s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 182s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 182s Northwest Division for the U.S. Department of Energy. 182s 182s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 182s Portions Copyright (c) 2002-2020, Nathan A. Baker. 182s Portions Copyright (c) 1999-2002, The Regents of the University of California. 182s Portions Copyright (c) 1995, Michael Holst. 182s All rights reserved. 182s 182s Redistribution and use in source and binary forms, with or without 182s modification, are permitted provided that the following conditions are met: 182s 182s * Redistributions of source code must retain the above copyright notice, this 182s list of conditions and the following disclaimer. 182s 182s * Redistributions in binary form must reproduce the above copyright notice, 182s this list of conditions and the following disclaimer in the documentation 182s and/or other materials provided with the distribution. 182s 182s * Neither the name of the developer nor the names of its contributors may be 182s used to endorse or promote products derived from this software without 182s specific prior written permission. 182s 182s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 182s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 182s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 182s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 182s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 182s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 182s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 182s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 182s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 182s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 182s ---------------------------------------------------------------------- 182s APBS uses FETK (the Finite Element ToolKit) to solve the 182s Poisson-Boltzmann equation numerically. FETK is a portable collection 182s of finite element modeling class libraries developed by the Michael Holst 182s research group and written in an object-oriented form of C. FEtk is 182s designed to solve general coupled systems of nonlinear partial differential 182s equations using adaptive finite element methods, inexact Newton methods, 182s and algebraic multilevel methods. More information about FEtk may be found 182s at . 182s ---------------------------------------------------------------------- 182s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 182s Aqua is a modified form of the Holst group PMG library 182s which has been modified by Patrice Koehl 182s for improved efficiency and 182s memory usage when solving the Poisson-Boltzmann equation. 182s ---------------------------------------------------------------------- 182s Please cite your use of APBS as: 182s 182s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 182s nanosystems: application to microtubules and the ribosome. Proc. 182s Natl. Acad. Sci. USA 98, 10037-10041 2001. 182s 182s 182s This executable compiled on Jan 3 2025 at 11:01:42 182s 182s Parsing input file apbs-smol.in... 182s rank 0 size 1... 182s Parsed input file. 182s Got paths for 3 molecules 182s Reading PQR-format atom data from acet.pqr. 182s asc_getToken: Error occurred (bailing out). 182s Vio_scanf: Format problem with input. 182s 18 atoms 182s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 182s Net charge -1.00e+00 e 182s Reading PQR-format atom data from hca.pqr. 182s asc_getToken: Error occurred (bailing out). 182s Vio_scanf: Format problem with input. 182s 2482 atoms 182s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 182s Net charge 1.00e+00 e 182s Reading PQR-format atom data from complex.pqr. 182s 2500 atoms 182s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 182s Net charge -1.02e-14 e 182s Preparing to run 9 PBE calculations. 182s ---------------------------------------- 182s CALCULATION #1 (acet): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 62.727 MB total, 62.727 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 1.500 x 1.500 x 1.500 182s Grid lengths: 96.000 x 96.000 x 96.000 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 1 182s Linearized traditional PBE 182s Single Debye-Huckel sphere boundary conditions 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 1.884888131017E+02 kJ/mol 182s Calculating forces... 182s ---------------------------------------- 182s CALCULATION #2 (acet): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 62.727 MB total, 123.701 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 0.581 x 0.581 x 0.581 182s Grid lengths: 37.181 x 37.181 x 37.181 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 1 182s Linearized traditional PBE 182s Boundary conditions from focusing 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 1.820045922544E+03 kJ/mol 182s Calculating forces... 182s ---------------------------------------- 182s CALCULATION #3 (acet): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 62.727 MB total, 123.701 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 0.225 x 0.225 x 0.225 182s Grid lengths: 14.400 x 14.400 x 14.400 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 1 182s Linearized traditional PBE 182s Boundary conditions from focusing 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 6.460002606908E+03 kJ/mol 182s Calculating forces... 182s ---------------------------------------- 182s CALCULATION #4 (hca): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 146.516 MB total, 146.516 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 1.500 x 1.500 x 1.500 182s Grid lengths: 96.000 x 96.000 x 96.000 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 2 182s Linearized traditional PBE 182s Single Debye-Huckel sphere boundary conditions 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 2.189161497021E+04 kJ/mol 182s Calculating forces... 182s [focusFillBound()]: WARNING: 182s Unusually large potential values 182s detected on the focusing boundary! 182s Convergence not guaranteed for NPBE/NRPBE calculations! 182s 182s ---------------------------------------- 182s CALCULATION #5 (hca): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 146.516 MB total, 245.092 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 0.581 x 0.581 x 0.581 182s Grid lengths: 37.181 x 37.181 x 37.181 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 2 182s Linearized traditional PBE 182s Boundary conditions from focusing 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 1.520000494925E+05 kJ/mol 182s Calculating forces... 182s [focusFillBound()]: WARNING: 182s Unusually large potential values 182s detected on the focusing boundary! 182s Convergence not guaranteed for NPBE/NRPBE calculations! 182s 182s ---------------------------------------- 182s CALCULATION #6 (hca): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 146.516 MB total, 245.092 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 0.225 x 0.225 x 0.225 182s Grid lengths: 14.400 x 14.400 x 14.400 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 2 182s Linearized traditional PBE 182s Boundary conditions from focusing 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 1.790436191580E+05 kJ/mol 182s Calculating forces... 182s ---------------------------------------- 182s CALCULATION #7 (complex): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 146.926 MB total, 245.092 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 1.500 x 1.500 x 1.500 182s Grid lengths: 96.000 x 96.000 x 96.000 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 3 182s Linearized traditional PBE 182s Single Debye-Huckel sphere boundary conditions 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 2.195842512312E+04 kJ/mol 182s Calculating forces... 182s [focusFillBound()]: WARNING: 182s Unusually large potential values 182s detected on the focusing boundary! 182s Convergence not guaranteed for NPBE/NRPBE calculations! 182s 182s ---------------------------------------- 182s CALCULATION #8 (complex): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 146.926 MB total, 245.725 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 0.581 x 0.581 x 0.581 182s Grid lengths: 37.181 x 37.181 x 37.181 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 3 182s Linearized traditional PBE 182s Boundary conditions from focusing 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 1.537771604355E+05 kJ/mol 182s Calculating forces... 182s [focusFillBound()]: WARNING: 182s Unusually large potential values 182s detected on the focusing boundary! 182s Convergence not guaranteed for NPBE/NRPBE calculations! 182s 182s ---------------------------------------- 182s CALCULATION #9 (complex): MULTIGRID 182s Setting up problem... 182s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 182s Debye length: 0 A 182s Current memory usage: 146.926 MB total, 245.725 MB high water 182s Using linear spline charge discretization. 182s Grid dimensions: 65 x 65 x 65 182s Grid spacings: 0.225 x 0.225 x 0.225 182s Grid lengths: 14.400 x 14.400 x 14.400 182s Grid center: (-6.028, 3.898, 15.179) 182s Multigrid levels: 5 182s Molecule ID: 3 182s Linearized traditional PBE 182s Boundary conditions from focusing 182s 2 ion species (0.000 M ionic strength): 182s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 182s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 182s Solute dielectric: 2.000 182s Solvent dielectric: 78.540 182s Using "molecular" surface definition;harmonic average smoothing 182s Solvent probe radius: 0.000 A 182s Temperature: 298.150 K 182s Electrostatic energies will be calculated 182s Total electrostatic energy = 1.854495619747E+05 kJ/mol 182s Calculating forces... 182s ---------------------------------------- 182s PRINT STATEMENTS 182s 182s print energy 3 (complex) - 1 (acet) - 2 (hca) end 182s Local net energy (PE 0) = -5.405979017066E+01 kJ/mol 182s Global net ELEC energy = -5.405979017066E+01 kJ/mol 182s ---------------------------------------- 182s CLEANING UP AND SHUTTING DOWN... 182s Destroying force arrays. 182s No energy arrays to destroy. 182s Destroying multigrid structures. 182s Destroying finite element structures. 182s Destroying 3 molecules 182s Final memory usage: 0.001 MB total, 245.725 MB high water 182s 182s 182s Thanks for using APBS! 182s 182s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 182s *** PASSED *** 182s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 182s *** PASSED *** 182s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 182s *** PASSED *** 182s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 182s *** PASSED *** 182s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 182s *** PASSED *** 182s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 182s *** PASSED *** 182s Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) 182s *** PASSED *** 182s Elapsed time: 4.043038 seconds 182s -------------------------------------------------------------------------------- 182s Total elapsed time: 8.307142 seconds 182s Test results have been logged 182s -------------------------------------------------------------------------------- 182s -------------------------------------------------------------------------------- 182s Testing input file apbs-mol.in 182s 183s Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 183s *** PASSED *** 183s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 183s *** PASSED *** 183s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 183s *** PASSED *** 183s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 183s *** PASSED *** 183s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 183s *** PASSED *** 183s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 183s *** PASSED *** 183s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 183s *** PASSED *** 183s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 183s *** PASSED *** 183s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 183s *** PASSED *** 183s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 183s *** PASSED *** 183s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 183s *** PASSED *** 183s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 183s *** PASSED *** 183s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 183s *** PASSED *** 183s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 183s *** PASSED *** 183s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 183s *** PASSED *** 183s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 183s *** PASSED *** 183s Elapsed time: 1.159272 seconds 183s -------------------------------------------------------------------------------- 183s -------------------------------------------------------------------------------- 183s Testing input file apbs-smol.in 183s 183s Checking for intermediate energies in input file apbs-smol.out 183s EXPECTED COMPUTED: 10 183s EXPECTED EXPECTED: 10 183s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] 183s 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'] 183s COMPUTED RESULT 188.4888131017 183s COMPUTED RESULT 1820.045922544 183s COMPUTED RESULT 6460.002606908 183s COMPUTED RESULT 21891.61497021 183s COMPUTED RESULT 152000.0494925 183s COMPUTED RESULT 179043.619158 183s COMPUTED RESULT 21958.42512312 183s COMPUTED RESULT 153777.1604355 183s COMPUTED RESULT 185449.5619747 183s COMPUTED RESULT -54.05979017066 183s Running tests for ionize section 183s BINARY: /usr/bin/apbs 183s INPUT: apbs-mol.in 183s COMMAND: ['/usr/bin/apbs', 'apbs-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 apbs-mol.in... 183s rank 0 size 1... 183s Parsed input file. 183s Got paths for 3 molecules 183s Reading PQR-format atom data from acetic-acid.pqr. 183s asc_getToken: Error occurred (bailing out). 183s Vio_scanf: Format problem with input. 183s 8 atoms 183s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 183s Net charge -1.67e-16 e 183s Reading PQR-format atom data from acetate.pqr. 183s asc_getToken: Error occurred (bailing out). 183s Vio_scanf: Format problem with input. 183s 8 atoms 183s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 183s Net charge -1.00e+00 e 183s Reading PQR-format atom data from proton.pqr. 183s 1 atoms 183s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 183s Net charge 1.00e+00 e 183s Preparing to run 12 PBE calculations. 183s ---------------------------------------- 183s CALCULATION #1 (acetic-solv): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 7.76163 A 183s Current memory usage: 61.598 MB total, 61.598 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.188 x 0.188 x 0.188 183s Grid lengths: 12.000 x 12.000 x 12.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.150 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 5.823898055191E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #2 (acetic-solv): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 7.76163 A 183s Current memory usage: 61.598 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.094 x 0.094 x 0.094 183s Grid lengths: 6.000 x 6.000 x 6.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.150 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 9.793274462353E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #3 (acetic-ref): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 0 A 183s Current memory usage: 61.422 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.188 x 0.188 x 0.188 183s Grid lengths: 12.000 x 12.000 x 12.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.000 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.000 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 5.846917564309E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #4 (acetic-ref): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 0 A 183s Current memory usage: 61.422 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.094 x 0.094 x 0.094 183s Grid lengths: 6.000 x 6.000 x 6.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 1 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.000 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.000 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 9.815953282539E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #5 (acetate-solv): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 7.76163 A 183s Current memory usage: 61.598 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.188 x 0.188 x 0.188 183s Grid lengths: 12.000 x 12.000 x 12.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.150 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 8.219846763777E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #6 (acetate-solv): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 7.76163 A 183s Current memory usage: 61.598 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.094 x 0.094 x 0.094 183s Grid lengths: 6.000 x 6.000 x 6.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.150 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 1.392741988698E+04 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #7 (acetate-ref): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 0 A 183s Current memory usage: 61.422 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.188 x 0.188 x 0.188 183s Grid lengths: 12.000 x 12.000 x 12.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.000 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.000 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 8.420373979905E+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 #8 (acetate-ref): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 0 A 183s Current memory usage: 61.422 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.094 x 0.094 x 0.094 183s Grid lengths: 6.000 x 6.000 x 6.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 2 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.000 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.000 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 1.412716615065E+04 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #9 (proton-solv): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 7.76163 A 183s Current memory usage: 61.412 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.188 x 0.188 x 0.188 183s Grid lengths: 12.000 x 12.000 x 12.