0s autopkgtest [15:35:16]: starting date and time: 2025-10-18 15:35:16+0000 0s autopkgtest [15:35:16]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:35:16]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z_o_jci7/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-1.secgroup --name adt-resolute-ppc64el-apbs-20251018-153516-juju-7f2275-prod-proposed-migration-environment-15-1e14156f-b220-420c-9c06-f3b65ba24780 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-apbs-20251018-153516-juju-7f2275-prod-proposed-migration-environment-15-1e14156f-b220-420c-9c06-f3b65ba24780 from image adt/ubuntu-resolute-ppc64el-server-20251018.img (UUID 746a0a80-14f1-4bf7-89b6-cbb5ab236a4e)... 54s autopkgtest [15:36:10]: testbed dpkg architecture: ppc64el 54s autopkgtest [15:36:10]: testbed apt version: 3.1.8ubuntu1 55s autopkgtest [15:36:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 55s autopkgtest [15:36:11]: testbed release detected to be: None 55s autopkgtest [15:36:11]: updating testbed package index (apt update) 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 56s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 56s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 56s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [73.4 kB] 57s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 57s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [222 kB] 57s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [3808 B] 57s Fetched 777 kB in 1s (762 kB/s) 57s Reading package lists... 58s Failed to check for VM: Permission denied 58s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 58s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 59s Reading package lists... 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 60s Calculating upgrade... 60s The following packages will be upgraded: 60s gir1.2-girepository-2.0 libgirepository-1.0-1 libpython3-stdlib python3 60s python3-minimal 60s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 185 kB of archives. 60s After this operation, 2048 B of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.7-2 [27.8 kB] 60s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.7-2 [23.9 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.7-2 [10.6 kB] 60s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgirepository-1.0-1 ppc64el 1.86.0-6 [97.4 kB] 60s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el gir1.2-girepository-2.0 ppc64el 1.86.0-6 [25.3 kB] 60s dpkg-preconfigure: unable to re-open stdin: No such file or directory 60s Fetched 185 kB in 0s (428 kB/s) 61s (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 ... 76461 files and directories currently installed.) 61s Preparing to unpack .../python3-minimal_3.13.7-2_ppc64el.deb ... 61s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 61s Setting up python3-minimal (3.13.7-2) ... 61s (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 ... 76461 files and directories currently installed.) 61s Preparing to unpack .../python3_3.13.7-2_ppc64el.deb ... 61s running python pre-rtupdate hooks for python3.13... 61s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 61s Preparing to unpack .../libpython3-stdlib_3.13.7-2_ppc64el.deb ... 61s Unpacking libpython3-stdlib:ppc64el (3.13.7-2) over (3.13.7-1) ... 61s Preparing to unpack .../libgirepository-1.0-1_1.86.0-6_ppc64el.deb ... 61s Unpacking libgirepository-1.0-1:ppc64el (1.86.0-6) over (1.84.0-1) ... 61s Preparing to unpack .../gir1.2-girepository-2.0_1.86.0-6_ppc64el.deb ... 61s Unpacking gir1.2-girepository-2.0:ppc64el (1.86.0-6) over (1.84.0-1) ... 61s Setting up libgirepository-1.0-1:ppc64el (1.86.0-6) ... 61s Setting up libpython3-stdlib:ppc64el (3.13.7-2) ... 61s Setting up python3 (3.13.7-2) ... 61s running python rtupdate hooks for python3.13... 61s running python post-rtupdate hooks for python3.13... 61s Setting up gir1.2-girepository-2.0:ppc64el (1.86.0-6) ... 61s Processing triggers for man-db (2.13.1-1) ... 62s Processing triggers for libc-bin (2.42-0ubuntu3) ... 62s autopkgtest [15:36:18]: upgrading testbed (apt dist-upgrade and autopurge) 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Solving dependencies... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s autopkgtest [15:36:22]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 66s autopkgtest [15:36:22]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 75s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 75s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 75s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 75s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 75s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 75s gpgv: Can't check signature: No public key 75s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 78s autopkgtest [15:36:34]: testing package apbs version 3.4.1-6build2 82s autopkgtest [15:36:38]: build not needed 89s autopkgtest [15:36:45]: test test-apbs: preparing testbed 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Solving dependencies... 90s The following NEW packages will be installed: 90s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax 90s libamd-comgr2 libamd3 libamdhip64-5 libapbs-dev libapbs3t64 libarpack2t64 90s libblas3 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdrm-amdgpu1 90s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfetk-dev 90s libfetk1.9t64 libgfortran5 libgomp1 libhsa-runtime64-1 libhsakmt1 90s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libjs-jquery libjs-mathjax 90s libjs-sphinxdoc libjs-underscore liblapack3 libllvm17t64 libmaloc-dev 90s libmaloc1 libopenmpi40 libpciaccess0 librdmacm1t64 libspqr4 90s libsuitesparseconfig7 libsuperlu7 libucx0 libumfpack6 libxnvctrl0 90s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 90s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 86.9 MB of archives. 90s After this operation, 373 MB of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-lato all 2.015-1 [2781 kB] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el apbs-data all 3.4.1-6build2 [1769 kB] 91s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libmaloc1 ppc64el 1.5-2 [103 kB] 91s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 91s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libsuperlu7 ppc64el 7.0.1+dfsg1-2 [237 kB] 91s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-5ubuntu1 [169 kB] 91s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsuitesparseconfig7 ppc64el 1:7.10.1+dfsg-1 [21.6 kB] 91s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libamd3 ppc64el 1:7.10.1+dfsg-1 [44.8 kB] 91s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcamd3 ppc64el 1:7.10.1+dfsg-1 [38.9 kB] 91s Get:10 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libccolamd3 ppc64el 1:7.10.1+dfsg-1 [39.6 kB] 91s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcolamd3 ppc64el 1:7.10.1+dfsg-1 [29.8 kB] 91s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-5ubuntu1 [620 kB] 91s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 91s Get:14 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcholmod5 ppc64el 1:7.10.1+dfsg-1 [913 kB] 91s Get:15 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libumfpack6 ppc64el 1:7.10.1+dfsg-1 [343 kB] 91s Get:16 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libfetk1.9t64 ppc64el 3.4.1-6build2 [660 kB] 91s Get:17 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libapbs3t64 ppc64el 3.4.1-6build2 [310 kB] 91s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 91s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 91s Get:20 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libarpack2t64 ppc64el 3.9.1-6 [107 kB] 91s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libevent-core-2.1-7t64 ppc64el 2.1.12-stable-10build1 [109 kB] 91s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libevent-pthreads-2.1-7t64 ppc64el 2.1.12-stable-10build1 [8140 B] 91s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el librdmacm1t64 ppc64el 56.1-1ubuntu1 [80.3 kB] 91s Get:24 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libfabric1 ppc64el 2.1.0-1.1 [786 kB] 91s Get:25 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhwloc15 ppc64el 2.12.2-1 [223 kB] 91s Get:26 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libllvm17t64 ppc64el 1:17.0.6-22build1 [27.0 MB] 92s Get:27 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3build3 [15.1 MB] 92s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdrm-amdgpu1 ppc64el 2.4.125-1 [25.5 kB] 92s Get:29 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhsakmt1 ppc64el 6.2.4+ds-1 [75.9 kB] 92s Get:30 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhsa-runtime64-1 ppc64el 6.1.2-3 [350 kB] 92s Get:31 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libamdhip64-5 ppc64el 5.7.1-6 [9342 kB] 92s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libibumad3 ppc64el 56.1-1ubuntu1 [33.8 kB] 92s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libibmad5 ppc64el 56.1-1ubuntu1 [47.1 kB] 92s Get:34 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libucx0 ppc64el 1.19.0+ds-1 [1361 kB] 92s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpciaccess0 ppc64el 0.18.1-1ubuntu2 [21.9 kB] 92s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu4 [12.6 kB] 92s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el ocl-icd-libopencl1 ppc64el 2.3.3-1 [47.9 kB] 92s Get:38 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhwloc-plugins ppc64el 2.12.2-1 [17.7 kB] 92s Get:39 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libopenmpi40 ppc64el 5.0.8-8ubuntu1 [3435 kB] 92s Get:40 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libspqr4 ppc64el 1:7.10.1+dfsg-1 [198 kB] 92s Get:41 http://ftpmaster.internal/ubuntu resolute/universe ppc64el apbs ppc64el 3.4.1-6build2 [80.3 kB] 92s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 92s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 92s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 92s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 92s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 92s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el apbs-doc all 3.4.1-6build2 [5850 kB] 92s Get:48 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libapbs-dev ppc64el 3.4.1-6build2 [99.5 kB] 92s Get:49 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libmaloc-dev ppc64el 1.5-2 [918 kB] 93s Get:50 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libfetk-dev ppc64el 3.4.1-6build2 [144 kB] 93s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-apbslib ppc64el 3.4.1-6build2 [218 kB] 93s Fetched 86.9 MB in 3s (29.2 MB/s) 93s Selecting previously unselected package fonts-lato. 93s (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 ... 76461 files and directories currently installed.) 93s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 93s Unpacking fonts-lato (2.015-1) ... 93s Selecting previously unselected package apbs-data. 93s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 93s Unpacking apbs-data (3.4.1-6build2) ... 93s Selecting previously unselected package libmaloc1:ppc64el. 93s Preparing to unpack .../02-libmaloc1_1.5-2_ppc64el.deb ... 93s Unpacking libmaloc1:ppc64el (1.5-2) ... 93s Selecting previously unselected package libblas3:ppc64el. 93s Preparing to unpack .../03-libblas3_3.12.1-6build1_ppc64el.deb ... 93s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 93s Selecting previously unselected package libsuperlu7:ppc64el. 93s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_ppc64el.deb ... 93s Unpacking libsuperlu7:ppc64el (7.0.1+dfsg1-2) ... 93s Selecting previously unselected package libgomp1:ppc64el. 93s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_ppc64el.deb ... 93s Unpacking libgomp1:ppc64el (15.2.0-5ubuntu1) ... 93s Selecting previously unselected package libsuitesparseconfig7:ppc64el. 93s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_ppc64el.deb ... 93s Unpacking libsuitesparseconfig7:ppc64el (1:7.10.1+dfsg-1) ... 93s Selecting previously unselected package libamd3:ppc64el. 93s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 93s Unpacking libamd3:ppc64el (1:7.10.1+dfsg-1) ... 93s Selecting previously unselected package libcamd3:ppc64el. 93s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 93s Unpacking libcamd3:ppc64el (1:7.10.1+dfsg-1) ... 93s Selecting previously unselected package libccolamd3:ppc64el. 93s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 93s Unpacking libccolamd3:ppc64el (1:7.10.1+dfsg-1) ... 93s Selecting previously unselected package libcolamd3:ppc64el. 93s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 93s Unpacking libcolamd3:ppc64el (1:7.10.1+dfsg-1) ... 93s Selecting previously unselected package libgfortran5:ppc64el. 93s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_ppc64el.deb ... 93s Unpacking libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 93s Selecting previously unselected package liblapack3:ppc64el. 93s Preparing to unpack .../12-liblapack3_3.12.1-6build1_ppc64el.deb ... 93s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 93s Selecting previously unselected package libcholmod5:ppc64el. 93s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_ppc64el.deb ... 93s Unpacking libcholmod5:ppc64el (1:7.10.1+dfsg-1) ... 93s Selecting previously unselected package libumfpack6:ppc64el. 93s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_ppc64el.deb ... 93s Unpacking libumfpack6:ppc64el (1:7.10.1+dfsg-1) ... 93s Selecting previously unselected package libfetk1.9t64:ppc64el. 93s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_ppc64el.deb ... 93s Unpacking libfetk1.9t64:ppc64el (3.4.1-6build2) ... 93s Selecting previously unselected package libapbs3t64:ppc64el. 93s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_ppc64el.deb ... 93s Unpacking libapbs3t64:ppc64el (3.4.1-6build2) ... 94s Selecting previously unselected package fonts-mathjax. 94s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 94s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 94s Selecting previously unselected package libjs-mathjax. 94s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 94s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 94s Selecting previously unselected package libarpack2t64:ppc64el. 94s Preparing to unpack .../19-libarpack2t64_3.9.1-6_ppc64el.deb ... 94s Unpacking libarpack2t64:ppc64el (3.9.1-6) ... 94s Selecting previously unselected package libevent-core-2.1-7t64:ppc64el. 94s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_ppc64el.deb ... 94s Unpacking libevent-core-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 94s Selecting previously unselected package libevent-pthreads-2.1-7t64:ppc64el. 94s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_ppc64el.deb ... 94s Unpacking libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 94s Selecting previously unselected package librdmacm1t64:ppc64el. 94s Preparing to unpack .../22-librdmacm1t64_56.1-1ubuntu1_ppc64el.deb ... 94s Unpacking librdmacm1t64:ppc64el (56.1-1ubuntu1) ... 94s Selecting previously unselected package libfabric1:ppc64el. 94s Preparing to unpack .../23-libfabric1_2.1.0-1.1_ppc64el.deb ... 94s Unpacking libfabric1:ppc64el (2.1.0-1.1) ... 94s Selecting previously unselected package libhwloc15:ppc64el. 94s Preparing to unpack .../24-libhwloc15_2.12.2-1_ppc64el.deb ... 94s Unpacking libhwloc15:ppc64el (2.12.2-1) ... 94s Selecting previously unselected package libllvm17t64:ppc64el. 94s Preparing to unpack .../25-libllvm17t64_1%3a17.0.6-22build1_ppc64el.deb ... 94s Unpacking libllvm17t64:ppc64el (1:17.0.6-22build1) ... 95s Selecting previously unselected package libamd-comgr2:ppc64el. 95s Preparing to unpack .../26-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build3_ppc64el.deb ... 