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.150 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 3.862359524598E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #10 (proton-solv): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 7.76163 A 183s Current memory usage: 61.412 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.094 x 0.094 x 0.094 183s Grid lengths: 6.000 x 6.000 x 6.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.150 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.150 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 6.288156251610E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s CALCULATION #11 (proton-ref): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 0 A 183s Current memory usage: 61.373 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.188 x 0.188 x 0.188 183s Grid lengths: 12.000 x 12.000 x 12.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Multiple Debye-Huckel sphere boundary conditions 183s 2 ion species (0.000 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.000 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 4.162533113906E+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 #12 (proton-ref): MULTIGRID 183s Setting up problem... 183s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 183s Debye length: 0 A 183s Current memory usage: 61.373 MB total, 122.404 MB high water 183s Using linear spline charge discretization. 183s Grid dimensions: 65 x 65 x 65 183s Grid spacings: 0.094 x 0.094 x 0.094 183s Grid lengths: 6.000 x 6.000 x 6.000 183s Grid center: (0.000, -0.154, 1.287) 183s Multigrid levels: 5 183s Molecule ID: 3 183s Linearized traditional PBE 183s Boundary conditions from focusing 183s 2 ion species (0.000 M ionic strength): 183s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 183s 2.000 A-radius, -1.000 e-charge, 0.000 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: 293.000 K 183s Electrostatic energies will be calculated 183s Total electrostatic energy = 6.585616091973E+03 kJ/mol 183s Calculating forces... 183s ---------------------------------------- 183s PRINT STATEMENTS 183s 183s print energy 1 (acetic-solv) - 2 (acetic-ref) end 183s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 183s Global net ELEC energy = -2.267882018629E+01 kJ/mol 183s 183s print energy 3 (acetate-solv) - 4 (acetate-ref) end 183s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 183s Global net ELEC energy = -1.997462636633E+02 kJ/mol 183s 183s print energy 5 (proton-solv) - 6 (proton-ref) end 183s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 183s Global net ELEC energy = -2.974598403628E+02 kJ/mol 183s 183s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 183s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 183s Global net ELEC energy = -4.745272838398E+02 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, 122.404 MB high water 183s 183s 183s Thanks for using APBS! 183s 184s Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 184s *** PASSED *** 184s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 184s *** PASSED *** 184s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 184s *** PASSED *** 184s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 184s *** PASSED *** 184s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 184s *** PASSED *** 184s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 184s *** PASSED *** 184s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 184s *** PASSED *** 184s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 184s *** PASSED *** 184s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 184s *** PASSED *** 184s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 184s *** PASSED *** 184s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 184s *** PASSED *** 184s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 184s *** PASSED *** 184s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 184s *** PASSED *** 184s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 184s *** PASSED *** 184s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 184s *** PASSED *** 184s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 184s *** PASSED *** 184s Elapsed time: 1.113297 seconds 184s -------------------------------------------------------------------------------- 184s Total elapsed time: 2.272569 seconds 184s Test results have been logged 184s -------------------------------------------------------------------------------- 184s -------------------------------------------------------------------------------- 184s Testing input file ion-pmf.in 184s 184s Checking for intermediate energies in input file apbs-mol.out 184s EXPECTED COMPUTED: 16 184s EXPECTED EXPECTED: 16 184s 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] 184s 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'] 184s COMPUTED RESULT 5823.898055191 184s COMPUTED RESULT 9793.274462353 184s COMPUTED RESULT 5846.917564309 184s COMPUTED RESULT 9815.953282539 184s COMPUTED RESULT 8219.846763777 184s COMPUTED RESULT 13927.41988698 184s COMPUTED RESULT 8420.373979905 184s COMPUTED RESULT 14127.16615065 184s COMPUTED RESULT 3862.359524598 184s COMPUTED RESULT 6288.15625161 184s COMPUTED RESULT 4162.533113906 184s COMPUTED RESULT 6585.616091973 184s COMPUTED RESULT -22.67882018629 184s COMPUTED RESULT -199.7462636633 184s COMPUTED RESULT -297.4598403628 184s COMPUTED RESULT -474.5272838398 184s BINARY: /usr/bin/apbs 184s INPUT: apbs-smol.in 184s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 184s asc_getToken: Error occurred (bailing out). 184s Vio_scanf: Format problem with input. 184s 184s 184s ---------------------------------------------------------------------- 184s APBS -- Adaptive Poisson-Boltzmann Solver 184s Version APBS 3.4.1 184s 184s Nathan A. Baker (nathan.baker@pnnl.gov) 184s Pacific Northwest National Laboratory 184s 184s Additional contributing authors listed in the code documentation. 184s 184s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 184s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 184s Northwest Division for the U.S. Department of Energy. 184s 184s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 184s Portions Copyright (c) 2002-2020, Nathan A. Baker. 184s Portions Copyright (c) 1999-2002, The Regents of the University of California. 184s Portions Copyright (c) 1995, Michael Holst. 184s All rights reserved. 184s 184s Redistribution and use in source and binary forms, with or without 184s modification, are permitted provided that the following conditions are met: 184s 184s * Redistributions of source code must retain the above copyright notice, this 184s list of conditions and the following disclaimer. 184s 184s * Redistributions in binary form must reproduce the above copyright notice, 184s this list of conditions and the following disclaimer in the documentation 184s and/or other materials provided with the distribution. 184s 184s * Neither the name of the developer nor the names of its contributors may be 184s used to endorse or promote products derived from this software without 184s specific prior written permission. 184s 184s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 184s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 184s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 184s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 184s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 184s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 184s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 184s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 184s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 184s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 184s ---------------------------------------------------------------------- 184s APBS uses FETK (the Finite Element ToolKit) to solve the 184s Poisson-Boltzmann equation numerically. FETK is a portable collection 184s of finite element modeling class libraries developed by the Michael Holst 184s research group and written in an object-oriented form of C. FEtk is 184s designed to solve general coupled systems of nonlinear partial differential 184s equations using adaptive finite element methods, inexact Newton methods, 184s and algebraic multilevel methods. More information about FEtk may be found 184s at . 184s ---------------------------------------------------------------------- 184s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 184s Aqua is a modified form of the Holst group PMG library 184s which has been modified by Patrice Koehl 184s for improved efficiency and 184s memory usage when solving the Poisson-Boltzmann equation. 184s ---------------------------------------------------------------------- 184s Please cite your use of APBS as: 184s 184s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 184s nanosystems: application to microtubules and the ribosome. Proc. 184s Natl. Acad. Sci. USA 98, 10037-10041 2001. 184s 184s 184s This executable compiled on Jan 3 2025 at 11:01:42 184s 184s Parsing input file apbs-smol.in... 184s rank 0 size 1... 184s Parsed input file. 184s Got paths for 3 molecules 184s Reading PQR-format atom data from acetic-acid.pqr. 184s asc_getToken: Error occurred (bailing out). 184s Vio_scanf: Format problem with input. 184s 8 atoms 184s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 184s Net charge -1.67e-16 e 184s Reading PQR-format atom data from acetate.pqr. 184s asc_getToken: Error occurred (bailing out). 184s Vio_scanf: Format problem with input. 184s 8 atoms 184s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 184s Net charge -1.00e+00 e 184s Reading PQR-format atom data from proton.pqr. 184s 1 atoms 184s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 184s Net charge 1.00e+00 e 184s Preparing to run 12 PBE calculations. 184s ---------------------------------------- 184s CALCULATION #1 (acetic-solv): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 7.76163 A 184s Current memory usage: 61.598 MB total, 61.598 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.188 x 0.188 x 0.188 184s Grid lengths: 12.000 x 12.000 x 12.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 2 ion species (0.150 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 78.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 5.824172730822E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #2 (acetic-solv): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 7.76163 A 184s Current memory usage: 61.598 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.094 x 0.094 x 0.094 184s Grid lengths: 6.000 x 6.000 x 6.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 2 ion species (0.150 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 78.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 9.793622759239E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #3 (acetic-ref): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.422 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.188 x 0.188 x 0.188 184s Grid lengths: 12.000 x 12.000 x 12.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 2 ion species (0.000 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 2.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 5.846917564309E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #4 (acetic-ref): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.422 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.094 x 0.094 x 0.094 184s Grid lengths: 6.000 x 6.000 x 6.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 1 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 2 ion species (0.000 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 2.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 9.815953282539E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #5 (acetate-solv): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 7.76163 A 184s Current memory usage: 61.598 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.188 x 0.188 x 0.188 184s Grid lengths: 12.000 x 12.000 x 12.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 2 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 2 ion species (0.150 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 78.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 8.221328580569E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #6 (acetate-solv): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 7.76163 A 184s Current memory usage: 61.598 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.094 x 0.094 x 0.094 184s Grid lengths: 6.000 x 6.000 x 6.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 2 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 2 ion species (0.150 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 78.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 1.392867783119E+04 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #7 (acetate-ref): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.422 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.188 x 0.188 x 0.188 184s Grid lengths: 12.000 x 12.000 x 12.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 2 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 2 ion species (0.000 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 2.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 8.420373979905E+03 kJ/mol 184s Calculating forces... 184s [focusFillBound()]: WARNING: 184s Unusually large potential values 184s detected on the focusing boundary! 184s Convergence not guaranteed for NPBE/NRPBE calculations! 184s 184s ---------------------------------------- 184s CALCULATION #8 (acetate-ref): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.422 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.094 x 0.094 x 0.094 184s Grid lengths: 6.000 x 6.000 x 6.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 2 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 2 ion species (0.000 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 2.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 1.412716615065E+04 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #9 (proton-solv): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 7.76163 A 184s Current memory usage: 61.412 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.188 x 0.188 x 0.188 184s Grid lengths: 12.000 x 12.000 x 12.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 3 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 2 ion species (0.150 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 78.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 3.863066835285E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #10 (proton-solv): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 7.76163 A 184s Current memory usage: 61.412 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.094 x 0.094 x 0.094 184s Grid lengths: 6.000 x 6.000 x 6.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 3 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 2 ion species (0.150 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 78.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 6.289649216644E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s CALCULATION #11 (proton-ref): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.373 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.188 x 0.188 x 0.188 184s Grid lengths: 12.000 x 12.000 x 12.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 3 184s Linearized traditional PBE 184s Multiple Debye-Huckel sphere boundary conditions 184s 2 ion species (0.000 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 2.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 4.162533113906E+03 kJ/mol 184s Calculating forces... 184s [focusFillBound()]: WARNING: 184s Unusually large potential values 184s detected on the focusing boundary! 184s Convergence not guaranteed for NPBE/NRPBE calculations! 184s 184s ---------------------------------------- 184s CALCULATION #12 (proton-ref): MULTIGRID 184s Setting up problem... 184s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 184s Debye length: 0 A 184s Current memory usage: 61.373 MB total, 122.404 MB high water 184s Using linear spline charge discretization. 184s Grid dimensions: 65 x 65 x 65 184s Grid spacings: 0.094 x 0.094 x 0.094 184s Grid lengths: 6.000 x 6.000 x 6.000 184s Grid center: (0.000, -0.154, 1.287) 184s Multigrid levels: 5 184s Molecule ID: 3 184s Linearized traditional PBE 184s Boundary conditions from focusing 184s 2 ion species (0.000 M ionic strength): 184s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 184s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 184s Solute dielectric: 2.000 184s Solvent dielectric: 2.000 184s Using "molecular" surface definition;harmonic average smoothing 184s Solvent probe radius: 0.000 A 184s Temperature: 293.000 K 184s Electrostatic energies will be calculated 184s Total electrostatic energy = 6.585616091973E+03 kJ/mol 184s Calculating forces... 184s ---------------------------------------- 184s PRINT STATEMENTS 184s 184s print energy 1 (acetic-solv) - 2 (acetic-ref) end 184s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 184s Global net ELEC energy = -2.233052329981E+01 kJ/mol 184s 184s print energy 3 (acetate-solv) - 4 (acetate-ref) end 184s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 184s Global net ELEC energy = -1.984883194538E+02 kJ/mol 184s 184s print energy 5 (proton-solv) - 6 (proton-ref) end 184s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 184s Global net ELEC energy = -2.959668753288E+02 kJ/mol 184s 184s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 184s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 184s Global net ELEC energy = -4.721246714828E+02 kJ/mol 184s ---------------------------------------- 184s CLEANING UP AND SHUTTING DOWN... 184s Destroying force arrays. 184s No energy arrays to destroy. 184s Destroying multigrid structures. 184s Destroying finite element structures. 184s Destroying 3 molecules 184s Final memory usage: 0.001 MB total, 122.404 MB high water 184s 184s 184s Thanks for using APBS! 184s 187s Checking for intermediate energies in input file apbs-smol.out 187s EXPECTED COMPUTED: 16 187s EXPECTED EXPECTED: 16 187s 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] 187s 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'] 187s COMPUTED RESULT 5824.172730822 187s COMPUTED RESULT 9793.622759239 187s COMPUTED RESULT 5846.917564309 187s COMPUTED RESULT 9815.953282539 187s COMPUTED RESULT 8221.328580569 187s COMPUTED RESULT 13928.67783119 187s COMPUTED RESULT 8420.373979905 187s COMPUTED RESULT 14127.16615065 187s COMPUTED RESULT 3863.066835285 187s COMPUTED RESULT 6289.649216644 187s COMPUTED RESULT 4162.533113906 187s COMPUTED RESULT 6585.616091973 187s COMPUTED RESULT -22.33052329981 187s COMPUTED RESULT -198.4883194538 187s COMPUTED RESULT -295.9668753288 187s COMPUTED RESULT -472.1246714828 187s Running tests for ion-pmf section 187s BINARY: /usr/bin/apbs 187s INPUT: ion-pmf.in 187s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 187s asc_getToken: Error occurred (bailing out). 187s Vio_scanf: Format problem with input. 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 ion-pmf.in... 187s rank 0 size 1... 187s Parsed input file. 187s Reading parameter data from parm.dat. 187s Got paths for 1 molecules 187s Reading PDB-format atom data from ion-pmf.pdb. 187s Vpmg_ibForce: No force for zero ionic strength! 187s Vpmg_ibForce: No force for zero ionic strength! 187s 2 atoms 187s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 187s Net charge 2.00e+00 e 187s Preparing to run 3 PBE calculations. 187s ---------------------------------------- 187s CALCULATION #1 (solv): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 187s Debye length: 0 A 187s Current memory usage: 61.106 MB total, 61.106 MB high water 187s Using cubic spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.210 x 0.210 x 0.210 187s Grid lengths: 13.440 x 13.440 x 13.440 187s Grid center: (0.000, 0.000, 0.000) 187s Multigrid levels: 5 187s Molecule ID: 1 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 0 ion species (0.000 M ionic strength): 187s Solute dielectric: 1.000 187s Solvent dielectric: 78.540 187s Using spline-based surface definition;window = 0.300 187s Temperature: 298.150 K 187s Electrostatic energies will be calculated 187s All-atom solvent forces will be calculated 187s Total electrostatic energy = 7.839535983197E+03 kJ/mol 187s Calculating forces... 187s Printing per-atom forces for molecule 1 (kJ/mol/A) 187s Legend: 187s tot n -- total force for atom n 187s qf n -- fixed charge force for atom n 187s db n -- dielectric boundary force for atom n 187s ib n -- ionic boundary force for atom n 187s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 187s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 187s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 187s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 187s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 187s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 187s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 187s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 187s Vpmg_ibForce: No force for zero ionic strength! 187s Vpmg_ibForce: No force for zero ionic strength! 187s ---------------------------------------- 187s CALCULATION #2 (ref): MULTIGRID 187s Setting up problem... 187s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 187s Debye length: 0 A 187s Current memory usage: 61.106 MB total, 61.155 MB high water 187s Using cubic spline charge discretization. 187s Grid dimensions: 65 x 65 x 65 187s Grid spacings: 0.210 x 0.210 x 0.210 187s Grid lengths: 13.440 x 13.440 x 13.440 187s Grid center: (0.000, 0.000, 0.000) 187s Multigrid levels: 5 187s Molecule ID: 1 187s Linearized traditional PBE 187s Multiple Debye-Huckel sphere boundary conditions 187s 0 ion species (0.000 M ionic strength): 187s Solute dielectric: 1.000 187s Solvent dielectric: 1.000 187s Using spline-based surface definition;window = 0.300 187s Temperature: 298.150 K 187s Electrostatic energies will be calculated 187s All-atom solvent forces will be calculated 187s Total electrostatic energy = 8.964727588811E+03 kJ/mol 187s Calculating forces... 187s Printing per-atom forces for molecule 1 (kJ/mol/A) 187s Legend: 187s tot n -- total force for atom n 187s qf n -- fixed charge force for atom n 187s db n -- dielectric boundary force for atom n 187s ib n -- ionic boundary force for atom n 187s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 187s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 187s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 187s mgF db 0 0.000e+00 0.000e+00 0.000e+00 187s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 187s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 187s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 187s mgF db 1 0.000e+00 0.000e+00 0.000e+00 187s ---------------------------------------- 187s CALCULATION #3 (asolv): APOLAR 187s Printing per atom forces (kJ/mol/A) 187s Legend: 187s tot n -- Total force for atom n 187s sasa n -- SASA force for atom n 187s sav n -- SAV force for atom n 187s wca n -- WCA force for atom n 187s 187s gamma 0.000720 187s pressure 0.000000 187s bconc 0.033000 187s 187s tot 0 2.715e-02 9.130e-07 9.130e-07 187s sasa 0 -1.100e+01 0.000e+00 0.000e+00 187s sav 0 0.000e+00 0.000e+00 0.000e+00 187s wca 0 -5.827e-01 -2.767e-05 -2.767e-05 187s tot 1 -2.723e-02 9.133e-07 9.133e-07 187s sasa 1 1.112e+01 0.000e+00 0.000e+00 187s sav 1 0.000e+00 0.000e+00 0.000e+00 187s wca 1 5.827e-01 -2.767e-05 -2.767e-05 187s 187s 187s Solvent Accessible Surface Area (SASA) for each atom: 187s SASA for atom 0: 1.153275282828E+02 187s SASA for atom 1: 1.153114143344E+02 187s 187s Total solvent accessible surface area: 230.639 A^2 187s 187s Surface tension*area energies (gamma * SASA) for each atom: 187s Surface tension*area energy for atom 0: 8.303582036361E-02 187s Surface tension*area energy for atom 1: 8.302421832080E-02 187s 187s Total surface tension energy: 0.16606 kJ/mol 187s 187s Total solvent accessible volume: 0 A^3 187s 187s Total pressure*volume energy: 0 kJ/mol 187s 187s WCA dispersion Energies for each atom: 187s WCA energy for atom 0: -6.909718359932E+00 187s WCA energy for atom 1: -6.909422551724E+00 187s 187s Total WCA energy: -13.8191 kJ/mol 187s 187s Total non-polar energy = -1.365308087297E+01 kJ/mol 187s ---------------------------------------- 187s PRINT STATEMENTS 187s 187s print energy 1 (solv) - 2 (ref) end 187s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 187s Global net ELEC energy = -1.125191605614E+03 kJ/mol 187s print force 1 (solv) - 2 (ref) end 187s Printing per-atom forces (kJ/mol/A). 187s Legend: 187s tot n -- Total force for atom n 187s qf n -- Fixed charge force for atom n 187s db n -- Dielectric boundary force for atom n 187s ib n -- Ionic boundary force for atom n 187s tot all -- Total force for system 187s qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 187s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 187s db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 187s tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 187s qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 187s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 187s db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 187s tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 187s tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 187s 187s print APOL energy 1 (asolv) end 187s Global net APOL energy = -1.365308087297E+01 kJ/mol 187s 187s print APOL force 1 (asolv) end 187s Printing per atom forces (kJ/mol/A) 187s Legend: 187s tot n -- Total force for atom n 187s sasa n -- SASA force for atom n 187s sav n -- SAV force for atom n 187s wca n -- WCA force for atom n 187s tot all -- Total force for system 187s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 187s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 187s wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 187s tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 187s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 187s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 187s wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 187s tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 187s tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 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 1 molecules 187s Final memory usage: 60.711 MB total, 62.250 MB high water 187s 187s 187s Thanks for using APBS! 187s 187s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 187s *** PASSED *** 187s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 187s *** PASSED *** 187s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 187s *** PASSED *** 187s Elapsed time: 3.456362 seconds 187s -------------------------------------------------------------------------------- 187s Total elapsed time: 3.456362 seconds 187s Test results have been logged 187s -------------------------------------------------------------------------------- 187s -------------------------------------------------------------------------------- 187s Testing input file apbs-mol-vdw.in 187s 193s Checking for intermediate energies in input file ion-pmf.out 193s EXPECTED COMPUTED: 4 193s EXPECTED EXPECTED: 4 193s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] 193s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 193s COMPUTED RESULT 7839.535983197 193s COMPUTED RESULT 8964.727588811 193s COMPUTED RESULT -1125.191605614 193s COMPUTED RESULT -13.65308087297 193s Running tests for pka-lig section 193s BINARY: /usr/bin/apbs 193s INPUT: apbs-mol-vdw.in 193s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 193s asc_getToken: Error occurred (bailing out). 193s Vio_scanf: Format problem with input. 193s 193s 193s ---------------------------------------------------------------------- 193s APBS -- Adaptive Poisson-Boltzmann Solver 193s Version APBS 3.4.1 193s 193s Nathan A. Baker (nathan.baker@pnnl.gov) 193s Pacific Northwest National Laboratory 193s 193s Additional contributing authors listed in the code documentation. 193s 193s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 193s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 193s Northwest Division for the U.S. Department of Energy. 193s 193s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 193s Portions Copyright (c) 2002-2020, Nathan A. Baker. 193s Portions Copyright (c) 1999-2002, The Regents of the University of California. 193s Portions Copyright (c) 1995, Michael Holst. 193s All rights reserved. 193s 193s Redistribution and use in source and binary forms, with or without 193s modification, are permitted provided that the following conditions are met: 193s 193s * Redistributions of source code must retain the above copyright notice, this 193s list of conditions and the following disclaimer. 193s 193s * Redistributions in binary form must reproduce the above copyright notice, 193s this list of conditions and the following disclaimer in the documentation 193s and/or other materials provided with the distribution. 193s 193s * Neither the name of the developer nor the names of its contributors may be 193s used to endorse or promote products derived from this software without 193s specific prior written permission. 193s 193s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 193s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 193s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 193s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 193s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 193s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 193s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 193s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 193s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 193s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 193s ---------------------------------------------------------------------- 193s APBS uses FETK (the Finite Element ToolKit) to solve the 193s Poisson-Boltzmann equation numerically. FETK is a portable collection 193s of finite element modeling class libraries developed by the Michael Holst 193s research group and written in an object-oriented form of C. FEtk is 193s designed to solve general coupled systems of nonlinear partial differential 193s equations using adaptive finite element methods, inexact Newton methods, 193s and algebraic multilevel methods. More information about FEtk may be found 193s at . 193s ---------------------------------------------------------------------- 193s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 193s Aqua is a modified form of the Holst group PMG library 193s which has been modified by Patrice Koehl 193s for improved efficiency and 193s memory usage when solving the Poisson-Boltzmann equation. 193s ---------------------------------------------------------------------- 193s Please cite your use of APBS as: 193s 193s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 193s nanosystems: application to microtubules and the ribosome. Proc. 193s Natl. Acad. Sci. USA 98, 10037-10041 2001. 193s 193s 193s This executable compiled on Jan 3 2025 at 11:01:42 193s 193s Parsing input file apbs-mol-vdw.in... 193s rank 0 size 1... 193s Parsed input file. 193s Got paths for 3 molecules 193s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 193s asc_getToken: Error occurred (bailing out). 193s Vio_scanf: Format problem with input. 193s 47 atoms 193s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 193s Net charge 1.11e-16 e 193s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 193s asc_getToken: Error occurred (bailing out). 193s Vio_scanf: Format problem with input. 193s 3423 atoms 193s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 193s Net charge 1.00e+00 e 193s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 193s 3470 atoms 193s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 193s Net charge 1.00e+00 e 193s Preparing to run 6 PBE calculations. 193s ---------------------------------------- 193s CALCULATION #1 (lig-coarse): MULTIGRID 193s Setting up problem... 193s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 193s Debye length: 0 A 193s Current memory usage: 204.292 MB total, 204.292 MB high water 193s Using linear spline charge discretization. 193s Grid dimensions: 97 x 97 x 97 193s Grid spacings: 0.729 x 0.729 x 0.729 193s Grid lengths: 70.000 x 70.000 x 70.000 193s Grid center: (28.969, -32.507, 27.022) 193s Multigrid levels: 4 193s Molecule ID: 1 193s Linearized traditional PBE 193s Single Debye-Huckel sphere boundary conditions 193s 2 ion species (0.000 M ionic strength): 193s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 193s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 193s Solute dielectric: 2.000 193s Solvent dielectric: 78.000 193s Using "molecular" surface definition; no smoothing 193s Solvent probe radius: 0.000 A 193s Temperature: 298.150 K 193s Electrostatic energies will be calculated 193s Total electrostatic energy = 2.224988750664E+03 kJ/mol 193s Calculating forces... 193s ---------------------------------------- 193s CALCULATION #2 (lig-fine): MULTIGRID 193s Setting up problem... 193s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 193s Debye length: 0 A 193s Current memory usage: 204.292 MB total, 406.001 MB high water 193s Using linear spline charge discretization. 193s Grid dimensions: 97 x 97 x 97 193s Grid spacings: 0.250 x 0.250 x 0.250 193s Grid lengths: 24.000 x 24.000 x 24.000 193s Grid center: (24.822, -33.153, 21.545) 193s Multigrid levels: 4 193s Molecule ID: 1 193s Linearized traditional PBE 193s Boundary conditions from focusing 193s 2 ion species (0.000 M ionic strength): 193s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 193s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 193s Solute dielectric: 2.000 193s Solvent dielectric: 78.000 193s Using "molecular" surface definition; no smoothing 193s Solvent probe radius: 0.000 A 193s Temperature: 298.150 K 193s Electrostatic energies will be calculated 193s Total electrostatic energy = 1.049695084686E+04 kJ/mol 193s Calculating forces... 193s ---------------------------------------- 193s CALCULATION #3 (pka-coarse): MULTIGRID 193s Setting up problem... 193s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 193s Debye length: 0 A 193s Current memory usage: 291.151 MB total, 406.001 MB high water 193s Using linear spline charge discretization. 193s Grid dimensions: 97 x 97 x 97 193s Grid spacings: 0.729 x 0.729 x 0.729 193s Grid lengths: 70.000 x 70.000 x 70.000 193s Grid center: (28.969, -32.507, 27.022) 193s Multigrid levels: 4 193s Molecule ID: 2 193s Linearized traditional PBE 193s Single Debye-Huckel sphere boundary conditions 193s 2 ion species (0.000 M ionic strength): 193s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 193s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 193s Solute dielectric: 2.000 193s Solvent dielectric: 78.000 193s Using "molecular" surface definition; no smoothing 193s Solvent probe radius: 0.000 A 193s Temperature: 298.150 K 193s Electrostatic energies will be calculated 193s Total electrostatic energy = 1.818450789522E+05 kJ/mol 193s Calculating forces... 193s [focusFillBound()]: WARNING: 193s Unusually large potential values 193s detected on the focusing boundary! 193s Convergence not guaranteed for NPBE/NRPBE calculations! 193s 193s ---------------------------------------- 193s CALCULATION #4 (pka-fine): MULTIGRID 193s Setting up problem... 193s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 193s Debye length: 0 A 193s Current memory usage: 291.151 MB total, 533.426 MB high water 193s Using linear spline charge discretization. 193s Grid dimensions: 97 x 97 x 97 193s Grid spacings: 0.250 x 0.250 x 0.250 193s Grid lengths: 24.000 x 24.000 x 24.000 193s Grid center: (24.822, -33.153, 21.545) 193s Multigrid levels: 4 193s Molecule ID: 2 193s Linearized traditional PBE 193s Boundary conditions from focusing 193s 2 ion species (0.000 M ionic strength): 193s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 193s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 193s Solute dielectric: 2.000 193s Solvent dielectric: 78.000 193s Using "molecular" surface definition; no smoothing 193s Solvent probe radius: 0.000 A 193s Temperature: 298.150 K 193s Electrostatic energies will be calculated 193s Total electrostatic energy = 3.008254338259E+05 kJ/mol 193s Calculating forces... 