95s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build3) ... 95s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 95s Preparing to unpack .../27-libdrm-amdgpu1_2.4.125-1_ppc64el.deb ... 95s 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.../48-libmaloc-dev_1.5-2_ppc64el.deb ... 96s Unpacking libmaloc-dev (1.5-2) ... 96s Selecting previously unselected package libfetk-dev:ppc64el. 96s Preparing to unpack .../49-libfetk-dev_3.4.1-6build2_ppc64el.deb ... 96s Unpacking libfetk-dev:ppc64el (3.4.1-6build2) ... 96s Selecting previously unselected package python3-apbslib. 96s Preparing to unpack .../50-python3-apbslib_3.4.1-6build2_ppc64el.deb ... 96s Unpacking python3-apbslib (3.4.1-6build2) ... 96s Setting up libmaloc1:ppc64el (1.5-2) ... 96s Setting up libpciaccess0:ppc64el (0.18.1-1ubuntu2) ... 96s Setting up fonts-lato (2.015-1) ... 96s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 96s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 96s Setting up libibumad3:ppc64el (56.1-1ubuntu1) ... 96s Setting up libibmad5:ppc64el (56.1-1ubuntu1) ... 96s Setting up apbs-data (3.4.1-6build2) ... 96s Setting up libgomp1:ppc64el (15.2.0-5ubuntu1) ... 96s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ... 96s Setting up libblas3:ppc64el (3.12.1-6build1) ... 96s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 96s Setting up libllvm17t64:ppc64el (1:17.0.6-22build1) ... 96s Setting up libhwloc15:ppc64el (2.12.2-1) ... 96s Setting up libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 96s Setting up ocl-icd-libopencl1:ppc64el (2.3.3-1) ... 96s Setting up libsuitesparseconfig7:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up librdmacm1t64:ppc64el (56.1-1ubuntu1) ... 96s Setting up libevent-core-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 96s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build3) ... 96s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 96s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 96s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 96s Setting up libmaloc-dev (1.5-2) ... 96s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 96s Setting up libdrm-amdgpu1:ppc64el (2.4.125-1) ... 96s Setting up libfabric1:ppc64el (2.1.0-1.1) ... 96s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 96s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 96s Setting up libarpack2t64:ppc64el (3.9.1-6) ... 96s Setting up libamd3:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up libcolamd3:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 96s Setting up libhwloc-plugins:ppc64el (2.12.2-1) ... 96s Setting up libcamd3:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up libsuperlu7:ppc64el (7.0.1+dfsg1-2) ... 96s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 96s Setting up libccolamd3:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up libhsakmt1:ppc64el (6.2.4+ds-1) ... 96s Setting up libcholmod5:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up libspqr4:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up apbs-doc (3.4.1-6build2) ... 96s Setting up libumfpack6:ppc64el (1:7.10.1+dfsg-1) ... 96s Setting up libhsa-runtime64-1:ppc64el (6.1.2-3) ... 96s Setting up libfetk1.9t64:ppc64el (3.4.1-6build2) ... 96s Setting up libapbs3t64:ppc64el (3.4.1-6build2) ... 96s Setting up libfetk-dev:ppc64el (3.4.1-6build2) ... 96s Setting up libamdhip64-5:ppc64el (5.7.1-6) ... 96s Setting up libapbs-dev:ppc64el (3.4.1-6build2) ... 96s Setting up python3-apbslib (3.4.1-6build2) ... 96s Setting up libucx0:ppc64el (1.19.0+ds-1) ... 96s Setting up libopenmpi40:ppc64el (5.0.8-8ubuntu1) ... 96s Setting up apbs (3.4.1-6build2) ... 96s Processing triggers for man-db (2.13.1-1) ... 97s Processing triggers for libc-bin (2.42-0ubuntu3) ... 99s autopkgtest [15:36:55]: test test-apbs: [----------------------- 99s TESTING WITH BINARY_NAME:apbs 99s START_DIR:/tmp/autopkgtest.LMAmNF/autopkgtest_tmp/build 99s -------------------------------------------------------------------------------- 99s Testing forces from apbs-forces.in 99s 99s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001159 seconds 99s -------------------------------------------------------------------------------- 99s -------------------------------------------------------------------------------- 99s Testing input file apbs-mol-auto.in 99s 101s CHECKING:/usr/local/sbin/apbs 101s CHECKING:/usr/local/bin/apbs 101s CHECKING:/usr/sbin/apbs 101s CHECKING:/usr/bin/apbs 101s NOTE: Using apbs binary:/usr/bin/apbs 101s Testing all sections 101s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 101s ================================================================================ 101s Running tests for born section 101s BINARY: /usr/bin/apbs 101s INPUT: apbs-mol-auto.in 101s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 101s asc_getToken: Error occurred (bailing out). 101s Vio_scanf: Format problem with input. 101s 101s 101s ---------------------------------------------------------------------- 101s APBS -- Adaptive Poisson-Boltzmann Solver 101s Version APBS 3.4.1 101s 101s Nathan A. Baker (nathan.baker@pnnl.gov) 101s Pacific Northwest National Laboratory 101s 101s Additional contributing authors listed in the code documentation. 101s 101s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 101s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 101s Northwest Division for the U.S. Department of Energy. 101s 101s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 101s Portions Copyright (c) 2002-2020, Nathan A. Baker. 101s Portions Copyright (c) 1999-2002, The Regents of the University of California. 101s Portions Copyright (c) 1995, Michael Holst. 101s All rights reserved. 101s 101s Redistribution and use in source and binary forms, with or without 101s modification, are permitted provided that the following conditions are met: 101s 101s * Redistributions of source code must retain the above copyright notice, this 101s list of conditions and the following disclaimer. 101s 101s * Redistributions in binary form must reproduce the above copyright notice, 101s this list of conditions and the following disclaimer in the documentation 101s and/or other materials provided with the distribution. 101s 101s * Neither the name of the developer nor the names of its contributors may be 101s used to endorse or promote products derived from this software without 101s specific prior written permission. 101s 101s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 101s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 101s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 101s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 101s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 101s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 101s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 101s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 101s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 101s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 101s ---------------------------------------------------------------------- 101s APBS uses FETK (the Finite Element ToolKit) to solve the 101s Poisson-Boltzmann equation numerically. FETK is a portable collection 101s of finite element modeling class libraries developed by the Michael Holst 101s research group and written in an object-oriented form of C. FEtk is 101s designed to solve general coupled systems of nonlinear partial differential 101s equations using adaptive finite element methods, inexact Newton methods, 101s and algebraic multilevel methods. More information about FEtk may be found 101s at . 101s ---------------------------------------------------------------------- 101s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 101s Aqua is a modified form of the Holst group PMG library 101s which has been modified by Patrice Koehl 101s for improved efficiency and 101s memory usage when solving the Poisson-Boltzmann equation. 101s ---------------------------------------------------------------------- 101s Please cite your use of APBS as: 101s 101s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 101s nanosystems: application to microtubules and the ribosome. Proc. 101s Natl. Acad. Sci. USA 98, 10037-10041 2001. 101s 101s 101s This executable compiled on Jan 3 2025 at 11:01:42 101s 101s Parsing input file apbs-mol-auto.in... 101s rank 0 size 1... 101s Parsed input file. 101s Got paths for 1 molecules 101s Reading PQR-format atom data from ion.pqr. 101s 1 atoms 101s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 101s Net charge 1.00e+00 e 101s Preparing to run 6 PBE calculations. 101s ---------------------------------------- 101s CALCULATION #1 (solvated): MULTIGRID 101s Setting up problem... 101s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 101s Debye length: 0 A 101s Current memory usage: 61.280 MB total, 61.280 MB high water 101s Using cubic spline charge discretization. 101s Grid dimensions: 65 x 65 x 65 101s Grid spacings: 0.781 x 0.781 x 0.781 101s Grid lengths: 50.000 x 50.000 x 50.000 101s Grid center: (0.000, 0.000, 0.000) 101s Multigrid levels: 5 101s Molecule ID: 1 101s Linearized traditional PBE 101s Multiple Debye-Huckel sphere boundary conditions 101s 0 ion species (0.000 M ionic strength): 101s Solute dielectric: 1.000 101s Solvent dielectric: 78.540 101s Using "molecular" surface definition; no smoothing 101s Solvent probe radius: 1.400 A 101s Temperature: 298.150 K 101s Electrostatic energies will be calculated 101s Total electrostatic energy = 9.607073836227E+02 kJ/mol 101s Calculating forces... 101s ---------------------------------------- 101s CALCULATION #2 (solvated): MULTIGRID 101s Setting up problem... 101s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 101s Debye length: 0 A 101s Current memory usage: 61.280 MB total, 122.102 MB high water 101s Using cubic spline charge discretization. 101s Grid dimensions: 65 x 65 x 65 101s Grid spacings: 0.383 x 0.383 x 0.383 101s Grid lengths: 24.495 x 24.495 x 24.495 101s Grid center: (0.000, 0.000, 0.000) 101s Multigrid levels: 5 101s Molecule ID: 1 101s Linearized traditional PBE 101s Boundary conditions from focusing 101s 0 ion species (0.000 M ionic strength): 101s Solute dielectric: 1.000 101s Solvent dielectric: 78.540 101s Using "molecular" surface definition; no smoothing 101s Solvent probe radius: 1.400 A 101s Temperature: 298.150 K 101s Electrostatic energies will be calculated 101s Total electrostatic energy = 2.200266567971E+03 kJ/mol 101s Calculating forces... 101s ---------------------------------------- 101s CALCULATION #3 (solvated): MULTIGRID 101s Setting up problem... 101s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 101s Debye length: 0 A 101s Current memory usage: 61.280 MB total, 122.102 MB high water 101s Using cubic spline charge discretization. 101s Grid dimensions: 65 x 65 x 65 101s Grid spacings: 0.188 x 0.188 x 0.188 101s Grid lengths: 12.000 x 12.000 x 12.000 101s Grid center: (0.000, 0.000, 0.000) 101s Multigrid levels: 5 101s Molecule ID: 1 101s Linearized traditional PBE 101s Boundary conditions from focusing 101s 0 ion species (0.000 M ionic strength): 101s Solute dielectric: 1.000 101s Solvent dielectric: 78.540 101s Using "molecular" surface definition; no smoothing 101s Solvent probe radius: 1.400 A 101s Temperature: 298.150 K 101s Electrostatic energies will be calculated 101s Potential to be written to potential.dx.gz 101s Total electrostatic energy = 4.732245131587E+03 kJ/mol 101s Calculating forces... 101s Writing potential to potential-PE0.dx.gz 101s ---------------------------------------- 101s CALCULATION #4 (reference): MULTIGRID 101s Setting up problem... 101s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 101s Debye length: 0 A 101s Current memory usage: 61.207 MB total, 122.102 MB high water 101s Using cubic spline charge discretization. 101s Grid dimensions: 65 x 65 x 65 101s Grid spacings: 0.781 x 0.781 x 0.781 101s Grid lengths: 50.000 x 50.000 x 50.000 101s Grid center: (0.000, 0.000, 0.000) 101s Multigrid levels: 5 101s Molecule ID: 1 101s Linearized traditional PBE 101s Multiple Debye-Huckel sphere boundary conditions 101s 0 ion species (0.000 M ionic strength): 101s Solute dielectric: 1.000 101s Solvent dielectric: 1.000 101s Using "molecular" surface definition; no smoothing 101s Solvent probe radius: 1.400 A 101s Temperature: 298.150 K 101s Electrostatic energies will be calculated 101s Total electrostatic energy = 1.190871482831E+03 kJ/mol 101s Calculating forces... 101s ---------------------------------------- 101s CALCULATION #5 (reference): MULTIGRID 101s Setting up problem... 101s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 101s Debye length: 0 A 101s Current memory usage: 61.207 MB total, 122.102 MB high water 101s Using cubic spline charge discretization. 101s Grid dimensions: 65 x 65 x 65 101s Grid spacings: 0.383 x 0.383 x 0.383 101s Grid lengths: 24.495 x 24.495 x 24.495 101s Grid center: (0.000, 0.000, 0.000) 101s Multigrid levels: 5 101s Molecule ID: 1 101s Linearized traditional PBE 101s Boundary conditions from focusing 101s 0 ion species (0.000 M ionic strength): 101s Solute dielectric: 1.000 101s Solvent dielectric: 1.000 101s Using "molecular" surface definition; no smoothing 101s Solvent probe radius: 1.400 A 101s Temperature: 298.150 K 101s Electrostatic energies will be calculated 101s Total electrostatic energy = 2.430874049735E+03 kJ/mol 101s Calculating forces... 101s [focusFillBound()]: WARNING: 101s Unusually large potential values 101s detected on the focusing boundary! 101s Convergence not guaranteed for NPBE/NRPBE calculations! 101s 101s ---------------------------------------- 101s CALCULATION #6 (reference): MULTIGRID 101s Setting up problem... 101s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 101s Debye length: 0 A 101s Current memory usage: 61.207 MB total, 122.102 MB high water 101s Using cubic spline charge discretization. 101s Grid dimensions: 65 x 65 x 65 101s Grid spacings: 0.188 x 0.188 x 0.188 101s Grid lengths: 12.000 x 12.000 x 12.000 101s Grid center: (0.000, 0.000, 0.000) 101s Multigrid levels: 5 101s Molecule ID: 1 101s Linearized traditional PBE 101s Boundary conditions from focusing 101s 0 ion species (0.000 M ionic strength): 101s Solute dielectric: 1.000 101s Solvent dielectric: 1.000 101s Using "molecular" surface definition; no smoothing 101s Solvent probe radius: 1.400 A 101s Temperature: 298.150 K 101s Electrostatic energies will be calculated 101s Total electrostatic energy = 4.962018684215E+03 kJ/mol 101s Calculating forces... 101s ---------------------------------------- 101s PRINT STATEMENTS 101s 101s print energy 1 (solvated) - 2 (reference) end 101s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 101s Global net ELEC energy = -2.297735526282E+02 kJ/mol 101s ---------------------------------------- 101s CLEANING UP AND SHUTTING DOWN... 101s Destroying force arrays. 101s No energy arrays to destroy. 101s Destroying multigrid structures. 101s Destroying finite element structures. 101s Destroying 1 molecules 101s Final memory usage: 0.001 MB total, 122.102 MB high water 101s 101s 101s Thanks for using APBS! 101s 101s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 101s *** PASSED *** 101s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 101s *** PASSED *** 101s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 101s *** PASSED *** 101s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 101s *** PASSED *** 101s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 101s *** PASSED *** 101s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 101s *** PASSED *** 101s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 101s *** PASSED *** 101s Elapsed time: 1.447571 seconds 101s -------------------------------------------------------------------------------- 101s -------------------------------------------------------------------------------- 101s Testing input file apbs-smol-auto.in 101s 102s Checking for intermediate energies in input file apbs-mol-auto.out 102s EXPECTED COMPUTED: 7 102s EXPECTED EXPECTED: 7 102s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 102s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 102s COMPUTED RESULT 960.7073836227 102s COMPUTED RESULT 2200.266567971 102s COMPUTED RESULT 4732.245131587 102s COMPUTED RESULT 1190.871482831 102s COMPUTED RESULT 2430.874049735 102s COMPUTED RESULT 4962.018684215 102s COMPUTED RESULT -229.7735526282 102s BINARY: /usr/bin/apbs 102s INPUT: apbs-smol-auto.in 102s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 102s asc_getToken: Error occurred (bailing out). 102s Vio_scanf: Format problem with input. 102s 102s 102s ---------------------------------------------------------------------- 102s APBS -- Adaptive Poisson-Boltzmann Solver 102s Version APBS 3.4.1 102s 102s Nathan A. Baker (nathan.baker@pnnl.gov) 102s Pacific Northwest National Laboratory 102s 102s Additional contributing authors listed in the code documentation. 102s 102s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 102s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 102s Northwest Division for the U.S. Department of Energy. 102s 102s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 102s Portions Copyright (c) 2002-2020, Nathan A. Baker. 102s Portions Copyright (c) 1999-2002, The Regents of the University of California. 102s Portions Copyright (c) 1995, Michael Holst. 102s All rights reserved. 102s 102s Redistribution and use in source and binary forms, with or without 102s modification, are permitted provided that the following conditions are met: 102s 102s * Redistributions of source code must retain the above copyright notice, this 102s list of conditions and the following disclaimer. 102s 102s * Redistributions in binary form must reproduce the above copyright notice, 102s this list of conditions and the following disclaimer in the documentation 102s and/or other materials provided with the distribution. 102s 102s * Neither the name of the developer nor the names of its contributors may be 102s used to endorse or promote products derived from this software without 102s specific prior written permission. 102s 102s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 102s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 102s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 102s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 102s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 102s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 102s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 102s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 102s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 102s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 102s ---------------------------------------------------------------------- 102s APBS uses FETK (the Finite Element ToolKit) to solve the 102s Poisson-Boltzmann equation numerically. FETK is a portable collection 102s of finite element modeling class libraries developed by the Michael Holst 102s research group and written in an object-oriented form of C. FEtk is 102s designed to solve general coupled systems of nonlinear partial differential 102s equations using adaptive finite element methods, inexact Newton methods, 102s and algebraic multilevel methods. More information about FEtk may be found 102s at . 102s ---------------------------------------------------------------------- 102s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 102s Aqua is a modified form of the Holst group PMG library 102s which has been modified by Patrice Koehl 102s for improved efficiency and 102s memory usage when solving the Poisson-Boltzmann equation. 102s ---------------------------------------------------------------------- 102s Please cite your use of APBS as: 102s 102s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 102s nanosystems: application to microtubules and the ribosome. Proc. 102s Natl. Acad. Sci. USA 98, 10037-10041 2001. 102s 102s 102s This executable compiled on Jan 3 2025 at 11:01:42 102s 102s Parsing input file apbs-smol-auto.in... 102s rank 0 size 1... 102s Parsed input file. 102s Got paths for 1 molecules 102s Reading PQR-format atom data from ion.pqr. 102s 1 atoms 102s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 102s Net charge 1.00e+00 e 102s Preparing to run 6 PBE calculations. 102s ---------------------------------------- 102s CALCULATION #1 (solvated): MULTIGRID 102s Setting up problem... 102s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 102s Debye length: 0 A 102s Current memory usage: 61.280 MB total, 61.280 MB high water 102s Using cubic spline charge discretization. 102s Grid dimensions: 65 x 65 x 65 102s Grid spacings: 0.781 x 0.781 x 0.781 102s Grid lengths: 50.000 x 50.000 x 50.000 102s Grid center: (0.000, 0.000, 0.000) 102s Multigrid levels: 5 102s Molecule ID: 1 102s Linearized traditional PBE 102s Multiple Debye-Huckel sphere boundary conditions 102s 0 ion species (0.000 M ionic strength): 102s Solute dielectric: 1.000 102s Solvent dielectric: 78.540 102s Using "molecular" surface definition;harmonic average smoothing 102s Solvent probe radius: 1.400 A 102s Temperature: 298.150 K 102s Electrostatic energies will be calculated 102s Total electrostatic energy = 9.532928767450E+02 kJ/mol 102s Calculating forces... 102s ---------------------------------------- 102s CALCULATION #2 (solvated): MULTIGRID 102s Setting up problem... 102s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 102s Debye length: 0 A 102s Current memory usage: 61.280 MB total, 122.102 MB high water 102s Using cubic spline charge discretization. 102s Grid dimensions: 65 x 65 x 65 102s Grid spacings: 0.383 x 0.383 x 0.383 102s Grid lengths: 24.495 x 24.495 x 24.495 102s Grid center: (0.000, 0.000, 0.000) 102s Multigrid levels: 5 102s Molecule ID: 1 102s Linearized traditional PBE 102s Boundary conditions from focusing 102s 0 ion species (0.000 M ionic strength): 102s Solute dielectric: 1.000 102s Solvent dielectric: 78.540 102s Using "molecular" surface definition;harmonic average smoothing 102s Solvent probe radius: 1.400 A 102s Temperature: 298.150 K 102s Electrostatic energies will be calculated 102s Total electrostatic energy = 2.201243880085E+03 kJ/mol 102s Calculating forces... 102s ---------------------------------------- 102s CALCULATION #3 (solvated): MULTIGRID 102s Setting up problem... 102s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 102s Debye length: 0 A 102s Current memory usage: 61.280 MB total, 122.102 MB high water 102s Using cubic spline charge discretization. 102s Grid dimensions: 65 x 65 x 65 102s Grid spacings: 0.188 x 0.188 x 0.188 102s Grid lengths: 12.000 x 12.000 x 12.000 102s Grid center: (0.000, 0.000, 0.000) 102s Multigrid levels: 5 102s Molecule ID: 1 102s Linearized traditional PBE 102s Boundary conditions from focusing 102s 0 ion species (0.000 M ionic strength): 102s Solute dielectric: 1.000 102s Solvent dielectric: 78.540 102s Using "molecular" surface definition;harmonic average smoothing 102s Solvent probe radius: 1.400 A 102s Temperature: 298.150 K 102s Electrostatic energies will be calculated 102s Total electrostatic energy = 4.733006258977E+03 kJ/mol 102s Calculating forces... 102s ---------------------------------------- 102s CALCULATION #4 (reference): MULTIGRID 102s Setting up problem... 102s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 102s Debye length: 0 A 102s Current memory usage: 61.207 MB total, 122.102 MB high water 102s Using cubic spline charge discretization. 102s Grid dimensions: 65 x 65 x 65 102s Grid spacings: 0.781 x 0.781 x 0.781 102s Grid lengths: 50.000 x 50.000 x 50.000 102s Grid center: (0.000, 0.000, 0.000) 102s Multigrid levels: 5 102s Molecule ID: 1 102s Linearized traditional PBE 102s Multiple Debye-Huckel sphere boundary conditions 102s 0 ion species (0.000 M ionic strength): 102s Solute dielectric: 1.000 102s Solvent dielectric: 1.000 102s Using "molecular" surface definition;harmonic average smoothing 102s Solvent probe radius: 1.400 A 102s Temperature: 298.150 K 102s Electrostatic energies will be calculated 102s Total electrostatic energy = 1.190871482831E+03 kJ/mol 102s Calculating forces... 102s ---------------------------------------- 102s CALCULATION #5 (reference): MULTIGRID 102s Setting up problem... 102s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 102s Debye length: 0 A 102s Current memory usage: 61.207 MB total, 122.102 MB high water 102s Using cubic spline charge discretization. 102s Grid dimensions: 65 x 65 x 65 102s Grid spacings: 0.383 x 0.383 x 0.383 102s Grid lengths: 24.495 x 24.495 x 24.495 102s Grid center: (0.000, 0.000, 0.000) 102s Multigrid levels: 5 102s Molecule ID: 1 102s Linearized traditional PBE 102s Boundary conditions from focusing 102s 0 ion species (0.000 M ionic strength): 102s Solute dielectric: 1.000 102s Solvent dielectric: 1.000 102s Using "molecular" surface definition;harmonic average smoothing 102s Solvent probe radius: 1.400 A 102s Temperature: 298.150 K 102s Electrostatic energies will be calculated 102s Total electrostatic energy = 2.430874049735E+03 kJ/mol 102s Calculating forces... 102s [focusFillBound()]: WARNING: 102s Unusually large potential values 102s detected on the focusing boundary! 102s Convergence not guaranteed for NPBE/NRPBE calculations! 102s 102s ---------------------------------------- 102s CALCULATION #6 (reference): MULTIGRID 102s Setting up problem... 102s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 102s Debye length: 0 A 102s Current memory usage: 61.207 MB total, 122.102 MB high water 102s Using cubic spline charge discretization. 102s Grid dimensions: 65 x 65 x 65 102s Grid spacings: 0.188 x 0.188 x 0.188 102s Grid lengths: 12.000 x 12.000 x 12.000 102s Grid center: (0.000, 0.000, 0.000) 102s Multigrid levels: 5 102s Molecule ID: 1 102s Linearized traditional PBE 102s Boundary conditions from focusing 102s 0 ion species (0.000 M ionic strength): 102s Solute dielectric: 1.000 102s Solvent dielectric: 1.000 102s Using "molecular" surface definition;harmonic average smoothing 102s Solvent probe radius: 1.400 A 102s Temperature: 298.150 K 102s Electrostatic energies will be calculated 102s Total electrostatic energy = 4.962018684215E+03 kJ/mol 102s Calculating forces... 102s ---------------------------------------- 102s PRINT STATEMENTS 102s 102s print energy 1 (solvated) - 2 (reference) end 102s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 102s Global net ELEC energy = -2.290124252387E+02 kJ/mol 102s ---------------------------------------- 102s CLEANING UP AND SHUTTING DOWN... 102s Destroying force arrays. 102s No energy arrays to destroy. 102s Destroying multigrid structures. 102s Destroying finite element structures. 102s Destroying 1 molecules 102s Final memory usage: 0.001 MB total, 122.102 MB high water 102s 102s 102s Thanks for using APBS! 102s 102s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 102s *** PASSED *** 102s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 102s *** PASSED *** 102s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 102s *** PASSED *** 102s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 102s *** PASSED *** 102s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 102s *** PASSED *** 102s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 102s *** PASSED *** 102s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 102s *** PASSED *** 102s Elapsed time: 1.25819 seconds 102s -------------------------------------------------------------------------------- 102s -------------------------------------------------------------------------------- 102s Testing input file apbs-mol-parallel.in 102s 102s Splitting the input file into 4 separate files using the inputgen utility 102s 104s Checking for intermediate energies in input file apbs-smol-auto.out 104s EXPECTED COMPUTED: 7 104s EXPECTED EXPECTED: 7 104s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 104s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 104s COMPUTED RESULT 953.292876745 104s COMPUTED RESULT 2201.243880085 104s COMPUTED RESULT 4733.006258977 104s COMPUTED RESULT 1190.871482831 104s COMPUTED RESULT 2430.874049735 104s COMPUTED RESULT 4962.018684215 104s COMPUTED RESULT -229.0124252387 104s BINARY: /usr/bin/apbs 104s INPUT: apbs-mol-parallel-PE0.in 104s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 104s asc_getToken: Error occurred (bailing out). 104s Vio_scanf: Format problem with input. 104s 104s 104s ---------------------------------------------------------------------- 104s APBS -- Adaptive Poisson-Boltzmann Solver 104s Version APBS 3.4.1 104s 104s Nathan A. Baker (nathan.baker@pnnl.gov) 104s Pacific Northwest National Laboratory 104s 104s Additional contributing authors listed in the code documentation. 104s 104s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 104s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 104s Northwest Division for the U.S. Department of Energy. 104s 104s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 104s Portions Copyright (c) 2002-2020, Nathan A. Baker. 104s Portions Copyright (c) 1999-2002, The Regents of the University of California. 104s Portions Copyright (c) 1995, Michael Holst. 104s All rights reserved. 104s 104s Redistribution and use in source and binary forms, with or without 104s modification, are permitted provided that the following conditions are met: 104s 104s * Redistributions of source code must retain the above copyright notice, this 104s list of conditions and the following disclaimer. 104s 104s * Redistributions in binary form must reproduce the above copyright notice, 104s this list of conditions and the following disclaimer in the documentation 104s and/or other materials provided with the distribution. 104s 104s * Neither the name of the developer nor the names of its contributors may be 104s used to endorse or promote products derived from this software without 104s specific prior written permission. 104s 104s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 104s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 104s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 104s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 104s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 104s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 104s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 104s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 104s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 104s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 104s ---------------------------------------------------------------------- 104s APBS uses FETK (the Finite Element ToolKit) to solve the 104s Poisson-Boltzmann equation numerically. FETK is a portable collection 104s of finite element modeling class libraries developed by the Michael Holst 104s research group and written in an object-oriented form of C. FEtk is 104s designed to solve general coupled systems of nonlinear partial differential 104s equations using adaptive finite element methods, inexact Newton methods, 104s and algebraic multilevel methods. More information about FEtk may be found 104s at . 