193s ---------------------------------------- 193s CALCULATION #5 (complex-coarse): MULTIGRID 193s Setting up problem... 193s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 193s Debye length: 0 A 193s Current memory usage: 292.063 MB total, 533.426 MB high water 193s Using linear spline charge discretization. 193s Grid dimensions: 97 x 97 x 97 193s Grid spacings: 0.729 x 0.729 x 0.729 193s Grid lengths: 70.000 x 70.000 x 70.000 193s Grid center: (28.969, -32.507, 27.022) 193s Multigrid levels: 4 193s Molecule ID: 3 193s Linearized traditional PBE 193s Single Debye-Huckel sphere boundary conditions 193s 2 ion species (0.000 M ionic strength): 193s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 193s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 193s Solute dielectric: 2.000 193s Solvent dielectric: 78.000 193s Using "molecular" surface definition; no smoothing 193s Solvent probe radius: 0.000 A 193s Temperature: 298.150 K 193s Electrostatic energies will be calculated 193s Total electrostatic energy = 1.840918409896E+05 kJ/mol 193s Calculating forces... 193s [focusFillBound()]: WARNING: 193s Unusually large potential values 193s detected on the focusing boundary! 193s Convergence not guaranteed for NPBE/NRPBE calculations! 193s 193s ---------------------------------------- 193s CALCULATION #6 (complex-fine): MULTIGRID 193s Setting up problem... 193s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 193s Debye length: 0 A 193s Current memory usage: 292.063 MB total, 534.806 MB high water 193s Using linear spline charge discretization. 193s Grid dimensions: 97 x 97 x 97 193s Grid spacings: 0.250 x 0.250 x 0.250 193s Grid lengths: 24.000 x 24.000 x 24.000 193s Grid center: (24.822, -33.153, 21.545) 193s Multigrid levels: 4 193s Molecule ID: 3 193s Linearized traditional PBE 193s Boundary conditions from focusing 193s 2 ion species (0.000 M ionic strength): 193s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 193s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 193s Solute dielectric: 2.000 193s Solvent dielectric: 78.000 193s Using "molecular" surface definition; no smoothing 193s Solvent probe radius: 0.000 A 193s Temperature: 298.150 K 193s Electrostatic energies will be calculated 193s Total electrostatic energy = 3.113304681884E+05 kJ/mol 193s Calculating forces... 193s ---------------------------------------- 193s PRINT STATEMENTS 193s 193s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 193s Local net energy (PE 0) = 8.083515648730E+00 kJ/mol 193s Global net ELEC energy = 8.083515648730E+00 kJ/mol 193s ---------------------------------------- 193s CLEANING UP AND SHUTTING DOWN... 193s Destroying force arrays. 193s No energy arrays to destroy. 193s Destroying multigrid structures. 193s Destroying finite element structures. 193s Destroying 3 molecules 193s Final memory usage: 0.001 MB total, 534.806 MB high water 193s 193s 193s Thanks for using APBS! 193s 193s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 193s *** PASSED *** 193s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 193s *** PASSED *** 193s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 193s *** PASSED *** 193s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 193s *** PASSED *** 193s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 193s *** PASSED *** 193s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 193s *** PASSED *** 193s Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) 193s *** PASSED *** 193s Elapsed time: 5.746147 seconds 193s -------------------------------------------------------------------------------- 193s -------------------------------------------------------------------------------- 193s Testing input file apbs-smol-vdw.in 193s 198s Checking for intermediate energies in input file apbs-mol-vdw.out 198s EXPECTED COMPUTED: 7 198s EXPECTED EXPECTED: 7 198s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] 198s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 198s COMPUTED RESULT 2224.988750664 198s COMPUTED RESULT 10496.95084686 198s COMPUTED RESULT 181845.0789522 198s COMPUTED RESULT 300825.4338259 198s COMPUTED RESULT 184091.8409896 198s COMPUTED RESULT 311330.4681884 198s COMPUTED RESULT 8.08351564873 198s BINARY: /usr/bin/apbs 198s INPUT: apbs-smol-vdw.in 198s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.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-vdw.in... 198s rank 0 size 1... 198s Parsed input file. 198s Got paths for 3 molecules 198s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 198s asc_getToken: Error occurred (bailing out). 198s Vio_scanf: Format problem with input. 198s 47 atoms 198s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 198s Net charge 1.11e-16 e 198s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 198s asc_getToken: Error occurred (bailing out). 198s Vio_scanf: Format problem with input. 198s 3423 atoms 198s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 198s Net charge 1.00e+00 e 198s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 198s 3470 atoms 198s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 198s Net charge 1.00e+00 e 198s Preparing to run 6 PBE calculations. 198s ---------------------------------------- 198s CALCULATION #1 (lig-coarse): 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: 204.292 MB total, 204.292 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 97 x 97 x 97 198s Grid spacings: 0.729 x 0.729 x 0.729 198s Grid lengths: 70.000 x 70.000 x 70.000 198s Grid center: (28.969, -32.507, 27.022) 198s Multigrid levels: 4 198s Molecule ID: 1 198s Linearized traditional PBE 198s Single 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: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 2.226793167046E+03 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #2 (lig-fine): 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: 204.292 MB total, 406.001 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 97 x 97 x 97 198s Grid spacings: 0.250 x 0.250 x 0.250 198s Grid lengths: 24.000 x 24.000 x 24.000 198s Grid center: (24.822, -33.153, 21.545) 198s Multigrid levels: 4 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: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 1.050504485887E+04 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #3 (pka-coarse): 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: 291.151 MB total, 406.001 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 97 x 97 x 97 198s Grid spacings: 0.729 x 0.729 x 0.729 198s Grid lengths: 70.000 x 70.000 x 70.000 198s Grid center: (28.969, -32.507, 27.022) 198s Multigrid levels: 4 198s Molecule ID: 2 198s Linearized traditional PBE 198s Single 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: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 1.827976621645E+05 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 #4 (pka-fine): 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: 291.151 MB total, 533.426 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 97 x 97 x 97 198s Grid spacings: 0.250 x 0.250 x 0.250 198s Grid lengths: 24.000 x 24.000 x 24.000 198s Grid center: (24.822, -33.153, 21.545) 198s Multigrid levels: 4 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: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 3.017228546773E+05 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s CALCULATION #5 (complex-coarse): 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: 292.063 MB total, 533.426 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 97 x 97 x 97 198s Grid spacings: 0.729 x 0.729 x 0.729 198s Grid lengths: 70.000 x 70.000 x 70.000 198s Grid center: (28.969, -32.507, 27.022) 198s Multigrid levels: 4 198s Molecule ID: 3 198s Linearized traditional PBE 198s Single 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: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 1.850819075387E+05 kJ/mol 198s Calculating forces... 198s [focusFillBound()]: WARNING: 198s Unusually large potential values 198s detected on the focusing boundary! 198s Convergence not guaranteed for NPBE/NRPBE calculations! 198s 198s ---------------------------------------- 198s CALCULATION #6 (complex-fine): 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: 292.063 MB total, 534.806 MB high water 198s Using linear spline charge discretization. 198s Grid dimensions: 97 x 97 x 97 198s Grid spacings: 0.250 x 0.250 x 0.250 198s Grid lengths: 24.000 x 24.000 x 24.000 198s Grid center: (24.822, -33.153, 21.545) 198s Multigrid levels: 4 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: 78.000 198s Using "molecular" surface definition;harmonic average smoothing 198s Solvent probe radius: 0.000 A 198s Temperature: 298.150 K 198s Electrostatic energies will be calculated 198s Total electrostatic energy = 3.122488625388E+05 kJ/mol 198s Calculating forces... 198s ---------------------------------------- 198s PRINT STATEMENTS 198s 198s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 198s Local net energy (PE 0) = 2.096300255723E+01 kJ/mol 198s Global net ELEC energy = 2.096300255723E+01 kJ/mol 198s ---------------------------------------- 198s CLEANING UP AND SHUTTING DOWN... 198s Destroying force arrays. 198s No energy arrays to destroy. 198s Destroying multigrid structures. 198s Destroying finite element structures. 198s Destroying 3 molecules 198s Final memory usage: 0.001 MB total, 534.806 MB high water 198s 198s 198s Thanks for using APBS! 198s 198s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 198s *** PASSED *** 198s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 198s *** PASSED *** 198s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 198s *** PASSED *** 198s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 198s *** PASSED *** 198s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 198s *** PASSED *** 198s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 198s *** PASSED *** 198s Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01) 198s *** PASSED *** 198s Elapsed time: 5.070731 seconds 198s -------------------------------------------------------------------------------- 198s -------------------------------------------------------------------------------- 198s Testing input file apbs-mol-surf.in 198s 203s Checking for intermediate energies in input file apbs-smol-vdw.out 203s EXPECTED COMPUTED: 7 203s EXPECTED EXPECTED: 7 203s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] 203s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 203s COMPUTED RESULT 2226.793167046 203s COMPUTED RESULT 10505.04485887 203s COMPUTED RESULT 182797.6621645 203s COMPUTED RESULT 301722.8546773 203s COMPUTED RESULT 185081.9075387 203s COMPUTED RESULT 312248.8625388 203s COMPUTED RESULT 20.96300255723 203s BINARY: /usr/bin/apbs 203s INPUT: apbs-mol-surf.in 203s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 203s asc_getToken: Error occurred (bailing out). 203s Vio_scanf: Format problem with input. 203s 203s 203s ---------------------------------------------------------------------- 203s APBS -- Adaptive Poisson-Boltzmann Solver 203s Version APBS 3.4.1 203s 203s Nathan A. Baker (nathan.baker@pnnl.gov) 203s Pacific Northwest National Laboratory 203s 203s Additional contributing authors listed in the code documentation. 203s 203s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 203s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 203s Northwest Division for the U.S. Department of Energy. 203s 203s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 203s Portions Copyright (c) 2002-2020, Nathan A. Baker. 203s Portions Copyright (c) 1999-2002, The Regents of the University of California. 203s Portions Copyright (c) 1995, Michael Holst. 203s All rights reserved. 203s 203s Redistribution and use in source and binary forms, with or without 203s modification, are permitted provided that the following conditions are met: 203s 203s * Redistributions of source code must retain the above copyright notice, this 203s list of conditions and the following disclaimer. 203s 203s * Redistributions in binary form must reproduce the above copyright notice, 203s this list of conditions and the following disclaimer in the documentation 203s and/or other materials provided with the distribution. 203s 203s * Neither the name of the developer nor the names of its contributors may be 203s used to endorse or promote products derived from this software without 203s specific prior written permission. 203s 203s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 203s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 203s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 203s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 203s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 203s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 203s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 203s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 203s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 203s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 203s ---------------------------------------------------------------------- 203s APBS uses FETK (the Finite Element ToolKit) to solve the 203s Poisson-Boltzmann equation numerically. FETK is a portable collection 203s of finite element modeling class libraries developed by the Michael Holst 203s research group and written in an object-oriented form of C. FEtk is 203s designed to solve general coupled systems of nonlinear partial differential 203s equations using adaptive finite element methods, inexact Newton methods, 203s and algebraic multilevel methods. More information about FEtk may be found 203s at . 203s ---------------------------------------------------------------------- 203s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 203s Aqua is a modified form of the Holst group PMG library 203s which has been modified by Patrice Koehl 203s for improved efficiency and 203s memory usage when solving the Poisson-Boltzmann equation. 203s ---------------------------------------------------------------------- 203s Please cite your use of APBS as: 203s 203s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 203s nanosystems: application to microtubules and the ribosome. Proc. 203s Natl. Acad. Sci. USA 98, 10037-10041 2001. 203s 203s 203s This executable compiled on Jan 3 2025 at 11:01:42 203s 203s Parsing input file apbs-mol-surf.in... 203s rank 0 size 1... 203s Parsed input file. 203s Got paths for 3 molecules 203s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 203s asc_getToken: Error occurred (bailing out). 203s Vio_scanf: Format problem with input. 203s 47 atoms 203s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 203s Net charge 1.11e-16 e 203s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 203s asc_getToken: Error occurred (bailing out). 203s Vio_scanf: Format problem with input. 203s 3423 atoms 203s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 203s Net charge 1.00e+00 e 203s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 203s 3470 atoms 203s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 203s Net charge 1.00e+00 e 203s Preparing to run 6 PBE calculations. 203s ---------------------------------------- 203s CALCULATION #1 (lig-coarse): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 203.877 MB total, 203.877 MB high water 203s Using linear spline charge discretization. 203s Grid dimensions: 97 x 97 x 97 203s Grid spacings: 0.729 x 0.729 x 0.729 203s Grid lengths: 70.000 x 70.000 x 70.000 203s Grid center: (28.969, -32.507, 27.022) 203s Multigrid levels: 4 203s Molecule ID: 1 203s Linearized traditional PBE 203s Single Debye-Huckel sphere boundary conditions 203s 2 ion species (0.000 M ionic strength): 203s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 203s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 203s Solute dielectric: 2.000 203s Solvent dielectric: 78.000 203s Using "molecular" surface definition; no smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 2.244350164274E+03 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s CALCULATION #2 (lig-fine): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 203.877 MB total, 405.586 MB high water 203s Using linear spline charge discretization. 203s Grid dimensions: 97 x 97 x 97 203s Grid spacings: 0.250 x 0.250 x 0.250 203s Grid lengths: 24.000 x 24.000 x 24.000 203s Grid center: (24.822, -33.153, 21.545) 203s Multigrid levels: 4 203s Molecule ID: 1 203s Linearized traditional PBE 203s Boundary conditions from focusing 203s 2 ion species (0.000 M ionic strength): 203s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 203s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 203s Solute dielectric: 2.000 203s Solvent dielectric: 78.000 203s Using "molecular" surface definition; no smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 1.052149475373E+04 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s CALCULATION #3 (pka-coarse): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 251.521 MB total, 405.586 MB high water 203s Using linear spline charge discretization. 203s Grid dimensions: 97 x 97 x 97 203s Grid spacings: 0.729 x 0.729 x 0.729 203s Grid lengths: 70.000 x 70.000 x 70.000 203s Grid center: (28.969, -32.507, 27.022) 203s Multigrid levels: 4 203s Molecule ID: 2 203s Linearized traditional PBE 203s Single Debye-Huckel sphere boundary conditions 203s 2 ion species (0.000 M ionic strength): 203s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 203s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 203s Solute dielectric: 2.000 203s Solvent dielectric: 78.000 203s Using "molecular" surface definition; no smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 1.862615690066E+05 kJ/mol 203s Calculating forces... 203s [focusFillBound()]: WARNING: 203s Unusually large potential values 203s detected on the focusing boundary! 