104s ---------------------------------------------------------------------- 104s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 104s Aqua is a modified form of the Holst group PMG library 104s which has been modified by Patrice Koehl 104s for improved efficiency and 104s memory usage when solving the Poisson-Boltzmann equation. 104s ---------------------------------------------------------------------- 104s Please cite your use of APBS as: 104s 104s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 104s nanosystems: application to microtubules and the ribosome. Proc. 104s Natl. Acad. Sci. USA 98, 10037-10041 2001. 104s 104s 104s This executable compiled on Jan 3 2025 at 11:01:42 104s 104s Parsing input file apbs-mol-parallel-PE0.in... 104s rank 0 size 1... 104s Parsed input file. 104s Got paths for 1 molecules 104s Reading PQR-format atom data from ion.pqr. 104s 1 atoms 104s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 104s Net charge 1.00e+00 e 104s Preparing to run 6 PBE calculations. 104s ---------------------------------------- 104s CALCULATION #1 (solvated): MULTIGRID 104s Setting up problem... 104s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 104s Debye length: 0 A 104s Current memory usage: 61.280 MB total, 61.280 MB high water 104s Using cubic spline charge discretization. 104s Partition overlap fraction = 0.1 104s Processor array = 2 x 2 x 1 104s Grid dimensions: 65 x 65 x 65 104s Grid spacings: 0.781 x 0.781 x 0.781 104s Grid lengths: 50.000 x 50.000 x 50.000 104s Grid center: (0.000, 0.000, 0.000) 104s Multigrid levels: 5 104s Molecule ID: 1 104s Linearized traditional PBE 104s Multiple Debye-Huckel sphere boundary conditions 104s 0 ion species (0.000 M ionic strength): 104s Solute dielectric: 1.000 104s Solvent dielectric: 78.540 104s Using "molecular" surface definition; no smoothing 104s Solvent probe radius: 1.400 A 104s Temperature: 298.150 K 104s Electrostatic energies will be calculated 104s Total electrostatic energy = 2.401768459022E+02 kJ/mol 104s Calculating forces... 104s ---------------------------------------- 104s CALCULATION #2 (solvated): MULTIGRID 104s Setting up problem... 104s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 104s Debye length: 0 A 104s Current memory usage: 61.280 MB total, 122.102 MB high water 104s Using cubic spline charge discretization. 104s Partition overlap fraction = 0.1 104s Processor array = 2 x 2 x 1 104s Grid dimensions: 65 x 65 x 65 104s Grid spacings: 0.296 x 0.296 x 0.383 104s Grid lengths: 18.944 x 18.944 x 24.495 104s Grid center: (-2.411, -2.411, 0.000) 104s Multigrid levels: 5 104s Molecule ID: 1 104s Linearized traditional PBE 104s Boundary conditions from focusing 104s 0 ion species (0.000 M ionic strength): 104s Solute dielectric: 1.000 104s Solvent dielectric: 78.540 104s Using "molecular" surface definition; no smoothing 104s Solvent probe radius: 1.400 A 104s Temperature: 298.150 K 104s Electrostatic energies will be calculated 104s Total electrostatic energy = 8.142935592471E+02 kJ/mol 104s Calculating forces... 104s [focusFillBound()]: WARNING: 104s Unusually large potential values 104s detected on the focusing boundary! 104s Convergence not guaranteed for NPBE/NRPBE calculations! 104s 104s ---------------------------------------- 104s CALCULATION #3 (solvated): MULTIGRID 104s Setting up problem... 104s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 104s Debye length: 0 A 104s Current memory usage: 61.280 MB total, 122.102 MB high water 104s Using cubic spline charge discretization. 104s Partition overlap fraction = 0.1 104s Processor array = 2 x 2 x 1 104s Grid dimensions: 65 x 65 x 65 104s Grid spacings: 0.112 x 0.112 x 0.188 104s Grid lengths: 7.178 x 7.178 x 12.000 104s Grid center: (-2.411, -2.411, 0.000) 104s Multigrid levels: 5 104s Molecule ID: 1 104s Linearized traditional PBE 104s Boundary conditions from focusing 104s 0 ion species (0.000 M ionic strength): 104s Solute dielectric: 1.000 104s Solvent dielectric: 78.540 104s Using "molecular" surface definition; no smoothing 104s Solvent probe radius: 1.400 A 104s Temperature: 298.150 K 104s Electrostatic energies will be calculated 104s Total electrostatic energy = 1.485255308186E+03 kJ/mol 104s Calculating forces... 104s ---------------------------------------- 104s CALCULATION #4 (reference): MULTIGRID 104s Setting up problem... 104s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 104s Debye length: 0 A 104s Current memory usage: 61.207 MB total, 122.102 MB high water 104s Using cubic spline charge discretization. 104s Partition overlap fraction = 0.1 104s Processor array = 2 x 2 x 1 104s Grid dimensions: 65 x 65 x 65 104s Grid spacings: 0.781 x 0.781 x 0.781 104s Grid lengths: 50.000 x 50.000 x 50.000 104s Grid center: (0.000, 0.000, 0.000) 104s Multigrid levels: 5 104s Molecule ID: 1 104s Linearized traditional PBE 104s Multiple Debye-Huckel sphere boundary conditions 104s 0 ion species (0.000 M ionic strength): 104s Solute dielectric: 1.000 104s Solvent dielectric: 1.000 104s Using "molecular" surface definition; no smoothing 104s Solvent probe radius: 1.400 A 104s Temperature: 298.150 K 104s Electrostatic energies will be calculated 104s Total electrostatic energy = 2.977178707009E+02 kJ/mol 104s Calculating forces... 104s ---------------------------------------- 104s CALCULATION #5 (reference): MULTIGRID 104s Setting up problem... 104s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 104s Debye length: 0 A 104s Current memory usage: 61.207 MB total, 122.102 MB high water 104s Using cubic spline charge discretization. 104s Partition overlap fraction = 0.1 104s Processor array = 2 x 2 x 1 104s Grid dimensions: 65 x 65 x 65 104s Grid spacings: 0.296 x 0.296 x 0.383 104s Grid lengths: 18.944 x 18.944 x 24.495 104s Grid center: (-2.411, -2.411, 0.000) 104s Multigrid levels: 5 104s Molecule ID: 1 104s Linearized traditional PBE 104s Boundary conditions from focusing 104s 0 ion species (0.000 M ionic strength): 104s Solute dielectric: 1.000 104s Solvent dielectric: 1.000 104s Using "molecular" surface definition; no smoothing 104s Solvent probe radius: 1.400 A 104s Temperature: 298.150 K 104s Electrostatic energies will be calculated 104s Total electrostatic energy = 8.799304557588E+02 kJ/mol 104s Calculating forces... 104s [focusFillBound()]: WARNING: 104s Unusually large potential values 104s detected on the focusing boundary! 104s Convergence not guaranteed for NPBE/NRPBE calculations! 104s 104s ---------------------------------------- 104s CALCULATION #6 (reference): MULTIGRID 104s Setting up problem... 104s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 104s Debye length: 0 A 104s Current memory usage: 61.207 MB total, 122.102 MB high water 104s Using cubic spline charge discretization. 104s Partition overlap fraction = 0.1 104s Processor array = 2 x 2 x 1 104s Grid dimensions: 65 x 65 x 65 104s Grid spacings: 0.112 x 0.112 x 0.188 104s Grid lengths: 7.178 x 7.178 x 12.000 104s Grid center: (-2.411, -2.411, 0.000) 104s Multigrid levels: 5 104s Molecule ID: 1 104s Linearized traditional PBE 104s Boundary conditions from focusing 104s 0 ion species (0.000 M ionic strength): 104s Solute dielectric: 1.000 104s Solvent dielectric: 1.000 104s Using "molecular" surface definition; no smoothing 104s Solvent probe radius: 1.400 A 104s Temperature: 298.150 K 104s Electrostatic energies will be calculated 104s Total electrostatic energy = 1.542873949131E+03 kJ/mol 104s Calculating forces... 104s ---------------------------------------- 104s PRINT STATEMENTS 104s 104s print energy 1 (solvated) - 2 (reference) end 104s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 104s Global net ELEC energy = -5.761864094552E+01 kJ/mol 104s ---------------------------------------- 104s CLEANING UP AND SHUTTING DOWN... 104s Destroying force arrays. 104s No energy arrays to destroy. 104s Destroying multigrid structures. 104s Destroying finite element structures. 104s Destroying 1 molecules 104s Final memory usage: 0.001 MB total, 122.102 MB high water 104s 104s 104s Thanks for using APBS! 104s 104s Processor 0 results: 104s 2.401768459022e+02 104s 8.142935592471e+02 104s 1.485255308186e+03 104s 2.977178707009e+02 104s 8.799304557588e+02 104s 1.542873949131e+03 104s -5.761864094552e+01 104s 105s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 105s BINARY: /usr/bin/apbs 105s INPUT: apbs-mol-parallel-PE1.in 105s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 105s asc_getToken: Error occurred (bailing out). 105s Vio_scanf: Format problem with input. 105s 105s 105s ---------------------------------------------------------------------- 105s APBS -- Adaptive Poisson-Boltzmann Solver 105s Version APBS 3.4.1 105s 105s Nathan A. Baker (nathan.baker@pnnl.gov) 105s Pacific Northwest National Laboratory 105s 105s Additional contributing authors listed in the code documentation. 105s 105s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 105s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 105s Northwest Division for the U.S. Department of Energy. 105s 105s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 105s Portions Copyright (c) 2002-2020, Nathan A. Baker. 105s Portions Copyright (c) 1999-2002, The Regents of the University of California. 105s Portions Copyright (c) 1995, Michael Holst. 105s All rights reserved. 105s 105s Redistribution and use in source and binary forms, with or without 105s modification, are permitted provided that the following conditions are met: 105s 105s * Redistributions of source code must retain the above copyright notice, this 105s list of conditions and the following disclaimer. 105s 105s * Redistributions in binary form must reproduce the above copyright notice, 105s this list of conditions and the following disclaimer in the documentation 105s and/or other materials provided with the distribution. 105s 105s * Neither the name of the developer nor the names of its contributors may be 105s used to endorse or promote products derived from this software without 105s specific prior written permission. 105s 105s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 105s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 105s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 105s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 105s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 105s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 105s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 105s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 105s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 105s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 105s ---------------------------------------------------------------------- 105s APBS uses FETK (the Finite Element ToolKit) to solve the 105s Poisson-Boltzmann equation numerically. FETK is a portable collection 105s of finite element modeling class libraries developed by the Michael Holst 105s research group and written in an object-oriented form of C. FEtk is 105s designed to solve general coupled systems of nonlinear partial differential 105s equations using adaptive finite element methods, inexact Newton methods, 105s and algebraic multilevel methods. More information about FEtk may be found 105s at . 105s ---------------------------------------------------------------------- 105s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 105s Aqua is a modified form of the Holst group PMG library 105s which has been modified by Patrice Koehl 105s for improved efficiency and 105s memory usage when solving the Poisson-Boltzmann equation. 105s ---------------------------------------------------------------------- 105s Please cite your use of APBS as: 105s 105s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 105s nanosystems: application to microtubules and the ribosome. Proc. 105s Natl. Acad. Sci. USA 98, 10037-10041 2001. 105s 105s 105s This executable compiled on Jan 3 2025 at 11:01:42 105s 105s Parsing input file apbs-mol-parallel-PE1.in... 105s rank 0 size 1... 105s Parsed input file. 105s Got paths for 1 molecules 105s Reading PQR-format atom data from ion.pqr. 105s 1 atoms 105s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 105s Net charge 1.00e+00 e 105s Preparing to run 6 PBE calculations. 105s ---------------------------------------- 105s CALCULATION #1 (solvated): MULTIGRID 105s Setting up problem... 105s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 105s Debye length: 0 A 105s Current memory usage: 61.280 MB total, 61.280 MB high water 105s Using cubic spline charge discretization. 105s Partition overlap fraction = 0.1 105s Processor array = 2 x 2 x 1 105s Grid dimensions: 65 x 65 x 65 105s Grid spacings: 0.781 x 0.781 x 0.781 105s Grid lengths: 50.000 x 50.000 x 50.000 105s Grid center: (0.000, 0.000, 0.000) 105s Multigrid levels: 5 105s Molecule ID: 1 105s Linearized traditional PBE 105s Multiple Debye-Huckel sphere boundary conditions 105s 0 ion species (0.000 M ionic strength): 105s Solute dielectric: 1.000 105s Solvent dielectric: 78.540 105s Using "molecular" surface definition; no smoothing 105s Solvent probe radius: 1.400 A 105s Temperature: 298.150 K 105s Electrostatic energies will be calculated 105s Total electrostatic energy = 2.401768459022E+02 kJ/mol 105s Calculating forces... 105s ---------------------------------------- 105s CALCULATION #2 (solvated): MULTIGRID 105s Setting up problem... 105s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 105s Debye length: 0 A 105s Current memory usage: 61.280 MB total, 122.102 MB high water 105s Using cubic spline charge discretization. 105s Partition overlap fraction = 0.1 105s Processor array = 2 x 2 x 1 105s Grid dimensions: 65 x 65 x 65 105s Grid spacings: 0.296 x 0.296 x 0.383 105s Grid lengths: 18.944 x 18.944 x 24.495 105s Grid center: (2.411, -2.411, 0.000) 105s Multigrid levels: 5 105s Molecule ID: 1 105s Linearized traditional PBE 105s Boundary conditions from focusing 105s 0 ion species (0.000 M ionic strength): 105s Solute dielectric: 1.000 105s Solvent dielectric: 78.540 105s Using "molecular" surface definition; no smoothing 105s Solvent probe radius: 1.400 A 105s Temperature: 298.150 K 105s Electrostatic energies will be calculated 105s Total electrostatic energy = 8.142778312125E+02 kJ/mol 105s Calculating forces... 105s [focusFillBound()]: WARNING: 105s Unusually large potential values 105s detected on the focusing boundary! 105s Convergence not guaranteed for NPBE/NRPBE calculations! 105s 105s ---------------------------------------- 105s CALCULATION #3 (solvated): MULTIGRID 105s Setting up problem... 105s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 105s Debye length: 0 A 105s Current memory usage: 61.280 MB total, 122.102 MB high water 105s Using cubic spline charge discretization. 105s Partition overlap fraction = 0.1 105s Processor array = 2 x 2 x 1 105s Grid dimensions: 65 x 65 x 65 105s Grid spacings: 0.112 x 0.112 x 0.188 105s Grid lengths: 7.178 x 7.178 x 12.000 105s Grid center: (2.411, -2.411, 0.000) 105s Multigrid levels: 5 105s Molecule ID: 1 105s Linearized traditional PBE 105s Boundary conditions from focusing 105s 0 ion species (0.000 M ionic strength): 105s Solute dielectric: 1.000 105s Solvent dielectric: 78.540 105s Using "molecular" surface definition; no smoothing 105s Solvent probe radius: 1.400 A 105s Temperature: 298.150 K 105s Electrostatic energies will be calculated 105s Total electrostatic energy = 1.485246667424E+03 kJ/mol 105s Calculating forces... 105s ---------------------------------------- 105s CALCULATION #4 (reference): MULTIGRID 105s Setting up problem... 105s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 105s Debye length: 0 A 105s Current memory usage: 61.207 MB total, 122.102 MB high water 105s Using cubic spline charge discretization. 105s Partition overlap fraction = 0.1 105s Processor array = 2 x 2 x 1 105s Grid dimensions: 65 x 65 x 65 105s Grid spacings: 0.781 x 0.781 x 0.781 105s Grid lengths: 50.000 x 50.000 x 50.000 105s Grid center: (0.000, 0.000, 0.000) 105s Multigrid levels: 5 105s Molecule ID: 1 105s Linearized traditional PBE 105s Multiple Debye-Huckel sphere boundary conditions 105s 0 ion species (0.000 M ionic strength): 105s Solute dielectric: 1.000 105s Solvent dielectric: 1.000 105s Using "molecular" surface definition; no smoothing 105s Solvent probe radius: 1.400 A 105s Temperature: 298.150 K 105s Electrostatic energies will be calculated 105s Total electrostatic energy = 2.977178707009E+02 kJ/mol 105s Calculating forces... 105s ---------------------------------------- 105s CALCULATION #5 (reference): MULTIGRID 105s Setting up problem... 105s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 105s Debye length: 0 A 105s Current memory usage: 61.207 MB total, 122.102 MB high water 105s Using cubic spline charge discretization. 105s Partition overlap fraction = 0.1 105s Processor array = 2 x 2 x 1 105s Grid dimensions: 65 x 65 x 65 105s Grid spacings: 0.296 x 0.296 x 0.383 105s Grid lengths: 18.944 x 18.944 x 24.495 105s Grid center: (2.411, -2.411, 0.000) 105s Multigrid levels: 5 105s Molecule ID: 1 105s Linearized traditional PBE 105s Boundary conditions from focusing 105s 0 ion species (0.000 M ionic strength): 105s Solute dielectric: 1.000 105s Solvent dielectric: 1.000 105s Using "molecular" surface definition; no smoothing 105s Solvent probe radius: 1.400 A 105s Temperature: 298.150 K 105s Electrostatic energies will be calculated 105s Total electrostatic energy = 8.799304557588E+02 kJ/mol 105s Calculating forces... 105s [focusFillBound()]: WARNING: 105s Unusually large potential values 105s detected on the focusing boundary! 105s Convergence not guaranteed for NPBE/NRPBE calculations! 105s 105s ---------------------------------------- 105s CALCULATION #6 (reference): MULTIGRID 105s Setting up problem... 105s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 105s Debye length: 0 A 105s Current memory usage: 61.207 MB total, 122.102 MB high water 105s Using cubic spline charge discretization. 105s Partition overlap fraction = 0.1 105s Processor array = 2 x 2 x 1 105s Grid dimensions: 65 x 65 x 65 105s Grid spacings: 0.112 x 0.112 x 0.188 105s Grid lengths: 7.178 x 7.178 x 12.000 105s Grid center: (2.411, -2.411, 0.000) 105s Multigrid levels: 5 105s Molecule ID: 1 105s Linearized traditional PBE 105s Boundary conditions from focusing 105s 0 ion species (0.000 M ionic strength): 105s Solute dielectric: 1.000 105s Solvent dielectric: 1.000 105s Using "molecular" surface definition; no smoothing 105s Solvent probe radius: 1.400 A 105s Temperature: 298.150 K 105s Electrostatic energies will be calculated 105s Total electrostatic energy = 1.542873949131E+03 kJ/mol 105s Calculating forces... 105s ---------------------------------------- 105s PRINT STATEMENTS 105s 105s print energy 1 (solvated) - 2 (reference) end 105s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 105s Global net ELEC energy = -5.762728170718E+01 kJ/mol 105s ---------------------------------------- 105s CLEANING UP AND SHUTTING DOWN... 105s Destroying force arrays. 105s No energy arrays to destroy. 105s Destroying multigrid structures. 105s Destroying finite element structures. 105s Destroying 1 molecules 105s Final memory usage: 0.001 MB total, 122.102 MB high water 105s 105s 105s Thanks for using APBS! 105s 105s Processor 1 results: 105s 2.401768459022e+02 105s 8.142778312125e+02 105s 1.485246667424e+03 105s 2.977178707009e+02 105s 8.799304557588e+02 105s 1.542873949131e+03 105s -5.762728170718e+01 105s 107s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 107s BINARY: /usr/bin/apbs 107s INPUT: apbs-mol-parallel-PE2.in 107s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 107s Processor 2 results: 107s 2.401768459091e+02 107s 8.142935605695e+02 107s asc_getToken: Error occurred (bailing out). 107s Vio_scanf: Format problem with input. 107s 107s 107s ---------------------------------------------------------------------- 107s APBS -- Adaptive Poisson-Boltzmann Solver 107s Version APBS 3.4.1 107s 107s Nathan A. Baker (nathan.baker@pnnl.gov) 107s Pacific Northwest National Laboratory 107s 107s Additional contributing authors listed in the code documentation. 107s 107s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 107s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 107s Northwest Division for the U.S. Department of Energy. 107s 107s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 107s Portions Copyright (c) 2002-2020, Nathan A. Baker. 107s Portions Copyright (c) 1999-2002, The Regents of the University of California. 107s Portions Copyright (c) 1995, Michael Holst. 107s All rights reserved. 107s 107s Redistribution and use in source and binary forms, with or without 107s modification, are permitted provided that the following conditions are met: 107s 107s * Redistributions of source code must retain the above copyright notice, this 107s list of conditions and the following disclaimer. 107s 107s * Redistributions in binary form must reproduce the above copyright notice, 107s this list of conditions and the following disclaimer in the documentation 107s and/or other materials provided with the distribution. 107s 107s * Neither the name of the developer nor the names of its contributors may be 107s used to endorse or promote products derived from this software without 107s specific prior written permission. 107s 107s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 107s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 107s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 107s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 107s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 107s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 107s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 107s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 107s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 107s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 107s ---------------------------------------------------------------------- 107s APBS uses FETK (the Finite Element ToolKit) to solve the 107s Poisson-Boltzmann equation numerically. FETK is a portable collection 107s of finite element modeling class libraries developed by the Michael Holst 107s research group and written in an object-oriented form of C. FEtk is 107s designed to solve general coupled systems of nonlinear partial differential 107s equations using adaptive finite element methods, inexact Newton methods, 107s and algebraic multilevel methods. More information about FEtk may be found 107s at . 107s ---------------------------------------------------------------------- 107s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 107s Aqua is a modified form of the Holst group PMG library 107s which has been modified by Patrice Koehl 107s for improved efficiency and 107s memory usage when solving the Poisson-Boltzmann equation. 107s ---------------------------------------------------------------------- 107s Please cite your use of APBS as: 107s 107s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 107s nanosystems: application to microtubules and the ribosome. Proc. 107s Natl. Acad. Sci. USA 98, 10037-10041 2001. 107s 107s 107s This executable compiled on Jan 3 2025 at 11:01:42 107s 107s Parsing input file apbs-mol-parallel-PE2.in... 107s rank 0 size 1... 107s Parsed input file. 107s Got paths for 1 molecules 107s Reading PQR-format atom data from ion.pqr. 107s 1 atoms 107s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 107s Net charge 1.00e+00 e 107s Preparing to run 6 PBE calculations. 107s ---------------------------------------- 107s CALCULATION #1 (solvated): MULTIGRID 107s Setting up problem... 107s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 107s Debye length: 0 A 107s Current memory usage: 61.280 MB total, 61.280 MB high water 107s Using cubic spline charge discretization. 107s Partition overlap fraction = 0.1 107s Processor array = 2 x 2 x 1 107s Grid dimensions: 65 x 65 x 65 107s Grid spacings: 0.781 x 0.781 x 0.781 107s Grid lengths: 50.000 x 50.000 x 50.000 107s Grid center: (0.000, 0.000, 0.000) 107s Multigrid levels: 5 107s Molecule ID: 1 107s Linearized traditional PBE 107s Multiple Debye-Huckel sphere boundary conditions 107s 0 ion species (0.000 M ionic strength): 107s Solute dielectric: 1.000 107s Solvent dielectric: 78.540 107s Using "molecular" surface definition; no smoothing 107s Solvent probe radius: 1.400 A 107s Temperature: 298.150 K 107s Electrostatic energies will be calculated 107s Total electrostatic energy = 2.401768459091E+02 kJ/mol 107s Calculating forces... 107s ---------------------------------------- 107s CALCULATION #2 (solvated): MULTIGRID 107s Setting up problem... 107s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 107s Debye length: 0 A 107s Current memory usage: 61.280 MB total, 122.102 MB high water 107s Using cubic spline charge discretization. 107s Partition overlap fraction = 0.1 107s Processor array = 2 x 2 x 1 107s Grid dimensions: 65 x 65 x 65 107s Grid spacings: 0.296 x 0.296 x 0.383 107s Grid lengths: 18.944 x 18.944 x 24.495 107s Grid center: (-2.411, 2.411, 0.000) 107s Multigrid levels: 5 107s Molecule ID: 1 107s Linearized traditional PBE 107s Boundary conditions from focusing 107s 0 ion species (0.000 M ionic strength): 107s Solute dielectric: 1.000 107s Solvent dielectric: 78.540 107s Using "molecular" surface definition; no smoothing 107s Solvent probe radius: 1.400 A 107s Temperature: 298.150 K 107s Electrostatic energies will be calculated 107s Total electrostatic energy = 8.142935605695E+02 kJ/mol 107s Calculating forces... 107s [focusFillBound()]: WARNING: 107s Unusually large potential values 107s detected on the focusing boundary! 107s Convergence not guaranteed for NPBE/NRPBE calculations! 107s 107s ---------------------------------------- 107s CALCULATION #3 (solvated): MULTIGRID 107s Setting up problem... 107s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 107s Debye length: 0 A 107s Current memory usage: 61.280 MB total, 122.102 MB high water 107s Using cubic spline charge discretization. 107s Partition overlap fraction = 0.1 107s Processor array = 2 x 2 x 1 107s Grid dimensions: 65 x 65 x 65 107s Grid spacings: 0.112 x 0.112 x 0.188 107s Grid lengths: 7.178 x 7.178 x 12.000 107s Grid center: (-2.411, 2.411, 0.000) 107s Multigrid levels: 5 107s Molecule ID: 1 107s Linearized traditional PBE 107s Boundary conditions from focusing 107s 0 ion species (0.000 M ionic strength): 107s Solute dielectric: 1.000 107s Solvent dielectric: 78.540 107s Using "molecular" surface definition; no smoothing 107s Solvent probe radius: 1.400 A 107s Temperature: 298.150 K 107s Electrostatic energies will be calculated 107s Total electrostatic energy = 1.485255306569E+03 kJ/mol 107s Calculating forces... 107s ---------------------------------------- 107s CALCULATION #4 (reference): MULTIGRID 107s Setting up problem... 107s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 107s Debye length: 0 A 107s Current memory usage: 61.207 MB total, 122.102 MB high water 107s Using cubic spline charge discretization. 107s Partition overlap fraction = 0.1 107s Processor array = 2 x 2 x 1 107s Grid dimensions: 65 x 65 x 65 107s Grid spacings: 0.781 x 0.781 x 0.781 107s Grid lengths: 50.000 x 50.000 x 50.000 107s Grid center: (0.000, 0.000, 0.000) 107s Multigrid levels: 5 107s Molecule ID: 1 107s Linearized traditional PBE 107s Multiple Debye-Huckel sphere boundary conditions 107s 0 ion species (0.000 M ionic strength): 107s Solute dielectric: 1.000 107s Solvent dielectric: 1.000 107s Using "molecular" surface definition; no smoothing 107s Solvent probe radius: 1.400 A 107s Temperature: 298.150 K 107s Electrostatic energies will be calculated 107s Total electrostatic energy = 2.977178707146E+02 kJ/mol 107s Calculating forces... 107s ---------------------------------------- 107s CALCULATION #5 (reference): MULTIGRID 107s Setting up problem... 107s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 107s Debye length: 0 A 107s Current memory usage: 61.207 MB total, 122.102 MB high water 107s Using cubic spline charge discretization. 107s Partition overlap fraction = 0.1 107s Processor array = 2 x 2 x 1 107s Grid dimensions: 65 x 65 x 65 107s Grid spacings: 0.296 x 0.296 x 0.383 107s Grid lengths: 18.944 x 18.944 x 24.495 107s Grid center: (-2.411, 2.411, 0.000) 107s Multigrid levels: 5 107s Molecule ID: 1 107s Linearized traditional PBE 107s Boundary conditions from focusing 107s 0 ion species (0.000 M ionic strength): 107s Solute dielectric: 1.000 107s Solvent dielectric: 1.000 107s Using "molecular" surface definition; no smoothing 107s Solvent probe radius: 1.400 A 107s Temperature: 298.150 K 107s Electrostatic energies will be calculated 107s Total electrostatic energy = 8.799304557596E+02 kJ/mol 107s Calculating forces... 107s [focusFillBound()]: WARNING: 107s Unusually large potential values 107s detected on the focusing boundary! 107s Convergence not guaranteed for NPBE/NRPBE calculations! 107s 107s ---------------------------------------- 107s CALCULATION #6 (reference): MULTIGRID 107s Setting up problem... 107s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 107s Debye length: 0 A 107s Current memory usage: 61.207 MB total, 122.102 MB high water 107s Using cubic spline charge discretization. 107s Partition overlap fraction = 0.1 107s Processor array = 2 x 2 x 1 107s Grid dimensions: 65 x 65 x 65 107s Grid spacings: 0.112 x 0.112 x 0.188 107s Grid lengths: 7.178 x 7.178 x 12.000 107s Grid center: (-2.411, 2.411, 0.000) 107s Multigrid levels: 5 107s Molecule ID: 1 107s Linearized traditional PBE 107s Boundary conditions from focusing 107s 0 ion species (0.000 M ionic strength): 107s Solute dielectric: 1.000 107s Solvent dielectric: 1.000 107s Using "molecular" surface definition; no smoothing 107s Solvent probe radius: 1.400 A 107s Temperature: 298.150 K 107s Electrostatic energies will be calculated 107s Total electrostatic energy = 1.542873949141E+03 kJ/mol 107s Calculating forces... 107s ---------------------------------------- 107s PRINT STATEMENTS 107s 107s print energy 1 (solvated) - 2 (reference) end 107s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 107s Global net ELEC energy = -5.761864257239E+01 kJ/mol 107s ---------------------------------------- 107s CLEANING UP AND SHUTTING DOWN... 107s Destroying force arrays. 107s No energy arrays to destroy. 107s Destroying multigrid structures. 107s Destroying finite element structures. 107s Destroying 1 molecules 107s Final memory usage: 0.001 MB total, 122.102 MB high water 107s 107s 107s Thanks for using APBS! 107s 107s 1.485255306569e+03 107s 2.977178707146e+02 107s 8.799304557596e+02 107s 1.542873949141e+03 107s -5.761864257239e+01 107s 108s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 108s BINARY: /usr/bin/apbs 108s INPUT: apbs-mol-parallel-PE3.in 108s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 108s Processor 3 results: 108s asc_getToken: Error occurred (bailing out). 108s Vio_scanf: Format problem with input. 108s 108s 108s ---------------------------------------------------------------------- 108s APBS -- Adaptive Poisson-Boltzmann Solver 108s Version APBS 3.4.1 108s 108s Nathan A. Baker (nathan.baker@pnnl.gov) 108s Pacific Northwest National Laboratory 108s 108s Additional contributing authors listed in the code documentation. 