203s Convergence not guaranteed for NPBE/NRPBE calculations! 203s 203s ---------------------------------------- 203s CALCULATION #4 (pka-fine): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 251.521 MB total, 493.795 MB high water 203s Using linear spline charge discretization. 203s Grid dimensions: 97 x 97 x 97 203s Grid spacings: 0.250 x 0.250 x 0.250 203s Grid lengths: 24.000 x 24.000 x 24.000 203s Grid center: (24.822, -33.153, 21.545) 203s Multigrid levels: 4 203s Molecule ID: 2 203s Linearized traditional PBE 203s Boundary conditions from focusing 203s 2 ion species (0.000 M ionic strength): 203s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 203s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 203s Solute dielectric: 2.000 203s Solvent dielectric: 78.000 203s Using "molecular" surface definition; no smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 3.051810884053E+05 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s CALCULATION #5 (complex-coarse): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 251.858 MB total, 493.795 MB high water 203s Using linear spline charge discretization. 203s Grid dimensions: 97 x 97 x 97 203s Grid spacings: 0.729 x 0.729 x 0.729 203s Grid lengths: 70.000 x 70.000 x 70.000 203s Grid center: (28.969, -32.507, 27.022) 203s Multigrid levels: 4 203s Molecule ID: 3 203s Linearized traditional PBE 203s Single Debye-Huckel sphere boundary conditions 203s 2 ion species (0.000 M ionic strength): 203s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 203s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 203s Solute dielectric: 2.000 203s Solvent dielectric: 78.000 203s Using "molecular" surface definition; no smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 1.886625455219E+05 kJ/mol 203s Calculating forces... 203s [focusFillBound()]: WARNING: 203s Unusually large potential values 203s detected on the focusing boundary! 203s Convergence not guaranteed for NPBE/NRPBE calculations! 203s 203s ---------------------------------------- 203s CALCULATION #6 (complex-fine): MULTIGRID 203s Setting up problem... 203s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 203s Debye length: 0 A 203s Current memory usage: 251.858 MB total, 494.601 MB high water 203s Using linear spline charge discretization. 203s Grid dimensions: 97 x 97 x 97 203s Grid spacings: 0.250 x 0.250 x 0.250 203s Grid lengths: 24.000 x 24.000 x 24.000 203s Grid center: (24.822, -33.153, 21.545) 203s Multigrid levels: 4 203s Molecule ID: 3 203s Linearized traditional PBE 203s Boundary conditions from focusing 203s 2 ion species (0.000 M ionic strength): 203s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 203s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 203s Solute dielectric: 2.000 203s Solvent dielectric: 78.000 203s Using "molecular" surface definition; no smoothing 203s Solvent probe radius: 1.400 A 203s Temperature: 298.150 K 203s Electrostatic energies will be calculated 203s Total electrostatic energy = 3.158218439277E+05 kJ/mol 203s Calculating forces... 203s ---------------------------------------- 203s PRINT STATEMENTS 203s 203s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 203s Local net energy (PE 0) = 1.192607686581E+02 kJ/mol 203s Global net ELEC energy = 1.192607686581E+02 kJ/mol 203s ---------------------------------------- 203s CLEANING UP AND SHUTTING DOWN... 203s Destroying force arrays. 203s No energy arrays to destroy. 203s Destroying multigrid structures. 203s Destroying finite element structures. 203s Destroying 3 molecules 203s Final memory usage: 0.001 MB total, 494.601 MB high water 203s 203s 203s Thanks for using APBS! 203s 203s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 203s *** PASSED *** 203s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 203s *** PASSED *** 203s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 203s *** PASSED *** 203s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 203s *** PASSED *** 203s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 203s *** PASSED *** 203s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 203s *** PASSED *** 203s Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) 203s *** PASSED *** 203s Elapsed time: 5.265612 seconds 203s -------------------------------------------------------------------------------- 203s -------------------------------------------------------------------------------- 203s Testing input file apbs-smol-surf.in 203s 208s Checking for intermediate energies in input file apbs-mol-surf.out 208s EXPECTED COMPUTED: 7 208s EXPECTED EXPECTED: 7 208s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] 208s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 208s COMPUTED RESULT 2244.350164274 208s COMPUTED RESULT 10521.49475373 208s COMPUTED RESULT 186261.5690066 208s COMPUTED RESULT 305181.0884053 208s COMPUTED RESULT 188662.5455219 208s COMPUTED RESULT 315821.8439277 208s COMPUTED RESULT 119.2607686581 208s BINARY: /usr/bin/apbs 208s INPUT: apbs-smol-surf.in 208s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 208s asc_getToken: Error occurred (bailing out). 208s Vio_scanf: Format problem with input. 208s 208s 208s ---------------------------------------------------------------------- 208s APBS -- Adaptive Poisson-Boltzmann Solver 208s Version APBS 3.4.1 208s 208s Nathan A. Baker (nathan.baker@pnnl.gov) 208s Pacific Northwest National Laboratory 208s 208s Additional contributing authors listed in the code documentation. 208s 208s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 208s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 208s Northwest Division for the U.S. Department of Energy. 208s 208s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 208s Portions Copyright (c) 2002-2020, Nathan A. Baker. 208s Portions Copyright (c) 1999-2002, The Regents of the University of California. 208s Portions Copyright (c) 1995, Michael Holst. 208s All rights reserved. 208s 208s Redistribution and use in source and binary forms, with or without 208s modification, are permitted provided that the following conditions are met: 208s 208s * Redistributions of source code must retain the above copyright notice, this 208s list of conditions and the following disclaimer. 208s 208s * Redistributions in binary form must reproduce the above copyright notice, 208s this list of conditions and the following disclaimer in the documentation 208s and/or other materials provided with the distribution. 208s 208s * Neither the name of the developer nor the names of its contributors may be 208s used to endorse or promote products derived from this software without 208s specific prior written permission. 208s 208s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 208s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 208s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 208s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 208s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 208s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 208s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 208s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 208s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 208s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 208s ---------------------------------------------------------------------- 208s APBS uses FETK (the Finite Element ToolKit) to solve the 208s Poisson-Boltzmann equation numerically. FETK is a portable collection 208s of finite element modeling class libraries developed by the Michael Holst 208s research group and written in an object-oriented form of C. FEtk is 208s designed to solve general coupled systems of nonlinear partial differential 208s equations using adaptive finite element methods, inexact Newton methods, 208s and algebraic multilevel methods. More information about FEtk may be found 208s at . 208s ---------------------------------------------------------------------- 208s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 208s Aqua is a modified form of the Holst group PMG library 208s which has been modified by Patrice Koehl 208s for improved efficiency and 208s memory usage when solving the Poisson-Boltzmann equation. 208s ---------------------------------------------------------------------- 208s Please cite your use of APBS as: 208s 208s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 208s nanosystems: application to microtubules and the ribosome. Proc. 208s Natl. Acad. Sci. USA 98, 10037-10041 2001. 208s 208s 208s This executable compiled on Jan 3 2025 at 11:01:42 208s 208s Parsing input file apbs-smol-surf.in... 208s rank 0 size 1... 208s Parsed input file. 208s Got paths for 3 molecules 208s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 208s asc_getToken: Error occurred (bailing out). 208s Vio_scanf: Format problem with input. 208s 47 atoms 208s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 208s Net charge 1.11e-16 e 208s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 208s asc_getToken: Error occurred (bailing out). 208s Vio_scanf: Format problem with input. 208s 3423 atoms 208s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 208s Net charge 1.00e+00 e 208s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 208s 3470 atoms 208s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 208s Net charge 1.00e+00 e 208s Preparing to run 6 PBE calculations. 208s ---------------------------------------- 208s CALCULATION #1 (lig-coarse): MULTIGRID 208s Setting up problem... 208s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 208s Debye length: 0 A 208s Current memory usage: 203.877 MB total, 203.877 MB high water 208s Using linear spline charge discretization. 208s Grid dimensions: 97 x 97 x 97 208s Grid spacings: 0.729 x 0.729 x 0.729 208s Grid lengths: 70.000 x 70.000 x 70.000 208s Grid center: (28.969, -32.507, 27.022) 208s Multigrid levels: 4 208s Molecule ID: 1 208s Linearized traditional PBE 208s Single Debye-Huckel sphere boundary conditions 208s 2 ion species (0.000 M ionic strength): 208s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 208s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 208s Solute dielectric: 2.000 208s Solvent dielectric: 78.000 208s Using "molecular" surface definition;harmonic average smoothing 208s Solvent probe radius: 1.400 A 208s Temperature: 298.150 K 208s Electrostatic energies will be calculated 208s Total electrostatic energy = 2.251466789420E+03 kJ/mol 208s Calculating forces... 208s ---------------------------------------- 208s CALCULATION #2 (lig-fine): MULTIGRID 208s Setting up problem... 208s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 208s Debye length: 0 A 208s Current memory usage: 203.877 MB total, 405.586 MB high water 208s Using linear spline charge discretization. 208s Grid dimensions: 97 x 97 x 97 208s Grid spacings: 0.250 x 0.250 x 0.250 208s Grid lengths: 24.000 x 24.000 x 24.000 208s Grid center: (24.822, -33.153, 21.545) 208s Multigrid levels: 4 208s Molecule ID: 1 208s Linearized traditional PBE 208s Boundary conditions from focusing 208s 2 ion species (0.000 M ionic strength): 208s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 208s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 208s Solute dielectric: 2.000 208s Solvent dielectric: 78.000 208s Using "molecular" surface definition;harmonic average smoothing 208s Solvent probe radius: 1.400 A 208s Temperature: 298.150 K 208s Electrostatic energies will be calculated 208s Total electrostatic energy = 1.052814502873E+04 kJ/mol 208s Calculating forces... 208s ---------------------------------------- 208s CALCULATION #3 (pka-coarse): MULTIGRID 208s Setting up problem... 208s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 208s Debye length: 0 A 208s Current memory usage: 251.521 MB total, 405.586 MB high water 208s Using linear spline charge discretization. 208s Grid dimensions: 97 x 97 x 97 208s Grid spacings: 0.729 x 0.729 x 0.729 208s Grid lengths: 70.000 x 70.000 x 70.000 208s Grid center: (28.969, -32.507, 27.022) 208s Multigrid levels: 4 208s Molecule ID: 2 208s Linearized traditional PBE 208s Single Debye-Huckel sphere boundary conditions 208s 2 ion species (0.000 M ionic strength): 208s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 208s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 208s Solute dielectric: 2.000 208s Solvent dielectric: 78.000 208s Using "molecular" surface definition;harmonic average smoothing 208s Solvent probe radius: 1.400 A 208s Temperature: 298.150 K 208s Electrostatic energies will be calculated 208s Total electrostatic energy = 1.864071689626E+05 kJ/mol 208s Calculating forces... 208s [focusFillBound()]: WARNING: 208s Unusually large potential values 208s detected on the focusing boundary! 208s Convergence not guaranteed for NPBE/NRPBE calculations! 208s 208s ---------------------------------------- 208s CALCULATION #4 (pka-fine): MULTIGRID 208s Setting up problem... 208s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 208s Debye length: 0 A 208s Current memory usage: 251.521 MB total, 493.795 MB high water 208s Using linear spline charge discretization. 208s Grid dimensions: 97 x 97 x 97 208s Grid spacings: 0.250 x 0.250 x 0.250 208s Grid lengths: 24.000 x 24.000 x 24.000 208s Grid center: (24.822, -33.153, 21.545) 208s Multigrid levels: 4 208s Molecule ID: 2 208s Linearized traditional PBE 208s Boundary conditions from focusing 208s 2 ion species (0.000 M ionic strength): 208s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 208s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 208s Solute dielectric: 2.000 208s Solvent dielectric: 78.000 208s Using "molecular" surface definition;harmonic average smoothing 208s Solvent probe radius: 1.400 A 208s Temperature: 298.150 K 208s Electrostatic energies will be calculated 208s Total electrostatic energy = 3.053319953673E+05 kJ/mol 208s Calculating forces... 208s ---------------------------------------- 208s CALCULATION #5 (complex-coarse): MULTIGRID 208s Setting up problem... 208s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 208s Debye length: 0 A 208s Current memory usage: 251.858 MB total, 493.795 MB high water 208s Using linear spline charge discretization. 208s Grid dimensions: 97 x 97 x 97 208s Grid spacings: 0.729 x 0.729 x 0.729 208s Grid lengths: 70.000 x 70.000 x 70.000 208s Grid center: (28.969, -32.507, 27.022) 208s Multigrid levels: 4 208s Molecule ID: 3 208s Linearized traditional PBE 208s Single Debye-Huckel sphere boundary conditions 208s 2 ion species (0.000 M ionic strength): 208s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 208s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 208s Solute dielectric: 2.000 208s Solvent dielectric: 78.000 208s Using "molecular" surface definition;harmonic average smoothing 208s Solvent probe radius: 1.400 A 208s Temperature: 298.150 K 208s Electrostatic energies will be calculated 208s Total electrostatic energy = 1.888027142979E+05 kJ/mol 208s Calculating forces... 208s [focusFillBound()]: WARNING: 208s Unusually large potential values 208s detected on the focusing boundary! 208s Convergence not guaranteed for NPBE/NRPBE calculations! 208s 208s ---------------------------------------- 208s CALCULATION #6 (complex-fine): MULTIGRID 208s Setting up problem... 208s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 208s Debye length: 0 A 208s Current memory usage: 251.858 MB total, 494.601 MB high water 208s Using linear spline charge discretization. 208s Grid dimensions: 97 x 97 x 97 208s Grid spacings: 0.250 x 0.250 x 0.250 208s Grid lengths: 24.000 x 24.000 x 24.000 208s Grid center: (24.822, -33.153, 21.545) 208s Multigrid levels: 4 208s Molecule ID: 3 208s Linearized traditional PBE 208s Boundary conditions from focusing 208s 2 ion species (0.000 M ionic strength): 208s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 208s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 208s Solute dielectric: 2.000 208s Solvent dielectric: 78.000 208s Using "molecular" surface definition;harmonic average smoothing 208s Solvent probe radius: 1.400 A 208s Temperature: 298.150 K 208s Electrostatic energies will be calculated 208s Total electrostatic energy = 3.159690177241E+05 kJ/mol 208s Calculating forces... 208s ---------------------------------------- 208s PRINT STATEMENTS 208s 208s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 208s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 208s Global net ELEC energy = 1.088773280806E+02 kJ/mol 208s ---------------------------------------- 208s CLEANING UP AND SHUTTING DOWN... 208s Destroying force arrays. 208s No energy arrays to destroy. 208s Destroying multigrid structures. 208s Destroying finite element structures. 208s Destroying 3 molecules 208s Final memory usage: 0.001 MB total, 494.601 MB high water 208s 208s 208s Thanks for using APBS! 208s 208s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 208s *** PASSED *** 208s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 208s *** PASSED *** 208s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 208s *** PASSED *** 208s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 208s *** PASSED *** 208s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 208s *** PASSED *** 208s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 208s *** PASSED *** 208s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 208s *** PASSED *** 208s Elapsed time: 4.907085 seconds 208s -------------------------------------------------------------------------------- 208s Total elapsed time: 20.989575 seconds 208s Test results have been logged 208s -------------------------------------------------------------------------------- 208s -------------------------------------------------------------------------------- 208s Testing input file complex-0_1.in 208s 209s Checking for intermediate energies in input file apbs-smol-surf.out 209s EXPECTED COMPUTED: 7 209s EXPECTED EXPECTED: 7 209s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 209s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 209s COMPUTED RESULT 2251.46678942 209s COMPUTED RESULT 10528.14502873 209s COMPUTED RESULT 186407.1689626 209s COMPUTED RESULT 305331.9953673 209s COMPUTED RESULT 188802.7142979 209s COMPUTED RESULT 315969.0177241 209s COMPUTED RESULT 108.8773280806 209s Running tests for point-pmf section 209s BINARY: /usr/bin/apbs 209s INPUT: complex-0_1.in 209s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 209s 209s ---------------------------------------------------------------------- 209s APBS -- Adaptive Poisson-Boltzmann Solver 209s Version APBS 3.4.1 209s 209s Nathan A. Baker (nathan.baker@pnnl.gov) 209s Pacific Northwest National Laboratory 209s 209s Additional contributing authors listed in the code documentation. 