108s 108s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 108s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 108s Northwest Division for the U.S. Department of Energy. 108s 108s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 108s Portions Copyright (c) 2002-2020, Nathan A. Baker. 108s Portions Copyright (c) 1999-2002, The Regents of the University of California. 108s Portions Copyright (c) 1995, Michael Holst. 108s All rights reserved. 108s 108s Redistribution and use in source and binary forms, with or without 108s modification, are permitted provided that the following conditions are met: 108s 108s * Redistributions of source code must retain the above copyright notice, this 108s list of conditions and the following disclaimer. 108s 108s * Redistributions in binary form must reproduce the above copyright notice, 108s this list of conditions and the following disclaimer in the documentation 108s and/or other materials provided with the distribution. 108s 108s * Neither the name of the developer nor the names of its contributors may be 108s used to endorse or promote products derived from this software without 108s specific prior written permission. 108s 108s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 108s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 108s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 108s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 108s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 108s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 108s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 108s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 108s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 108s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 108s ---------------------------------------------------------------------- 108s APBS uses FETK (the Finite Element ToolKit) to solve the 108s Poisson-Boltzmann equation numerically. FETK is a portable collection 108s of finite element modeling class libraries developed by the Michael Holst 108s research group and written in an object-oriented form of C. FEtk is 108s designed to solve general coupled systems of nonlinear partial differential 108s equations using adaptive finite element methods, inexact Newton methods, 108s and algebraic multilevel methods. More information about FEtk may be found 108s at . 108s ---------------------------------------------------------------------- 108s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 108s Aqua is a modified form of the Holst group PMG library 108s which has been modified by Patrice Koehl 108s for improved efficiency and 108s memory usage when solving the Poisson-Boltzmann equation. 108s ---------------------------------------------------------------------- 108s Please cite your use of APBS as: 108s 108s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 108s nanosystems: application to microtubules and the ribosome. Proc. 108s Natl. Acad. Sci. USA 98, 10037-10041 2001. 108s 108s 108s This executable compiled on Jan 3 2025 at 11:01:42 108s 108s Parsing input file apbs-mol-parallel-PE3.in... 108s rank 0 size 1... 108s Parsed input file. 108s Got paths for 1 molecules 108s Reading PQR-format atom data from ion.pqr. 108s 1 atoms 108s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 108s Net charge 1.00e+00 e 108s Preparing to run 6 PBE calculations. 108s ---------------------------------------- 108s CALCULATION #1 (solvated): MULTIGRID 108s Setting up problem... 108s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 108s Debye length: 0 A 108s Current memory usage: 61.280 MB total, 61.280 MB high water 108s Using cubic spline charge discretization. 108s Partition overlap fraction = 0.1 108s Processor array = 2 x 2 x 1 108s Grid dimensions: 65 x 65 x 65 108s Grid spacings: 0.781 x 0.781 x 0.781 108s Grid lengths: 50.000 x 50.000 x 50.000 108s Grid center: (0.000, 0.000, 0.000) 108s Multigrid levels: 5 108s Molecule ID: 1 108s Linearized traditional PBE 108s Multiple Debye-Huckel sphere boundary conditions 108s 0 ion species (0.000 M ionic strength): 108s Solute dielectric: 1.000 108s Solvent dielectric: 78.540 108s Using "molecular" surface definition; no smoothing 108s Solvent probe radius: 1.400 A 108s Temperature: 298.150 K 108s Electrostatic energies will be calculated 108s Total electrostatic energy = 2.401768459091E+02 kJ/mol 108s Calculating forces... 108s ---------------------------------------- 108s CALCULATION #2 (solvated): MULTIGRID 108s Setting up problem... 108s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 108s Debye length: 0 A 108s Current memory usage: 61.280 MB total, 122.102 MB high water 108s Using cubic spline charge discretization. 108s Partition overlap fraction = 0.1 108s Processor array = 2 x 2 x 1 108s Grid dimensions: 65 x 65 x 65 108s Grid spacings: 0.296 x 0.296 x 0.383 108s Grid lengths: 18.944 x 18.944 x 24.495 108s Grid center: (2.411, 2.411, 0.000) 108s Multigrid levels: 5 108s Molecule ID: 1 108s Linearized traditional PBE 108s Boundary conditions from focusing 108s 0 ion species (0.000 M ionic strength): 108s Solute dielectric: 1.000 108s Solvent dielectric: 78.540 108s Using "molecular" surface definition; no smoothing 108s Solvent probe radius: 1.400 A 108s Temperature: 298.150 K 108s Electrostatic energies will be calculated 108s Total electrostatic energy = 8.142778325440E+02 kJ/mol 108s Calculating forces... 108s [focusFillBound()]: WARNING: 108s Unusually large potential values 108s detected on the focusing boundary! 108s Convergence not guaranteed for NPBE/NRPBE calculations! 108s 108s ---------------------------------------- 108s CALCULATION #3 (solvated): MULTIGRID 108s Setting up problem... 108s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 108s Debye length: 0 A 108s Current memory usage: 61.280 MB total, 122.102 MB high water 108s Using cubic spline charge discretization. 108s Partition overlap fraction = 0.1 108s Processor array = 2 x 2 x 1 108s Grid dimensions: 65 x 65 x 65 108s Grid spacings: 0.112 x 0.112 x 0.188 108s Grid lengths: 7.178 x 7.178 x 12.000 108s Grid center: (2.411, 2.411, 0.000) 108s Multigrid levels: 5 108s Molecule ID: 1 108s Linearized traditional PBE 108s Boundary conditions from focusing 108s 0 ion species (0.000 M ionic strength): 108s Solute dielectric: 1.000 108s Solvent dielectric: 78.540 108s Using "molecular" surface definition; no smoothing 108s Solvent probe radius: 1.400 A 108s Temperature: 298.150 K 108s Electrostatic energies will be calculated 108s Total electrostatic energy = 1.485246665692E+03 kJ/mol 108s Calculating forces... 108s ---------------------------------------- 108s CALCULATION #4 (reference): MULTIGRID 108s Setting up problem... 108s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 108s Debye length: 0 A 108s Current memory usage: 61.207 MB total, 122.102 MB high water 108s Using cubic spline charge discretization. 108s Partition overlap fraction = 0.1 108s Processor array = 2 x 2 x 1 108s Grid dimensions: 65 x 65 x 65 108s Grid spacings: 0.781 x 0.781 x 0.781 108s Grid lengths: 50.000 x 50.000 x 50.000 108s Grid center: (0.000, 0.000, 0.000) 108s Multigrid levels: 5 108s Molecule ID: 1 108s Linearized traditional PBE 108s Multiple Debye-Huckel sphere boundary conditions 108s 0 ion species (0.000 M ionic strength): 108s Solute dielectric: 1.000 108s Solvent dielectric: 1.000 108s Using "molecular" surface definition; no smoothing 108s Solvent probe radius: 1.400 A 108s Temperature: 298.150 K 108s Electrostatic energies will be calculated 108s Total electrostatic energy = 2.977178707146E+02 kJ/mol 108s Calculating forces... 108s ---------------------------------------- 108s CALCULATION #5 (reference): MULTIGRID 108s Setting up problem... 108s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 108s Debye length: 0 A 108s Current memory usage: 61.207 MB total, 122.102 MB high water 108s Using cubic spline charge discretization. 108s Partition overlap fraction = 0.1 108s Processor array = 2 x 2 x 1 108s Grid dimensions: 65 x 65 x 65 108s Grid spacings: 0.296 x 0.296 x 0.383 108s Grid lengths: 18.944 x 18.944 x 24.495 108s Grid center: (2.411, 2.411, 0.000) 108s Multigrid levels: 5 108s Molecule ID: 1 108s Linearized traditional PBE 108s Boundary conditions from focusing 108s 0 ion species (0.000 M ionic strength): 108s Solute dielectric: 1.000 108s Solvent dielectric: 1.000 108s Using "molecular" surface definition; no smoothing 108s Solvent probe radius: 1.400 A 108s Temperature: 298.150 K 108s Electrostatic energies will be calculated 108s Total electrostatic energy = 8.799304557596E+02 kJ/mol 108s Calculating forces... 108s [focusFillBound()]: WARNING: 108s Unusually large potential values 108s detected on the focusing boundary! 108s Convergence not guaranteed for NPBE/NRPBE calculations! 108s 108s ---------------------------------------- 108s CALCULATION #6 (reference): MULTIGRID 108s Setting up problem... 108s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 108s Debye length: 0 A 108s Current memory usage: 61.207 MB total, 122.102 MB high water 108s Using cubic spline charge discretization. 108s Partition overlap fraction = 0.1 108s Processor array = 2 x 2 x 1 108s Grid dimensions: 65 x 65 x 65 108s Grid spacings: 0.112 x 0.112 x 0.188 108s Grid lengths: 7.178 x 7.178 x 12.000 108s Grid center: (2.411, 2.411, 0.000) 108s Multigrid levels: 5 108s Molecule ID: 1 108s Linearized traditional PBE 108s Boundary conditions from focusing 108s 0 ion species (0.000 M ionic strength): 108s Solute dielectric: 1.000 108s Solvent dielectric: 1.000 108s Using "molecular" surface definition; no smoothing 108s Solvent probe radius: 1.400 A 108s Temperature: 298.150 K 108s Electrostatic energies will be calculated 108s Total electrostatic energy = 1.542873949141E+03 kJ/mol 108s Calculating forces... 108s ---------------------------------------- 108s PRINT STATEMENTS 108s 108s print energy 1 (solvated) - 2 (reference) end 108s Local net energy (PE 0) = -5.762728344953E+01 kJ/mol 108s Global net ELEC energy = -5.762728344953E+01 kJ/mol 108s ---------------------------------------- 108s CLEANING UP AND SHUTTING DOWN... 108s Destroying force arrays. 108s No energy arrays to destroy. 108s Destroying multigrid structures. 108s Destroying finite element structures. 108s Destroying 1 molecules 108s Final memory usage: 0.001 MB total, 122.102 MB high water 108s 108s 108s Thanks for using APBS! 108s 108s 2.401768459091e+02 108s 8.142778325440e+02 108s 1.485246665692e+03 108s 2.977178707146e+02 108s 8.799304557596e+02 108s 1.542873949141e+03 108s -5.762728344953e+01 108s 108s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 108s *** PASSED *** 108s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 108s *** PASSED *** 108s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 108s *** PASSED *** 108s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 108s *** PASSED *** 108s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 108s *** PASSED *** 108s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 108s *** PASSED *** 108s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 108s *** PASSED *** 108s Elapsed time: 6.0616 seconds 108s -------------------------------------------------------------------------------- 108s -------------------------------------------------------------------------------- 108s Testing input file apbs-smol-parallel.in 108s 108s Splitting the input file into 4 separate files using the inputgen utility 108s 109s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 109s EXPECTED COMPUTED: 7 109s EXPECTED EXPECTED: 7 109s COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 109s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 109s COMPUTED RESULT 960.7073836226 109s COMPUTED RESULT 3257.1427835730997 109s COMPUTED RESULT 5941.0039478710005 109s COMPUTED RESULT 1190.8714828309999 109s COMPUTED RESULT 3519.7218230368003 109s COMPUTED RESULT 6171.495796544 109s COMPUTED RESULT -230.49184867462003 109s BINARY: /usr/bin/apbs 109s INPUT: apbs-smol-parallel-PE0.in 109s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 109s asc_getToken: Error occurred (bailing out). 109s Vio_scanf: Format problem with input. 109s 109s 109s ---------------------------------------------------------------------- 109s APBS -- Adaptive Poisson-Boltzmann Solver 109s Version APBS 3.4.1 109s 109s Nathan A. Baker (nathan.baker@pnnl.gov) 109s Pacific Northwest National Laboratory 109s 109s Additional contributing authors listed in the code documentation. 109s 109s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 109s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 109s Northwest Division for the U.S. Department of Energy. 109s 109s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 109s Portions Copyright (c) 2002-2020, Nathan A. Baker. 109s Portions Copyright (c) 1999-2002, The Regents of the University of California. 109s Portions Copyright (c) 1995, Michael Holst. 109s All rights reserved. 109s 109s Redistribution and use in source and binary forms, with or without 109s modification, are permitted provided that the following conditions are met: 109s 109s * Redistributions of source code must retain the above copyright notice, this 109s list of conditions and the following disclaimer. 109s 109s * Redistributions in binary form must reproduce the above copyright notice, 109s this list of conditions and the following disclaimer in the documentation 109s and/or other materials provided with the distribution. 109s 109s * Neither the name of the developer nor the names of its contributors may be 109s used to endorse or promote products derived from this software without 109s specific prior written permission. 109s 109s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 109s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 109s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 109s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 109s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 109s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 109s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 109s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 109s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 109s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 109s ---------------------------------------------------------------------- 109s APBS uses FETK (the Finite Element ToolKit) to solve the 109s Poisson-Boltzmann equation numerically. FETK is a portable collection 109s of finite element modeling class libraries developed by the Michael Holst 109s research group and written in an object-oriented form of C. FEtk is 109s designed to solve general coupled systems of nonlinear partial differential 109s equations using adaptive finite element methods, inexact Newton methods, 109s and algebraic multilevel methods. More information about FEtk may be found 109s at . 109s ---------------------------------------------------------------------- 109s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 109s Aqua is a modified form of the Holst group PMG library 109s which has been modified by Patrice Koehl 109s for improved efficiency and 109s memory usage when solving the Poisson-Boltzmann equation. 109s ---------------------------------------------------------------------- 109s Please cite your use of APBS as: 109s 109s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 109s nanosystems: application to microtubules and the ribosome. Proc. 109s Natl. Acad. Sci. USA 98, 10037-10041 2001. 109s 109s 109s This executable compiled on Jan 3 2025 at 11:01:42 109s 109s Parsing input file apbs-smol-parallel-PE0.in... 109s rank 0 size 1... 