209s 209s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 209s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 209s Northwest Division for the U.S. Department of Energy. 209s 209s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 209s Portions Copyright (c) 2002-2020, Nathan A. Baker. 209s Portions Copyright (c) 1999-2002, The Regents of the University of California. 209s Portions Copyright (c) 1995, Michael Holst. 209s All rights reserved. 209s 209s Redistribution and use in source and binary forms, with or without 209s modification, are permitted provided that the following conditions are met: 209s 209s * Redistributions of source code must retain the above copyright notice, this 209s list of conditions and the following disclaimer. 209s 209s * Redistributions in binary form must reproduce the above copyright notice, 209s this list of conditions and the following disclaimer in the documentation 209s and/or other materials provided with the distribution. 209s 209s * Neither the name of the developer nor the names of its contributors may be 209s used to endorse or promote products derived from this software without 209s specific prior written permission. 209s 209s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 209s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 209s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 209s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 209s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 209s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 209s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 209s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 209s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 209s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 209s ---------------------------------------------------------------------- 209s APBS uses FETK (the Finite Element ToolKit) to solve the 209s Poisson-Boltzmann equation numerically. FETK is a portable collection 209s of finite element modeling class libraries developed by the Michael Holst 209s research group and written in an object-oriented form of C. FEtk is 209s designed to solve general coupled systems of nonlinear partial differential 209s equations using adaptive finite element methods, inexact Newton methods, 209s and algebraic multilevel methods. More information about FEtk may be found 209s at . 209s ---------------------------------------------------------------------- 209s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 209s Aqua is a modified form of the Holst group PMG library 209s which has been modified by Patrice Koehl 209s for improved efficiency and 209s memory usage when solving the Poisson-Boltzmann equation. 209s ---------------------------------------------------------------------- 209s Please cite your use of APBS as: 209s 209s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 209s nanosystems: application to microtubules and the ribosome. Proc. 209s Natl. Acad. Sci. USA 98, 10037-10041 2001. 209s 209s 209s This executable compiled on Jan 3 2025 at 11:01:42 209s 209s Parsing input file complex-0_1.in... 209s rank 0 size 1... 209s Parsed input file. 209s Got paths for 3 molecules 209s Reading PQR-format atom data from mol0.pqr. 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 1 atoms 209s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 1.00e+00 e 209s Reading PQR-format atom data from mol1.pqr. 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 1 atoms 209s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 1.00e+00 e 209s Reading PQR-format atom data from complex-0_1.pqr. 209s 2 atoms 209s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 209s Net charge 2.00e+00 e 209s Preparing to run 3 PBE calculations. 209s ---------------------------------------- 209s CALCULATION #1 (point1): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.060 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 9.776035707281E+01 kJ/mol 209s Fixed charge energy = 97.7604 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 96.5336 kJ/mol 209s Per-atom energies: 209s Atom 0: 9.776035707281E+01 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #2 (point2): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.067 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 2 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 8.975920687031E+01 kJ/mol 209s Fixed charge energy = 89.7592 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 88.6151 kJ/mol 209s Per-atom energies: 209s Atom 0: 8.975920687031E+01 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #3 (complex): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.067 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 3 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 2.058277719334E+02 kJ/mol 209s Fixed charge energy = 205.828 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 201.106 kJ/mol 209s Per-atom energies: 209s Atom 0: 1.069144350786E+02 kJ/mol 209s Atom 1: 9.891333685475E+01 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s PRINT STATEMENTS 209s 209s print energy 3 (complex) - 1 (point1) - 2 (point2) end 209s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 209s Global net ELEC energy = 1.830820799027E+01 kJ/mol 209s ---------------------------------------- 209s CLEANING UP AND SHUTTING DOWN... 209s Destroying force arrays. 209s No energy arrays to destroy. 209s Destroying multigrid structures. 209s Destroying finite element structures. 209s Destroying 3 molecules 209s Final memory usage: 0.001 MB total, 61.067 MB high water 209s 209s 209s Thanks for using APBS! 209s 209s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 209s *** PASSED *** 209s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 209s *** PASSED *** 209s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 209s *** PASSED *** 209s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 209s *** PASSED *** 209s Elapsed time: 0.355453 seconds 209s -------------------------------------------------------------------------------- 209s -------------------------------------------------------------------------------- 209s Testing input file complex-0_2.in 209s 209s Checking for intermediate energies in input file complex-0_1.out 209s EXPECTED COMPUTED: 13 209s EXPECTED EXPECTED: 13 209s 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] 209s 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'] 209s COMPUTED RESULT 97.76035707281 209s COMPUTED RESULT 89.75920687031 209s COMPUTED RESULT 205.8277719334 209s COMPUTED RESULT 0.0 209s COMPUTED RESULT 0.0 209s COMPUTED RESULT 0.0 209s COMPUTED RESULT 97.7604 209s COMPUTED RESULT 89.7592 209s COMPUTED RESULT 205.828 209s COMPUTED RESULT 96.5336 209s COMPUTED RESULT 88.6151 209s COMPUTED RESULT 201.106 209s COMPUTED RESULT 18.30820799027 209s BINARY: /usr/bin/apbs 209s INPUT: complex-0_2.in 209s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 209s 209s ---------------------------------------------------------------------- 209s APBS -- Adaptive Poisson-Boltzmann Solver 209s Version APBS 3.4.1 209s 209s Nathan A. Baker (nathan.baker@pnnl.gov) 209s Pacific Northwest National Laboratory 209s 209s Additional contributing authors listed in the code documentation. 209s 209s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 209s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 209s Northwest Division for the U.S. Department of Energy. 209s 209s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 209s Portions Copyright (c) 2002-2020, Nathan A. Baker. 209s Portions Copyright (c) 1999-2002, The Regents of the University of California. 209s Portions Copyright (c) 1995, Michael Holst. 209s All rights reserved. 209s 209s Redistribution and use in source and binary forms, with or without 209s modification, are permitted provided that the following conditions are met: 209s 209s * Redistributions of source code must retain the above copyright notice, this 209s list of conditions and the following disclaimer. 209s 209s * Redistributions in binary form must reproduce the above copyright notice, 209s this list of conditions and the following disclaimer in the documentation 209s and/or other materials provided with the distribution. 209s 209s * Neither the name of the developer nor the names of its contributors may be 209s used to endorse or promote products derived from this software without 209s specific prior written permission. 209s 209s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 209s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 209s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 209s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 209s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 209s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 209s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 209s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 209s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 209s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 209s ---------------------------------------------------------------------- 209s APBS uses FETK (the Finite Element ToolKit) to solve the 209s Poisson-Boltzmann equation numerically. FETK is a portable collection 209s of finite element modeling class libraries developed by the Michael Holst 209s research group and written in an object-oriented form of C. FEtk is 209s designed to solve general coupled systems of nonlinear partial differential 209s equations using adaptive finite element methods, inexact Newton methods, 209s and algebraic multilevel methods. More information about FEtk may be found 209s at . 209s ---------------------------------------------------------------------- 209s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 209s Aqua is a modified form of the Holst group PMG library 209s which has been modified by Patrice Koehl 209s for improved efficiency and 209s memory usage when solving the Poisson-Boltzmann equation. 209s ---------------------------------------------------------------------- 209s Please cite your use of APBS as: 209s 209s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 209s nanosystems: application to microtubules and the ribosome. Proc. 209s Natl. Acad. Sci. USA 98, 10037-10041 2001. 209s 209s 209s This executable compiled on Jan 3 2025 at 11:01:42 209s 209s Parsing input file complex-0_2.in... 209s rank 0 size 1... 209s Parsed input file. 209s Got paths for 3 molecules 209s Reading PQR-format atom data from mol0.pqr. 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 1 atoms 209s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 1.00e+00 e 209s Reading PQR-format atom data from mol2.pqr. 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 1 atoms 209s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 1.00e+00 e 209s Reading PQR-format atom data from complex-0_2.pqr. 209s 2 atoms 209s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 2.00e+00 e 209s Preparing to run 3 PBE calculations. 209s ---------------------------------------- 209s CALCULATION #1 (point1): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.060 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 9.776035707281E+01 kJ/mol 209s Fixed charge energy = 97.7604 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 96.5336 kJ/mol 209s Per-atom energies: 209s Atom 0: 9.776035707281E+01 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #2 (point2): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.067 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 2 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 1.017611498797E+02 kJ/mol 209s Fixed charge energy = 101.761 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 100.656 kJ/mol 209s Per-atom energies: 209s Atom 0: 1.017611498797E+02 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #3 (complex): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.068 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 3 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 2.084282010393E+02 kJ/mol 209s Fixed charge energy = 208.428 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 203.83 kJ/mol 209s Per-atom energies: 209s Atom 0: 1.022136878480E+02 kJ/mol 209s Atom 1: 1.062145131913E+02 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s PRINT STATEMENTS 209s 209s print energy 3 (complex) - 1 (point1) - 2 (point2) end 209s Local net energy (PE 0) = 8.906694086750E+00 kJ/mol 209s Global net ELEC energy = 8.906694086750E+00 kJ/mol 209s ---------------------------------------- 209s CLEANING UP AND SHUTTING DOWN... 209s Destroying force arrays. 209s No energy arrays to destroy. 209s Destroying multigrid structures. 209s Destroying finite element structures. 209s Destroying 3 molecules 209s Final memory usage: 0.001 MB total, 61.068 MB high water 209s 209s 209s Thanks for using APBS! 209s 209s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 209s *** PASSED *** 209s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 209s *** PASSED *** 209s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 209s *** PASSED *** 209s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) 209s *** PASSED *** 209s Elapsed time: 0.362034 seconds 209s -------------------------------------------------------------------------------- 209s -------------------------------------------------------------------------------- 209s Testing input file complex-0_3.in 209s 209s Checking for intermediate energies in input file complex-0_2.out 209s EXPECTED COMPUTED: 13 209s EXPECTED EXPECTED: 13 209s 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] 209s 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'] 209s COMPUTED RESULT 97.76035707281 209s COMPUTED RESULT 101.7611498797 209s COMPUTED RESULT 208.4282010393 209s COMPUTED RESULT 0.0 209s COMPUTED RESULT 0.0 209s COMPUTED RESULT 0.0 209s COMPUTED RESULT 97.7604 209s COMPUTED RESULT 101.761 209s COMPUTED RESULT 208.428 209s COMPUTED RESULT 96.5336 209s COMPUTED RESULT 100.656 209s COMPUTED RESULT 203.83 209s COMPUTED RESULT 8.90669408675 209s BINARY: /usr/bin/apbs 209s INPUT: complex-0_3.in 209s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 209s 209s ---------------------------------------------------------------------- 209s APBS -- Adaptive Poisson-Boltzmann Solver 209s Version APBS 3.4.1 209s 209s Nathan A. Baker (nathan.baker@pnnl.gov) 209s Pacific Northwest National Laboratory 209s 209s Additional contributing authors listed in the code documentation. 209s 209s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 209s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 209s Northwest Division for the U.S. Department of Energy. 209s 209s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 209s Portions Copyright (c) 2002-2020, Nathan A. Baker. 209s Portions Copyright (c) 1999-2002, The Regents of the University of California. 209s Portions Copyright (c) 1995, Michael Holst. 209s All rights reserved. 209s 209s Redistribution and use in source and binary forms, with or without 209s modification, are permitted provided that the following conditions are met: 209s 209s * Redistributions of source code must retain the above copyright notice, this 209s list of conditions and the following disclaimer. 209s 209s * Redistributions in binary form must reproduce the above copyright notice, 209s this list of conditions and the following disclaimer in the documentation 209s and/or other materials provided with the distribution. 209s 209s * Neither the name of the developer nor the names of its contributors may be 209s used to endorse or promote products derived from this software without 209s specific prior written permission. 209s 209s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 209s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 209s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 209s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 209s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 209s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 209s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 209s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 209s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 209s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 209s ---------------------------------------------------------------------- 209s APBS uses FETK (the Finite Element ToolKit) to solve the 209s Poisson-Boltzmann equation numerically. FETK is a portable collection 209s of finite element modeling class libraries developed by the Michael Holst 209s research group and written in an object-oriented form of C. FEtk is 209s designed to solve general coupled systems of nonlinear partial differential 209s equations using adaptive finite element methods, inexact Newton methods, 209s and algebraic multilevel methods. More information about FEtk may be found 209s at . 209s ---------------------------------------------------------------------- 209s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 209s Aqua is a modified form of the Holst group PMG library 209s which has been modified by Patrice Koehl 209s for improved efficiency and 209s memory usage when solving the Poisson-Boltzmann equation. 209s ---------------------------------------------------------------------- 209s Please cite your use of APBS as: 209s 209s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 209s nanosystems: application to microtubules and the ribosome. Proc. 209s Natl. Acad. Sci. USA 98, 10037-10041 2001. 209s 209s 209s This executable compiled on Jan 3 2025 at 11:01:42 209s 209s Parsing input file complex-0_3.in... 209s rank 0 size 1... 209s Parsed input file. 209s Got paths for 3 molecules 209s Reading PQR-format atom data from mol0.pqr. 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 1 atoms 209s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 1.00e+00 e 209s Reading PQR-format atom data from mol3.pqr. 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 1 atoms 209s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 1.00e+00 e 209s Reading PQR-format atom data from complex-0_3.pqr. 209s 2 atoms 209s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 209s Net charge 2.00e+00 e 209s Preparing to run 3 PBE calculations. 209s ---------------------------------------- 209s CALCULATION #1 (point1): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.060 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 9.776035707281E+01 kJ/mol 209s Fixed charge energy = 97.7604 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 96.5336 kJ/mol 209s Per-atom energies: 209s Atom 0: 9.776035707281E+01 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #2 (point2): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.067 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 2 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 1.337661883222E+02 kJ/mol 209s Fixed charge energy = 133.766 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 132.672 kJ/mol 209s Per-atom energies: 209s Atom 0: 1.337661883222E+02 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #3 (complex): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.060 MB total, 61.068 MB high water 209s Using linear spline charge discretization. 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.210 x 0.210 x 0.210 209s Grid lengths: 13.440 x 13.440 x 13.440 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 3 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 78.540 209s Solvent dielectric: 78.540 209s Using spline-based surface definition;window = 0.300 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 2.374361452120E+02 kJ/mol 209s Fixed charge energy = 237.436 kJ/mol 209s Mobile charge energy = 0 kJ/mol 209s Dielectric energy = 232.924 kJ/mol 209s Per-atom energies: 209s Atom 0: 1.007151570480E+02 kJ/mol 209s Atom 1: 1.367209881640E+02 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s PRINT STATEMENTS 209s 209s print energy 3 (complex) - 1 (point1) - 2 (point2) end 209s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 209s Global net ELEC energy = 5.909599816984E+00 kJ/mol 209s ---------------------------------------- 209s CLEANING UP AND SHUTTING DOWN... 209s Destroying force arrays. 209s No energy arrays to destroy. 209s Destroying multigrid structures. 209s Destroying finite element structures. 209s Destroying 3 molecules 209s Final memory usage: 0.001 MB total, 61.068 MB high water 209s 209s 209s Thanks for using APBS! 209s 209s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 209s *** PASSED *** 209s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 209s *** PASSED *** 209s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 209s *** PASSED *** 209s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 209s *** PASSED *** 209s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 209s *** PASSED *** 209s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 209s *** PASSED *** 209s Elapsed time: 0.354609 seconds 209s -------------------------------------------------------------------------------- 209s -------------------------------------------------------------------------------- 209s Testing input file complex-0_4.in 209s 210s Checking for intermediate energies in input file complex-0_3.out 210s EXPECTED COMPUTED: 13 210s EXPECTED EXPECTED: 13 210s 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] 210s 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'] 210s COMPUTED RESULT 97.76035707281 210s COMPUTED RESULT 133.7661883222 210s COMPUTED RESULT 237.436145212 210s COMPUTED RESULT 0.0 210s COMPUTED RESULT 0.0 210s COMPUTED RESULT 0.0 210s COMPUTED RESULT 97.7604 210s COMPUTED RESULT 133.766 210s COMPUTED RESULT 237.436 210s COMPUTED RESULT 96.5336 210s COMPUTED RESULT 132.672 210s COMPUTED RESULT 232.924 210s COMPUTED RESULT 5.909599816984 210s BINARY: /usr/bin/apbs 210s INPUT: complex-0_4.in 210s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 210s asc_getToken: Error occurred (bailing out). 210s Vio_scanf: Format problem with input. 210s 210s 210s ---------------------------------------------------------------------- 210s APBS -- Adaptive Poisson-Boltzmann Solver 210s Version APBS 3.4.1 210s 210s Nathan A. Baker (nathan.baker@pnnl.gov) 210s Pacific Northwest National Laboratory 210s 210s Additional contributing authors listed in the code documentation. 210s 210s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 210s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 210s Northwest Division for the U.S. Department of Energy. 210s 210s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 210s Portions Copyright (c) 2002-2020, Nathan A. Baker. 210s Portions Copyright (c) 1999-2002, The Regents of the University of California. 210s Portions Copyright (c) 1995, Michael Holst. 210s All rights reserved. 210s 210s Redistribution and use in source and binary forms, with or without 210s modification, are permitted provided that the following conditions are met: 210s 210s * Redistributions of source code must retain the above copyright notice, this 210s list of conditions and the following disclaimer. 210s 210s * Redistributions in binary form must reproduce the above copyright notice, 210s this list of conditions and the following disclaimer in the documentation 210s and/or other materials provided with the distribution. 210s 210s * Neither the name of the developer nor the names of its contributors may be 210s used to endorse or promote products derived from this software without 210s specific prior written permission. 210s 210s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 210s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 210s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 210s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 210s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 210s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 210s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 210s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 210s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 210s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 210s ---------------------------------------------------------------------- 210s APBS uses FETK (the Finite Element ToolKit) to solve the 210s Poisson-Boltzmann equation numerically. FETK is a portable collection 210s of finite element modeling class libraries developed by the Michael Holst 210s research group and written in an object-oriented form of C. FEtk is 210s designed to solve general coupled systems of nonlinear partial differential 210s equations using adaptive finite element methods, inexact Newton methods, 210s and algebraic multilevel methods. More information about FEtk may be found 210s at . 210s ---------------------------------------------------------------------- 210s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 210s Aqua is a modified form of the Holst group PMG library 210s which has been modified by Patrice Koehl 210s for improved efficiency and 210s memory usage when solving the Poisson-Boltzmann equation. 210s ---------------------------------------------------------------------- 210s Please cite your use of APBS as: 210s 210s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 210s nanosystems: application to microtubules and the ribosome. Proc. 210s Natl. Acad. Sci. USA 98, 10037-10041 2001. 210s 210s 210s This executable compiled on Jan 3 2025 at 11:01:42 210s 210s Parsing input file complex-0_4.in... 210s rank 0 size 1... 210s Parsed input file. 210s Got paths for 3 molecules 210s Reading PQR-format atom data from mol0.pqr. 210s asc_getToken: Error occurred (bailing out). 210s Vio_scanf: Format problem with input. 210s 1 atoms 210s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 210s Net charge 1.00e+00 e 210s Reading PQR-format atom data from mol4.pqr. 210s asc_getToken: Error occurred (bailing out). 210s Vio_scanf: Format problem with input. 210s 1 atoms 210s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 210s Net charge 1.00e+00 e 210s Reading PQR-format atom data from complex-0_4.pqr. 210s 2 atoms 210s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 210s Net charge 2.00e+00 e 210s Preparing to run 3 PBE calculations. 210s ---------------------------------------- 210s CALCULATION #1 (point1): MULTIGRID 210s Setting up problem... 210s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 210s Debye length: 0 A 210s Current memory usage: 61.060 MB total, 61.060 MB high water 210s Using linear spline charge discretization. 210s Grid dimensions: 65 x 65 x 65 210s Grid spacings: 0.210 x 0.210 x 0.210 210s Grid lengths: 13.440 x 13.440 x 13.440 210s Grid center: (0.000, 0.000, 0.000) 210s Multigrid levels: 5 210s Molecule ID: 1 210s Linearized traditional PBE 210s Multiple Debye-Huckel sphere boundary conditions 210s 0 ion species (0.000 M ionic strength): 210s Solute dielectric: 78.540 210s Solvent dielectric: 78.540 210s Using spline-based surface definition;window = 0.300 210s Temperature: 298.150 K 210s Electrostatic energies will be calculated 210s Total electrostatic energy = 9.776035707281E+01 kJ/mol 210s Fixed charge energy = 97.7604 kJ/mol 210s Mobile charge energy = 0 kJ/mol 210s Dielectric energy = 96.5336 kJ/mol 210s Per-atom energies: 210s Atom 0: 9.776035707281E+01 kJ/mol 210s Calculating forces... 210s ---------------------------------------- 210s CALCULATION #2 (point2): MULTIGRID 210s Setting up problem... 210s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 210s Debye length: 0 A 210s Current memory usage: 61.060 MB total, 61.067 MB high water 210s Using linear spline charge discretization. 210s Grid dimensions: 65 x 65 x 65 210s Grid spacings: 0.210 x 0.210 x 0.210 210s Grid lengths: 13.440 x 13.440 x 13.440 210s Grid center: (0.000, 0.000, 0.000) 210s Multigrid levels: 5 210s Molecule ID: 2 210s Linearized traditional PBE 210s Multiple Debye-Huckel sphere boundary conditions 210s 0 ion species (0.000 M ionic strength): 210s Solute dielectric: 78.540 210s Solvent dielectric: 78.540 210s Using spline-based surface definition;window = 0.300 210s Temperature: 298.150 K 210s Electrostatic energies will be calculated 210s Total electrostatic energy = 1.017611498797E+02 kJ/mol 210s Fixed charge energy = 101.761 kJ/mol 210s Mobile charge energy = 0 kJ/mol 210s Dielectric energy = 100.654 kJ/mol 210s Per-atom energies: 210s Atom 0: 1.017611498797E+02 kJ/mol 210s Calculating forces... 210s ---------------------------------------- 210s CALCULATION #3 (complex): MULTIGRID 210s Setting up problem... 210s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 210s Debye length: 0 A 210s Current memory usage: 61.061 MB total, 61.068 MB high water 210s Using linear spline charge discretization. 210s Grid dimensions: 65 x 65 x 65 210s Grid spacings: 0.210 x 0.210 x 0.210 210s Grid lengths: 13.440 x 13.440 x 13.440 210s Grid center: (0.000, 0.000, 0.000) 210s Multigrid levels: 5 210s Molecule ID: 3 210s Linearized traditional PBE 210s Multiple Debye-Huckel sphere boundary conditions 210s 0 ion species (0.000 M ionic strength): 210s Solute dielectric: 78.540 210s Solvent dielectric: 78.540 210s Using spline-based surface definition;window = 0.300 210s Temperature: 298.150 K 210s Electrostatic energies will be calculated 210s Total electrostatic energy = 2.039516519000E+02 kJ/mol 210s Fixed charge energy = 203.952 kJ/mol 210s Mobile charge energy = 0 kJ/mol 210s Dielectric energy = 199.493 kJ/mol 210s Per-atom energies: 210s Atom 0: 9.997541697022E+01 kJ/mol 210s Atom 1: 1.039762349297E+02 kJ/mol 210s Calculating forces... 210s ---------------------------------------- 210s PRINT STATEMENTS 210s 210s print energy 3 (complex) - 1 (point1) - 2 (point2) end 210s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 210s Global net ELEC energy = 4.430144947418E+00 kJ/mol 210s ---------------------------------------- 210s CLEANING UP AND SHUTTING DOWN... 210s Destroying force arrays. 210s No energy arrays to destroy. 210s Destroying multigrid structures. 210s Destroying finite element structures. 210s Destroying 3 molecules 210s Final memory usage: 0.001 MB total, 61.068 MB high water 210s 210s 210s Thanks for using APBS! 210s 210s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 210s *** PASSED *** 210s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 210s *** PASSED *** 210s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 210s *** PASSED *** 210s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 210s *** PASSED *** 210s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 210s *** PASSED *** 210s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 210s *** PASSED *** 210s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 210s *** PASSED *** 210s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 210s *** PASSED *** 210s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 210s *** PASSED *** 210s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 210s *** PASSED *** 210s Elapsed time: 0.369331 seconds 210s -------------------------------------------------------------------------------- 210s Total elapsed time: 1.441427 seconds 210s Test results have been logged 210s -------------------------------------------------------------------------------- 210s -------------------------------------------------------------------------------- 210s Testing input file apbs-mol.in 210s 210s Checking for intermediate energies in input file complex-0_4.out 210s EXPECTED COMPUTED: 13 210s EXPECTED EXPECTED: 13 210s 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] 210s 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'] 210s COMPUTED RESULT 97.76035707281 210s COMPUTED RESULT 101.7611498797 210s COMPUTED RESULT 203.9516519 210s COMPUTED RESULT 0.0 210s COMPUTED RESULT 0.0 210s COMPUTED RESULT 0.0 210s COMPUTED RESULT 97.7604 210s COMPUTED RESULT 101.761 210s COMPUTED RESULT 203.952 210s COMPUTED RESULT 96.5336 210s COMPUTED RESULT 100.654 210s COMPUTED RESULT 199.493 210s COMPUTED RESULT 4.430144947418 210s Running tests for solv section 210s BINARY: /usr/bin/apbs 210s INPUT: apbs-mol.in 210s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 210s asc_getToken: Error occurred (bailing out). 210s Vio_scanf: Format problem with input. 210s 210s 210s ---------------------------------------------------------------------- 210s APBS -- Adaptive Poisson-Boltzmann Solver 210s Version APBS 3.4.1 210s 210s Nathan A. Baker (nathan.baker@pnnl.gov) 210s Pacific Northwest National Laboratory 210s 210s Additional contributing authors listed in the code documentation. 210s 210s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 210s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 210s Northwest Division for the U.S. Department of Energy. 210s 210s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 210s Portions Copyright (c) 2002-2020, Nathan A. Baker. 210s Portions Copyright (c) 1999-2002, The Regents of the University of California. 210s Portions Copyright (c) 1995, Michael Holst. 210s All rights reserved. 210s 210s Redistribution and use in source and binary forms, with or without 210s modification, are permitted provided that the following conditions are met: 210s 210s * Redistributions of source code must retain the above copyright notice, this 210s list of conditions and the following disclaimer. 210s 210s * Redistributions in binary form must reproduce the above copyright notice, 210s this list of conditions and the following disclaimer in the documentation 210s and/or other materials provided with the distribution. 210s 210s * Neither the name of the developer nor the names of its contributors may be 210s used to endorse or promote products derived from this software without 210s specific prior written permission. 210s 210s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 210s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 210s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 210s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 210s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 210s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 210s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 210s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 210s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 210s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 210s ---------------------------------------------------------------------- 210s APBS uses FETK (the Finite Element ToolKit) to solve the 210s Poisson-Boltzmann equation numerically. FETK is a portable collection 210s of finite element modeling class libraries developed by the Michael Holst 210s research group and written in an object-oriented form of C. FEtk is 210s designed to solve general coupled systems of nonlinear partial differential 210s equations using adaptive finite element methods, inexact Newton methods, 210s and algebraic multilevel methods. More information about FEtk may be found 210s at . 210s ---------------------------------------------------------------------- 210s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 210s Aqua is a modified form of the Holst group PMG library 210s which has been modified by Patrice Koehl 210s for improved efficiency and 210s memory usage when solving the Poisson-Boltzmann equation. 210s ---------------------------------------------------------------------- 210s Please cite your use of APBS as: 210s 210s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 210s nanosystems: application to microtubules and the ribosome. Proc. 210s Natl. Acad. Sci. USA 98, 10037-10041 2001. 210s 210s 210s This executable compiled on Jan 3 2025 at 11:01:42 210s 210s Parsing input file apbs-mol.in... 210s rank 0 size 1... 