109s Parsed input file. 109s Got paths for 1 molecules 109s Reading PQR-format atom data from ion.pqr. 109s 1 atoms 109s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 109s Net charge 1.00e+00 e 109s Preparing to run 6 PBE calculations. 109s ---------------------------------------- 109s CALCULATION #1 (solvated): MULTIGRID 109s Setting up problem... 109s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 109s Debye length: 0 A 109s Current memory usage: 61.280 MB total, 61.280 MB high water 109s Using cubic spline charge discretization. 109s Partition overlap fraction = 0.1 109s Processor array = 2 x 2 x 1 109s Grid dimensions: 65 x 65 x 65 109s Grid spacings: 0.781 x 0.781 x 0.781 109s Grid lengths: 50.000 x 50.000 x 50.000 109s Grid center: (0.000, 0.000, 0.000) 109s Multigrid levels: 5 109s Molecule ID: 1 109s Linearized traditional PBE 109s Multiple Debye-Huckel sphere boundary conditions 109s 0 ion species (0.000 M ionic strength): 109s Solute dielectric: 1.000 109s Solvent dielectric: 78.540 109s Using "molecular" surface definition;harmonic average smoothing 109s Solvent probe radius: 1.400 A 109s Temperature: 298.150 K 109s Electrostatic energies will be calculated 109s Total electrostatic energy = 2.383232191816E+02 kJ/mol 109s Calculating forces... 109s ---------------------------------------- 109s CALCULATION #2 (solvated): MULTIGRID 109s Setting up problem... 109s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 109s Debye length: 0 A 109s Current memory usage: 61.280 MB total, 122.102 MB high water 109s Using cubic spline charge discretization. 109s Partition overlap fraction = 0.1 109s Processor array = 2 x 2 x 1 109s Grid dimensions: 65 x 65 x 65 109s Grid spacings: 0.296 x 0.296 x 0.383 109s Grid lengths: 18.944 x 18.944 x 24.495 109s Grid center: (-2.411, -2.411, 0.000) 109s Multigrid levels: 5 109s Molecule ID: 1 109s Linearized traditional PBE 109s Boundary conditions from focusing 109s 0 ion species (0.000 M ionic strength): 109s Solute dielectric: 1.000 109s Solvent dielectric: 78.540 109s Using "molecular" surface definition;harmonic average smoothing 109s Solvent probe radius: 1.400 A 109s Temperature: 298.150 K 109s Electrostatic energies will be calculated 109s Total electrostatic energy = 8.145369591602E+02 kJ/mol 109s Calculating forces... 109s [focusFillBound()]: WARNING: 109s Unusually large potential values 109s detected on the focusing boundary! 109s Convergence not guaranteed for NPBE/NRPBE calculations! 109s 109s ---------------------------------------- 109s CALCULATION #3 (solvated): MULTIGRID 109s Setting up problem... 109s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 109s Debye length: 0 A 109s Current memory usage: 61.280 MB total, 122.102 MB high water 109s Using cubic spline charge discretization. 109s Partition overlap fraction = 0.1 109s Processor array = 2 x 2 x 1 109s Grid dimensions: 65 x 65 x 65 109s Grid spacings: 0.112 x 0.112 x 0.188 109s Grid lengths: 7.178 x 7.178 x 12.000 109s Grid center: (-2.411, -2.411, 0.000) 109s Multigrid levels: 5 109s Molecule ID: 1 109s Linearized traditional PBE 109s Boundary conditions from focusing 109s 0 ion species (0.000 M ionic strength): 109s Solute dielectric: 1.000 109s Solvent dielectric: 78.540 109s Using "molecular" surface definition;harmonic average smoothing 109s Solvent probe radius: 1.400 A 109s Temperature: 298.150 K 109s Electrostatic energies will be calculated 109s Total electrostatic energy = 1.485524998001E+03 kJ/mol 109s Calculating forces... 109s ---------------------------------------- 109s CALCULATION #4 (reference): MULTIGRID 109s Setting up problem... 109s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 109s Debye length: 0 A 109s Current memory usage: 61.207 MB total, 122.102 MB high water 109s Using cubic spline charge discretization. 109s Partition overlap fraction = 0.1 109s Processor array = 2 x 2 x 1 109s Grid dimensions: 65 x 65 x 65 109s Grid spacings: 0.781 x 0.781 x 0.781 109s Grid lengths: 50.000 x 50.000 x 50.000 109s Grid center: (0.000, 0.000, 0.000) 109s Multigrid levels: 5 109s Molecule ID: 1 109s Linearized traditional PBE 109s Multiple Debye-Huckel sphere boundary conditions 109s 0 ion species (0.000 M ionic strength): 109s Solute dielectric: 1.000 109s Solvent dielectric: 1.000 109s Using "molecular" surface definition;harmonic average smoothing 109s Solvent probe radius: 1.400 A 109s Temperature: 298.150 K 109s Electrostatic energies will be calculated 109s Total electrostatic energy = 2.977178707009E+02 kJ/mol 109s Calculating forces... 109s ---------------------------------------- 109s CALCULATION #5 (reference): MULTIGRID 109s Setting up problem... 109s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 109s Debye length: 0 A 109s Current memory usage: 61.207 MB total, 122.102 MB high water 109s Using cubic spline charge discretization. 109s Partition overlap fraction = 0.1 109s Processor array = 2 x 2 x 1 109s Grid dimensions: 65 x 65 x 65 109s Grid spacings: 0.296 x 0.296 x 0.383 109s Grid lengths: 18.944 x 18.944 x 24.495 109s Grid center: (-2.411, -2.411, 0.000) 109s Multigrid levels: 5 109s Molecule ID: 1 109s Linearized traditional PBE 109s Boundary conditions from focusing 109s 0 ion species (0.000 M ionic strength): 109s Solute dielectric: 1.000 109s Solvent dielectric: 1.000 109s Using "molecular" surface definition;harmonic average smoothing 109s Solvent probe radius: 1.400 A 109s Temperature: 298.150 K 109s Electrostatic energies will be calculated 109s Total electrostatic energy = 8.799304557588E+02 kJ/mol 109s Calculating forces... 109s [focusFillBound()]: WARNING: 109s Unusually large potential values 109s detected on the focusing boundary! 109s Convergence not guaranteed for NPBE/NRPBE calculations! 109s 109s ---------------------------------------- 109s CALCULATION #6 (reference): MULTIGRID 109s Setting up problem... 109s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 109s Debye length: 0 A 109s Current memory usage: 61.207 MB total, 122.102 MB high water 109s Using cubic spline charge discretization. 109s Partition overlap fraction = 0.1 109s Processor array = 2 x 2 x 1 109s Grid dimensions: 65 x 65 x 65 109s Grid spacings: 0.112 x 0.112 x 0.188 109s Grid lengths: 7.178 x 7.178 x 12.000 109s Grid center: (-2.411, -2.411, 0.000) 109s Multigrid levels: 5 109s Molecule ID: 1 109s Linearized traditional PBE 109s Boundary conditions from focusing 109s 0 ion species (0.000 M ionic strength): 109s Solute dielectric: 1.000 109s Solvent dielectric: 1.000 109s Using "molecular" surface definition;harmonic average smoothing 109s Solvent probe radius: 1.400 A 109s Temperature: 298.150 K 109s Electrostatic energies will be calculated 109s Total electrostatic energy = 1.542873949131E+03 kJ/mol 109s Calculating forces... 109s ---------------------------------------- 109s PRINT STATEMENTS 109s 109s print energy 1 (solvated) - 2 (reference) end 109s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 109s Global net ELEC energy = -5.734895113069E+01 kJ/mol 109s ---------------------------------------- 109s CLEANING UP AND SHUTTING DOWN... 109s Destroying force arrays. 109s No energy arrays to destroy. 109s Destroying multigrid structures. 109s Destroying finite element structures. 109s Destroying 1 molecules 109s Final memory usage: 0.001 MB total, 122.102 MB high water 109s 109s 109s Thanks for using APBS! 109s 109s Processor 0 results: 110s 2.383232191816e+02 110s 8.145369591602e+02 110s 1.485524998001e+03 110s 2.977178707009e+02 110s 8.799304557588e+02 110s 1.542873949131e+03 110s -5.734895113069e+01 110s 111s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 111s BINARY: /usr/bin/apbs 111s INPUT: apbs-smol-parallel-PE1.in 111s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 111s asc_getToken: Error occurred (bailing out). 111s Vio_scanf: Format problem with input. 111s 111s 111s ---------------------------------------------------------------------- 111s APBS -- Adaptive Poisson-Boltzmann Solver 111s Version APBS 3.4.1 111s 111s Nathan A. Baker (nathan.baker@pnnl.gov) 111s Pacific Northwest National Laboratory 111s 111s Additional contributing authors listed in the code documentation. 111s 111s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 111s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 111s Northwest Division for the U.S. Department of Energy. 111s 111s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 111s Portions Copyright (c) 2002-2020, Nathan A. Baker. 111s Portions Copyright (c) 1999-2002, The Regents of the University of California. 111s Portions Copyright (c) 1995, Michael Holst. 111s All rights reserved. 111s 111s Redistribution and use in source and binary forms, with or without 111s modification, are permitted provided that the following conditions are met: 111s 111s * Redistributions of source code must retain the above copyright notice, this 111s list of conditions and the following disclaimer. 111s 111s * Redistributions in binary form must reproduce the above copyright notice, 111s this list of conditions and the following disclaimer in the documentation 111s and/or other materials provided with the distribution. 111s 111s * Neither the name of the developer nor the names of its contributors may be 111s used to endorse or promote products derived from this software without 111s specific prior written permission. 111s 111s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 111s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 111s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 111s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 111s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 111s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 111s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 111s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 111s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 111s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 111s ---------------------------------------------------------------------- 111s APBS uses FETK (the Finite Element ToolKit) to solve the 111s Poisson-Boltzmann equation numerically. FETK is a portable collection 111s of finite element modeling class libraries developed by the Michael Holst 111s research group and written in an object-oriented form of C. FEtk is 111s designed to solve general coupled systems of nonlinear partial differential 111s equations using adaptive finite element methods, inexact Newton methods, 111s and algebraic multilevel methods. More information about FEtk may be found 111s at . 111s ---------------------------------------------------------------------- 111s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 111s Aqua is a modified form of the Holst group PMG library 111s which has been modified by Patrice Koehl 111s for improved efficiency and 111s memory usage when solving the Poisson-Boltzmann equation. 111s ---------------------------------------------------------------------- 111s Please cite your use of APBS as: 111s 111s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 111s nanosystems: application to microtubules and the ribosome. Proc. 111s Natl. Acad. Sci. USA 98, 10037-10041 2001. 111s 111s 111s This executable compiled on Jan 3 2025 at 11:01:42 111s 111s Parsing input file apbs-smol-parallel-PE1.in... 111s rank 0 size 1... 111s Parsed input file. 111s Got paths for 1 molecules 111s Reading PQR-format atom data from ion.pqr. 111s 1 atoms 111s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 111s Net charge 1.00e+00 e 111s Preparing to run 6 PBE calculations. 111s ---------------------------------------- 111s CALCULATION #1 (solvated): MULTIGRID 111s Setting up problem... 111s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 111s Debye length: 0 A 111s Current memory usage: 61.280 MB total, 61.280 MB high water 111s Using cubic spline charge discretization. 111s Partition overlap fraction = 0.1 111s Processor array = 2 x 2 x 1 111s Grid dimensions: 65 x 65 x 65 111s Grid spacings: 0.781 x 0.781 x 0.781 111s Grid lengths: 50.000 x 50.000 x 50.000 111s Grid center: (0.000, 0.000, 0.000) 111s Multigrid levels: 5 111s Molecule ID: 1 111s Linearized traditional PBE 111s Multiple Debye-Huckel sphere boundary conditions 111s 0 ion species (0.000 M ionic strength): 111s Solute dielectric: 1.000 111s Solvent dielectric: 78.540 111s Using "molecular" surface definition;harmonic average smoothing 111s Solvent probe radius: 1.400 A 111s Temperature: 298.150 K 111s Electrostatic energies will be calculated 111s Total electrostatic energy = 2.383232191816E+02 kJ/mol 111s Calculating forces... 111s ---------------------------------------- 111s CALCULATION #2 (solvated): MULTIGRID 111s Setting up problem... 111s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 111s Debye length: 0 A 111s Current memory usage: 61.280 MB total, 122.102 MB high water 111s Using cubic spline charge discretization. 111s Partition overlap fraction = 0.1 111s Processor array = 2 x 2 x 1 111s Grid dimensions: 65 x 65 x 65 111s Grid spacings: 0.296 x 0.296 x 0.383 111s Grid lengths: 18.944 x 18.944 x 24.495 111s Grid center: (2.411, -2.411, 0.000) 111s Multigrid levels: 5 111s Molecule ID: 1 111s Linearized traditional PBE 111s Boundary conditions from focusing 111s 0 ion species (0.000 M ionic strength): 111s Solute dielectric: 1.000 111s Solvent dielectric: 78.540 111s Using "molecular" surface definition;harmonic average smoothing 111s Solvent probe radius: 1.400 A 111s Temperature: 298.150 K 111s Electrostatic energies will be calculated 111s Total electrostatic energy = 8.145419898332E+02 kJ/mol 111s Calculating forces... 111s [focusFillBound()]: WARNING: 111s Unusually large potential values 111s detected on the focusing boundary! 111s Convergence not guaranteed for NPBE/NRPBE calculations! 111s 111s ---------------------------------------- 111s CALCULATION #3 (solvated): MULTIGRID 111s Setting up problem... 111s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 111s Debye length: 0 A 111s Current memory usage: 61.280 MB total, 122.102 MB high water 111s Using cubic spline charge discretization. 111s Partition overlap fraction = 0.1 111s Processor array = 2 x 2 x 1 111s Grid dimensions: 65 x 65 x 65 111s Grid spacings: 0.112 x 0.112 x 0.188 111s Grid lengths: 7.178 x 7.178 x 12.000 111s Grid center: (2.411, -2.411, 0.000) 111s Multigrid levels: 5 111s Molecule ID: 1 111s Linearized traditional PBE 111s Boundary conditions from focusing 111s 0 ion species (0.000 M ionic strength): 111s Solute dielectric: 1.000 111s Solvent dielectric: 78.540 111s Using "molecular" surface definition;harmonic average smoothing 111s Solvent probe radius: 1.400 A 111s Temperature: 298.150 K 111s Electrostatic energies will be calculated 111s Total electrostatic energy = 1.485529328612E+03 kJ/mol 111s Calculating forces... 111s ---------------------------------------- 111s CALCULATION #4 (reference): MULTIGRID 111s Setting up problem... 111s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 111s Debye length: 0 A 111s Current memory usage: 61.207 MB total, 122.102 MB high water 111s Using cubic spline charge discretization. 111s Partition overlap fraction = 0.1 111s Processor array = 2 x 2 x 1 111s Grid dimensions: 65 x 65 x 65 111s Grid spacings: 0.781 x 0.781 x 0.781 111s Grid lengths: 50.000 x 50.000 x 50.000 111s Grid center: (0.000, 0.000, 0.000) 111s Multigrid levels: 5 111s Molecule ID: 1 111s Linearized traditional PBE 111s Multiple Debye-Huckel sphere boundary conditions 111s 0 ion species (0.000 M ionic strength): 111s Solute dielectric: 1.000 111s Solvent dielectric: 1.000 111s Using "molecular" surface definition;harmonic average smoothing 111s Solvent probe radius: 1.400 A 111s Temperature: 298.150 K 111s Electrostatic energies will be calculated 111s Total electrostatic energy = 2.977178707009E+02 kJ/mol 111s Calculating forces... 