210s Parsed input file. 210s Got paths for 2 molecules 210s Reading PQR-format atom data from methanol.pqr. 210s asc_getToken: Error occurred (bailing out). 210s Vio_scanf: Format problem with input. 210s 3 atoms 210s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 210s Net charge 5.55e-17 e 210s Reading PQR-format atom data from methoxide.pqr. 210s 2 atoms 210s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 210s Net charge -1.00e+00 e 210s Preparing to run 4 PBE calculations. 210s ---------------------------------------- 210s CALCULATION #1 (methanol-solv): MULTIGRID 210s Setting up problem... 210s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 210s Debye length: 0 A 210s Current memory usage: 61.253 MB total, 61.253 MB high water 210s Using linear spline charge discretization. 210s Grid dimensions: 65 x 65 x 65 210s Grid spacings: 0.250 x 0.250 x 0.250 210s Grid lengths: 16.000 x 16.000 x 16.000 210s Grid center: (0.309, 0.000, -0.242) 210s Multigrid levels: 5 210s Molecule ID: 1 210s Linearized traditional PBE 210s Multiple Debye-Huckel sphere boundary conditions 210s 2 ion species (0.000 M ionic strength): 210s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 210s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 210s Solute dielectric: 2.000 210s Solvent dielectric: 78.000 210s Using "molecular" surface definition; no smoothing 210s Solvent probe radius: 0.000 A 210s Temperature: 300.000 K 210s Electrostatic energies will be calculated 210s Total electrostatic energy = 1.847663548071E+03 kJ/mol 210s Calculating forces... 210s ---------------------------------------- 210s CALCULATION #2 (methanol-ref): MULTIGRID 210s Setting up problem... 210s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 210s Debye length: 0 A 210s Current memory usage: 61.253 MB total, 61.328 MB high water 210s Using linear spline charge discretization. 210s Grid dimensions: 65 x 65 x 65 210s Grid spacings: 0.250 x 0.250 x 0.250 210s Grid lengths: 16.000 x 16.000 x 16.000 210s Grid center: (0.309, 0.000, -0.242) 210s Multigrid levels: 5 210s Molecule ID: 1 210s Linearized traditional PBE 210s Multiple Debye-Huckel sphere boundary conditions 210s 2 ion species (0.000 M ionic strength): 210s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 210s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 210s Solute dielectric: 2.000 210s Solvent dielectric: 1.000 210s Using "molecular" surface definition; no smoothing 210s Solvent probe radius: 0.000 A 210s Temperature: 300.000 K 210s Electrostatic energies will be calculated 210s Total electrostatic energy = 1.883912182952E+03 kJ/mol 210s Calculating forces... 210s ---------------------------------------- 210s CALCULATION #3 (methoxide-solv): MULTIGRID 210s Setting up problem... 210s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 210s Debye length: 0 A 210s Current memory usage: 61.250 MB total, 61.328 MB high water 210s Using linear spline charge discretization. 210s Grid dimensions: 65 x 65 x 65 210s Grid spacings: 0.250 x 0.250 x 0.250 210s Grid lengths: 16.000 x 16.000 x 16.000 210s Grid center: (0.000, 0.000, -0.128) 210s Multigrid levels: 5 210s Molecule ID: 2 210s Linearized traditional PBE 210s Multiple Debye-Huckel sphere boundary conditions 210s 2 ion species (0.000 M ionic strength): 210s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 210s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 210s Solute dielectric: 2.000 210s Solvent dielectric: 78.000 210s Using "molecular" surface definition; no smoothing 210s Solvent probe radius: 0.000 A 210s Temperature: 300.000 K 210s Electrostatic energies will be calculated 210s Total electrostatic energy = 2.732623683321E+03 kJ/mol 210s Calculating forces... 210s ---------------------------------------- 210s CALCULATION #4 (methoxide-ref): MULTIGRID 210s Setting up problem... 210s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 210s Debye length: 0 A 210s Current memory usage: 61.250 MB total, 61.328 MB high water 210s Using linear spline charge discretization. 210s Grid dimensions: 65 x 65 x 65 210s Grid spacings: 0.250 x 0.250 x 0.250 210s Grid lengths: 16.000 x 16.000 x 16.000 210s Grid center: (0.000, 0.000, -0.128) 210s Multigrid levels: 5 210s Molecule ID: 2 210s Linearized traditional PBE 210s Multiple Debye-Huckel sphere boundary conditions 210s 2 ion species (0.000 M ionic strength): 210s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 210s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 210s Solute dielectric: 2.000 210s Solvent dielectric: 1.000 210s Using "molecular" surface definition; no smoothing 210s Solvent probe radius: 0.000 A 210s Temperature: 300.000 K 210s Electrostatic energies will be calculated 210s Total electrostatic energy = 3.123035854133E+03 kJ/mol 210s Calculating forces... 210s ---------------------------------------- 210s PRINT STATEMENTS 210s 210s print energy 1 (methanol-solv) - 2 (methanol-ref) end 210s Local net energy (PE 0) = -3.624863488074E+01 kJ/mol 210s Global net ELEC energy = -3.624863488074E+01 kJ/mol 210s 210s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 210s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 210s Global net ELEC energy = -3.904121708125E+02 kJ/mol 210s 210s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 210s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 210s Global net ELEC energy = -3.541635359318E+02 kJ/mol 210s ---------------------------------------- 210s CLEANING UP AND SHUTTING DOWN... 210s Destroying force arrays. 210s No energy arrays to destroy. 210s Destroying multigrid structures. 210s Destroying finite element structures. 210s Destroying 2 molecules 210s Final memory usage: 0.001 MB total, 61.328 MB high water 210s 210s 210s Thanks for using APBS! 210s 210s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 210s *** PASSED *** 210s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 210s *** PASSED *** 210s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 210s *** PASSED *** 210s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 210s *** PASSED *** 210s Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) 210s *** PASSED *** 210s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 210s *** PASSED *** 210s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 210s *** PASSED *** 210s Elapsed time: 0.452782 seconds 210s -------------------------------------------------------------------------------- 210s -------------------------------------------------------------------------------- 210s Testing input file apbs-smol.in 210s 211s Checking for intermediate energies in input file apbs-mol.out 211s EXPECTED COMPUTED: 7 211s EXPECTED EXPECTED: 7 211s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] 211s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 211s COMPUTED RESULT 1847.663548071 211s COMPUTED RESULT 1883.912182952 211s COMPUTED RESULT 2732.623683321 211s COMPUTED RESULT 3123.035854133 211s COMPUTED RESULT -36.24863488074 211s COMPUTED RESULT -390.4121708125 211s COMPUTED RESULT -354.1635359318 211s BINARY: /usr/bin/apbs 211s INPUT: apbs-smol.in 211s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 211s asc_getToken: Error occurred (bailing out). 211s Vio_scanf: Format problem with input. 211s 211s 211s ---------------------------------------------------------------------- 211s APBS -- Adaptive Poisson-Boltzmann Solver 211s Version APBS 3.4.1 211s 211s Nathan A. Baker (nathan.baker@pnnl.gov) 211s Pacific Northwest National Laboratory 211s 211s Additional contributing authors listed in the code documentation. 211s 211s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 211s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 211s Northwest Division for the U.S. Department of Energy. 211s 211s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 211s Portions Copyright (c) 2002-2020, Nathan A. Baker. 211s Portions Copyright (c) 1999-2002, The Regents of the University of California. 211s Portions Copyright (c) 1995, Michael Holst. 211s All rights reserved. 211s 211s Redistribution and use in source and binary forms, with or without 211s modification, are permitted provided that the following conditions are met: 211s 211s * Redistributions of source code must retain the above copyright notice, this 211s list of conditions and the following disclaimer. 211s 211s * Redistributions in binary form must reproduce the above copyright notice, 211s this list of conditions and the following disclaimer in the documentation 211s and/or other materials provided with the distribution. 211s 211s * Neither the name of the developer nor the names of its contributors may be 211s used to endorse or promote products derived from this software without 211s specific prior written permission. 211s 211s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 211s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 211s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 211s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 211s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 211s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 211s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 211s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 211s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 211s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 211s ---------------------------------------------------------------------- 211s APBS uses FETK (the Finite Element ToolKit) to solve the 211s Poisson-Boltzmann equation numerically. FETK is a portable collection 211s of finite element modeling class libraries developed by the Michael Holst 211s research group and written in an object-oriented form of C. FEtk is 211s designed to solve general coupled systems of nonlinear partial differential 211s equations using adaptive finite element methods, inexact Newton methods, 211s and algebraic multilevel methods. More information about FEtk may be found 211s at . 211s ---------------------------------------------------------------------- 211s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 211s Aqua is a modified form of the Holst group PMG library 211s which has been modified by Patrice Koehl 211s for improved efficiency and 211s memory usage when solving the Poisson-Boltzmann equation. 211s ---------------------------------------------------------------------- 211s Please cite your use of APBS as: 211s 211s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 211s nanosystems: application to microtubules and the ribosome. Proc. 211s Natl. Acad. Sci. USA 98, 10037-10041 2001. 211s 211s 211s This executable compiled on Jan 3 2025 at 11:01:42 211s 211s Parsing input file apbs-smol.in... 211s rank 0 size 1... 211s Parsed input file. 211s Got paths for 2 molecules 211s Reading PQR-format atom data from methanol.pqr. 211s asc_getToken: Error occurred (bailing out). 211s Vio_scanf: Format problem with input. 211s 3 atoms 211s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 211s Net charge 5.55e-17 e 211s Reading PQR-format atom data from methoxide.pqr. 211s 2 atoms 211s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 211s Net charge -1.00e+00 e 211s Preparing to run 4 PBE calculations. 211s ---------------------------------------- 211s CALCULATION #1 (methanol-solv): MULTIGRID 211s Setting up problem... 211s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 211s Debye length: 0 A 211s Current memory usage: 61.253 MB total, 61.253 MB high water 211s Using linear spline charge discretization. 211s Grid dimensions: 65 x 65 x 65 211s Grid spacings: 0.250 x 0.250 x 0.250 211s Grid lengths: 16.000 x 16.000 x 16.000 211s Grid center: (0.309, 0.000, -0.242) 211s Multigrid levels: 5 211s Molecule ID: 1 211s Linearized traditional PBE 211s Multiple Debye-Huckel sphere boundary conditions 211s 2 ion species (0.000 M ionic strength): 211s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 211s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 211s Solute dielectric: 2.000 211s Solvent dielectric: 78.000 211s Using "molecular" surface definition;harmonic average smoothing 211s Solvent probe radius: 0.000 A 211s Temperature: 300.000 K 211s Electrostatic energies will be calculated 211s Total electrostatic energy = 1.847860440020E+03 kJ/mol 211s Calculating forces... 211s ---------------------------------------- 211s CALCULATION #2 (methanol-ref): MULTIGRID 211s Setting up problem... 211s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 211s Debye length: 0 A 211s Current memory usage: 61.253 MB total, 61.328 MB high water 211s Using linear spline charge discretization. 211s Grid dimensions: 65 x 65 x 65 211s Grid spacings: 0.250 x 0.250 x 0.250 211s Grid lengths: 16.000 x 16.000 x 16.000 211s Grid center: (0.309, 0.000, -0.242) 211s Multigrid levels: 5 211s Molecule ID: 1 211s Linearized traditional PBE 211s Multiple Debye-Huckel sphere boundary conditions 211s 2 ion species (0.000 M ionic strength): 211s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 211s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 211s Solute dielectric: 2.000 211s Solvent dielectric: 1.000 211s Using "molecular" surface definition;harmonic average smoothing 211s Solvent probe radius: 0.000 A 211s Temperature: 300.000 K 211s Electrostatic energies will be calculated 211s Total electrostatic energy = 1.885436377745E+03 kJ/mol 211s Calculating forces... 211s ---------------------------------------- 211s CALCULATION #3 (methoxide-solv): MULTIGRID 211s Setting up problem... 211s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 211s Debye length: 0 A 211s Current memory usage: 61.250 MB total, 61.328 MB high water 211s Using linear spline charge discretization. 211s Grid dimensions: 65 x 65 x 65 211s Grid spacings: 0.250 x 0.250 x 0.250 211s Grid lengths: 16.000 x 16.000 x 16.000 211s Grid center: (0.000, 0.000, -0.128) 211s Multigrid levels: 5 211s Molecule ID: 2 211s Linearized traditional PBE 211s Multiple Debye-Huckel sphere boundary conditions 211s 2 ion species (0.000 M ionic strength): 211s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 211s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 211s Solute dielectric: 2.000 211s Solvent dielectric: 78.000 211s Using "molecular" surface definition;harmonic average smoothing 211s Solvent probe radius: 0.000 A 211s Temperature: 300.000 K 211s Electrostatic energies will be calculated 211s Total electrostatic energy = 2.734040568569E+03 kJ/mol 211s Calculating forces... 211s ---------------------------------------- 211s CALCULATION #4 (methoxide-ref): MULTIGRID 211s Setting up problem... 211s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 211s Debye length: 0 A 211s Current memory usage: 61.250 MB total, 61.328 MB high water 211s Using linear spline charge discretization. 211s Grid dimensions: 65 x 65 x 65 211s Grid spacings: 0.250 x 0.250 x 0.250 211s Grid lengths: 16.000 x 16.000 x 16.000 211s Grid center: (0.000, 0.000, -0.128) 211s Multigrid levels: 5 211s Molecule ID: 2 211s Linearized traditional PBE 211s Multiple Debye-Huckel sphere boundary conditions 211s 2 ion species (0.000 M ionic strength): 211s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 211s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 211s Solute dielectric: 2.000 211s Solvent dielectric: 1.000 211s Using "molecular" surface definition;harmonic average smoothing 211s Solvent probe radius: 0.000 A 211s Temperature: 300.000 K 211s Electrostatic energies will be calculated 211s Total electrostatic energy = 3.125279428954E+03 kJ/mol 211s Calculating forces... 211s ---------------------------------------- 211s PRINT STATEMENTS 211s 211s print energy 1 (methanol-solv) - 2 (methanol-ref) end 211s Local net energy (PE 0) = -3.757593772493E+01 kJ/mol 211s Global net ELEC energy = -3.757593772493E+01 kJ/mol 211s 211s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 211s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 211s Global net ELEC energy = -3.912388603848E+02 kJ/mol 211s 211s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 211s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 211s Global net ELEC energy = -3.536629226599E+02 kJ/mol 211s ---------------------------------------- 211s CLEANING UP AND SHUTTING DOWN... 211s Destroying force arrays. 211s No energy arrays to destroy. 211s Destroying multigrid structures. 211s Destroying finite element structures. 211s Destroying 2 molecules 211s Final memory usage: 0.001 MB total, 61.328 MB high water 211s 211s 211s Thanks for using APBS! 211s 211s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 211s *** PASSED *** 211s Checking for intermediate energies in input file apbs-smol.out 211s EXPECTED COMPUTED: 7 211s EXPECTED EXPECTED: 7 211s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] 211s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 211s COMPUTED RESULT 1847.86044002 211s COMPUTED RESULT 1885.436377745 211s COMPUTED RESULT 2734.040568569 211s COMPUTED RESULT 3125.279428954 211s COMPUTED RESULT -37.57593772493 211s COMPUTED RESULT -391.2388603848 211s COMPUTED RESULT -353.6629226599 211s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 211s *** PASSED *** 211s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 211s *** PASSED *** 211s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 211s *** PASSED *** 211s Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) 211s *** PASSED *** 211s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 211s *** PASSED *** 211s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 211s *** PASSED *** 211s Elapsed time: 0.486568 seconds 211s -------------------------------------------------------------------------------- 211s Total elapsed time: 0.93935 seconds 211s Test results have been logged 211s -------------------------------------------------------------------------------- 211s autopkgtest [06:47:51]: test test-apbs: -----------------------] 212s autopkgtest [06:47:52]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 212s test-apbs PASS 212s autopkgtest [06:47:52]: @@@@@@@@@@@@@@@@@@@@ summary 212s test-apbs PASS