111s ---------------------------------------- 111s CALCULATION #5 (reference): MULTIGRID 111s Setting up problem... 111s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 111s Debye length: 0 A 111s Current memory usage: 61.207 MB total, 122.102 MB high water 111s Using cubic spline charge discretization. 111s Partition overlap fraction = 0.1 111s Processor array = 2 x 2 x 1 111s Grid dimensions: 65 x 65 x 65 111s Grid spacings: 0.296 x 0.296 x 0.383 111s Grid lengths: 18.944 x 18.944 x 24.495 111s Grid center: (2.411, -2.411, 0.000) 111s Multigrid levels: 5 111s Molecule ID: 1 111s Linearized traditional PBE 111s Boundary conditions from focusing 111s 0 ion species (0.000 M ionic strength): 111s Solute dielectric: 1.000 111s Solvent dielectric: 1.000 111s Using "molecular" surface definition;harmonic average smoothing 111s Solvent probe radius: 1.400 A 111s Temperature: 298.150 K 111s Electrostatic energies will be calculated 111s Total electrostatic energy = 8.799304557588E+02 kJ/mol 111s Calculating forces... 111s [focusFillBound()]: WARNING: 111s Unusually large potential values 111s detected on the focusing boundary! 111s Convergence not guaranteed for NPBE/NRPBE calculations! 111s 111s ---------------------------------------- 111s CALCULATION #6 (reference): MULTIGRID 111s Setting up problem... 111s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 111s Debye length: 0 A 111s Current memory usage: 61.207 MB total, 122.102 MB high water 111s Using cubic spline charge discretization. 111s Partition overlap fraction = 0.1 111s Processor array = 2 x 2 x 1 111s Grid dimensions: 65 x 65 x 65 111s Grid spacings: 0.112 x 0.112 x 0.188 111s Grid lengths: 7.178 x 7.178 x 12.000 111s Grid center: (2.411, -2.411, 0.000) 111s Multigrid levels: 5 111s Molecule ID: 1 111s Linearized traditional PBE 111s Boundary conditions from focusing 111s 0 ion species (0.000 M ionic strength): 111s Solute dielectric: 1.000 111s Solvent dielectric: 1.000 111s Using "molecular" surface definition;harmonic average smoothing 111s Solvent probe radius: 1.400 A 111s Temperature: 298.150 K 111s Electrostatic energies will be calculated 111s Total electrostatic energy = 1.542873949131E+03 kJ/mol 111s Calculating forces... 111s ---------------------------------------- 111s PRINT STATEMENTS 111s 111s print energy 1 (solvated) - 2 (reference) end 111s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 111s Global net ELEC energy = -5.734462051928E+01 kJ/mol 111s ---------------------------------------- 111s CLEANING UP AND SHUTTING DOWN... 111s Destroying force arrays. 111s No energy arrays to destroy. 111s Destroying multigrid structures. 111s Destroying finite element structures. 111s Destroying 1 molecules 111s Final memory usage: 0.001 MB total, 122.102 MB high water 111s 111s 111s Thanks for using APBS! 111s 111s Processor 1 results: 111s 2.383232191816e+02 111s 8.145419898332e+02 111s 1.485529328612e+03 111s 2.977178707009e+02 111s 8.799304557588e+02 111s 1.542873949131e+03 111s -5.734462051928e+01 111s 113s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 113s BINARY: /usr/bin/apbs 113s INPUT: apbs-smol-parallel-PE2.in 113s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 113s asc_getToken: Error occurred (bailing out). 113s Vio_scanf: Format problem with input. 113s 113s 113s ---------------------------------------------------------------------- 113s APBS -- Adaptive Poisson-Boltzmann Solver 113s Version APBS 3.4.1 113s 113s Nathan A. Baker (nathan.baker@pnnl.gov) 113s Pacific Northwest National Laboratory 113s 113s Additional contributing authors listed in the code documentation. 113s 113s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 113s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 113s Northwest Division for the U.S. Department of Energy. 113s 113s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 113s Portions Copyright (c) 2002-2020, Nathan A. Baker. 113s Portions Copyright (c) 1999-2002, The Regents of the University of California. 113s Portions Copyright (c) 1995, Michael Holst. 113s All rights reserved. 113s 113s Redistribution and use in source and binary forms, with or without 113s modification, are permitted provided that the following conditions are met: 113s 113s * Redistributions of source code must retain the above copyright notice, this 113s list of conditions and the following disclaimer. 113s 113s * Redistributions in binary form must reproduce the above copyright notice, 113s this list of conditions and the following disclaimer in the documentation 113s and/or other materials provided with the distribution. 113s 113s * Neither the name of the developer nor the names of its contributors may be 113s used to endorse or promote products derived from this software without 113s specific prior written permission. 113s 113s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 113s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 113s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 113s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 113s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 113s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 113s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 113s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 113s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 113s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 113s ---------------------------------------------------------------------- 113s APBS uses FETK (the Finite Element ToolKit) to solve the 113s Poisson-Boltzmann equation numerically. FETK is a portable collection 113s of finite element modeling class libraries developed by the Michael Holst 113s research group and written in an object-oriented form of C. FEtk is 113s designed to solve general coupled systems of nonlinear partial differential 113s equations using adaptive finite element methods, inexact Newton methods, 113s and algebraic multilevel methods. More information about FEtk may be found 113s at . 113s ---------------------------------------------------------------------- 113s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 113s Aqua is a modified form of the Holst group PMG library 113s which has been modified by Patrice Koehl 113s for improved efficiency and 113s memory usage when solving the Poisson-Boltzmann equation. 113s ---------------------------------------------------------------------- 113s Please cite your use of APBS as: 113s 113s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 113s nanosystems: application to microtubules and the ribosome. Proc. 113s Natl. Acad. Sci. USA 98, 10037-10041 2001. 113s 113s 113s This executable compiled on Jan 3 2025 at 11:01:42 113s 113s Parsing input file apbs-smol-parallel-PE2.in... 113s rank 0 size 1... 113s Parsed input file. 113s Got paths for 1 molecules 113s Reading PQR-format atom data from ion.pqr. 113s 1 atoms 113s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 113s Net charge 1.00e+00 e 113s Preparing to run 6 PBE calculations. 113s ---------------------------------------- 113s CALCULATION #1 (solvated): MULTIGRID 113s Setting up problem... 113s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 113s Debye length: 0 A 113s Current memory usage: 61.280 MB total, 61.280 MB high water 113s Using cubic spline charge discretization. 113s Partition overlap fraction = 0.1 113s Processor array = 2 x 2 x 1 113s Grid dimensions: 65 x 65 x 65 113s Grid spacings: 0.781 x 0.781 x 0.781 113s Grid lengths: 50.000 x 50.000 x 50.000 113s Grid center: (0.000, 0.000, 0.000) 113s Multigrid levels: 5 113s Molecule ID: 1 113s Linearized traditional PBE 113s Multiple Debye-Huckel sphere boundary conditions 113s 0 ion species (0.000 M ionic strength): 113s Solute dielectric: 1.000 113s Solvent dielectric: 78.540 113s Using "molecular" surface definition;harmonic average smoothing 113s Solvent probe radius: 1.400 A 113s Temperature: 298.150 K 113s Electrostatic energies will be calculated 113s Total electrostatic energy = 2.383232191909E+02 kJ/mol 113s Calculating forces... 113s ---------------------------------------- 113s CALCULATION #2 (solvated): MULTIGRID 113s Setting up problem... 113s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 113s Debye length: 0 A 113s Current memory usage: 61.280 MB total, 122.102 MB high water 113s Using cubic spline charge discretization. 113s Partition overlap fraction = 0.1 113s Processor array = 2 x 2 x 1 113s Grid dimensions: 65 x 65 x 65 113s Grid spacings: 0.296 x 0.296 x 0.383 113s Grid lengths: 18.944 x 18.944 x 24.495 113s Grid center: (-2.411, 2.411, 0.000) 113s Multigrid levels: 5 113s Molecule ID: 1 113s Linearized traditional PBE 113s Boundary conditions from focusing 113s 0 ion species (0.000 M ionic strength): 113s Solute dielectric: 1.000 113s Solvent dielectric: 78.540 113s Using "molecular" surface definition;harmonic average smoothing 113s Solvent probe radius: 1.400 A 113s Temperature: 298.150 K 113s Electrostatic energies will be calculated 113s Total electrostatic energy = 8.145369593489E+02 kJ/mol 113s Calculating forces... 113s [focusFillBound()]: WARNING: 113s Unusually large potential values 113s detected on the focusing boundary! 113s Convergence not guaranteed for NPBE/NRPBE calculations! 113s 113s ---------------------------------------- 113s CALCULATION #3 (solvated): MULTIGRID 113s Setting up problem... 113s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 113s Debye length: 0 A 113s Current memory usage: 61.280 MB total, 122.102 MB high water 113s Using cubic spline charge discretization. 113s Partition overlap fraction = 0.1 113s Processor array = 2 x 2 x 1 113s Grid dimensions: 65 x 65 x 65 113s Grid spacings: 0.112 x 0.112 x 0.188 113s Grid lengths: 7.178 x 7.178 x 12.000 113s Grid center: (-2.411, 2.411, 0.000) 113s Multigrid levels: 5 113s Molecule ID: 1 113s Linearized traditional PBE 113s Boundary conditions from focusing 113s 0 ion species (0.000 M ionic strength): 113s Solute dielectric: 1.000 113s Solvent dielectric: 78.540 113s Using "molecular" surface definition;harmonic average smoothing 113s Solvent probe radius: 1.400 A 113s Temperature: 298.150 K 113s Electrostatic energies will be calculated 113s Total electrostatic energy = 1.485524997676E+03 kJ/mol 113s Calculating forces... 113s ---------------------------------------- 113s CALCULATION #4 (reference): MULTIGRID 113s Setting up problem... 113s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 113s Debye length: 0 A 113s Current memory usage: 61.207 MB total, 122.102 MB high water 113s Using cubic spline charge discretization. 113s Partition overlap fraction = 0.1 113s Processor array = 2 x 2 x 1 113s Grid dimensions: 65 x 65 x 65 113s Grid spacings: 0.781 x 0.781 x 0.781 113s Grid lengths: 50.000 x 50.000 x 50.000 113s Grid center: (0.000, 0.000, 0.000) 113s Multigrid levels: 5 113s Molecule ID: 1 113s Linearized traditional PBE 113s Multiple Debye-Huckel sphere boundary conditions 113s 0 ion species (0.000 M ionic strength): 113s Solute dielectric: 1.000 113s Solvent dielectric: 1.000 113s Using "molecular" surface definition;harmonic average smoothing 113s Solvent probe radius: 1.400 A 113s Temperature: 298.150 K 113s Electrostatic energies will be calculated 113s Total electrostatic energy = 2.977178707146E+02 kJ/mol 113s Calculating forces... 113s ---------------------------------------- 113s CALCULATION #5 (reference): MULTIGRID 113s Setting up problem... 113s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 113s Debye length: 0 A 113s Current memory usage: 61.207 MB total, 122.102 MB high water 113s Using cubic spline charge discretization. 113s Partition overlap fraction = 0.1 113s Processor array = 2 x 2 x 1 113s Grid dimensions: 65 x 65 x 65 113s Grid spacings: 0.296 x 0.296 x 0.383 113s Grid lengths: 18.944 x 18.944 x 24.495 113s Grid center: (-2.411, 2.411, 0.000) 113s Multigrid levels: 5 113s Molecule ID: 1 113s Linearized traditional PBE 113s Boundary conditions from focusing 113s 0 ion species (0.000 M ionic strength): 113s Solute dielectric: 1.000 113s Solvent dielectric: 1.000 113s Using "molecular" surface definition;harmonic average smoothing 113s Solvent probe radius: 1.400 A 113s Temperature: 298.150 K 113s Electrostatic energies will be calculated 113s Total electrostatic energy = 8.799304557596E+02 kJ/mol 113s Calculating forces... 113s [focusFillBound()]: WARNING: 113s Unusually large potential values 113s detected on the focusing boundary! 113s Convergence not guaranteed for NPBE/NRPBE calculations! 113s 113s ---------------------------------------- 113s CALCULATION #6 (reference): MULTIGRID 113s Setting up problem... 113s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 113s Debye length: 0 A 113s Current memory usage: 61.207 MB total, 122.102 MB high water 113s Using cubic spline charge discretization. 113s Partition overlap fraction = 0.1 113s Processor array = 2 x 2 x 1 113s Grid dimensions: 65 x 65 x 65 113s Grid spacings: 0.112 x 0.112 x 0.188 113s Grid lengths: 7.178 x 7.178 x 12.000 113s Grid center: (-2.411, 2.411, 0.000) 113s Multigrid levels: 5 113s Molecule ID: 1 113s Linearized traditional PBE 113s Boundary conditions from focusing 113s 0 ion species (0.000 M ionic strength): 113s Solute dielectric: 1.000 113s Solvent dielectric: 1.000 113s Using "molecular" surface definition;harmonic average smoothing 113s Solvent probe radius: 1.400 A 113s Temperature: 298.150 K 113s Electrostatic energies will be calculated 113s Total electrostatic energy = 1.542873949141E+03 kJ/mol 113s Calculating forces... 113s ---------------------------------------- 113s PRINT STATEMENTS 113s 113s print energy 1 (solvated) - 2 (reference) end 113s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 113s Global net ELEC energy = -5.734895146550E+01 kJ/mol 113s ---------------------------------------- 113s CLEANING UP AND SHUTTING DOWN... 113s Destroying force arrays. 113s No energy arrays to destroy. 113s Destroying multigrid structures. 113s Destroying finite element structures. 113s Destroying 1 molecules 113s Final memory usage: 0.001 MB total, 122.102 MB high water 113s 113s 113s Thanks for using APBS! 113s 113s Processor 2 results: 113s 2.383232191909e+02 113s 8.145369593489e+02 113s 1.485524997676e+03 113s 2.977178707146e+02 113s 8.799304557596e+02 113s 1.542873949141e+03 113s -5.734895146550e+01 113s 114s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 114s BINARY: /usr/bin/apbs 114s INPUT: apbs-smol-parallel-PE3.in 114s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 114s asc_getToken: Error occurred (bailing out). 114s Vio_scanf: Format problem with input. 114s 114s 114s ---------------------------------------------------------------------- 114s APBS -- Adaptive Poisson-Boltzmann Solver 114s Version APBS 3.4.1 114s 114s Nathan A. Baker (nathan.baker@pnnl.gov) 114s Pacific Northwest National Laboratory 114s 114s Additional contributing authors listed in the code documentation. 114s 114s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 114s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 114s Northwest Division for the U.S. Department of Energy. 114s 114s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 114s Portions Copyright (c) 2002-2020, Nathan A. Baker. 114s Portions Copyright (c) 1999-2002, The Regents of the University of California. 114s Portions Copyright (c) 1995, Michael Holst. 114s All rights reserved. 114s 114s Redistribution and use in source and binary forms, with or without 114s modification, are permitted provided that the following conditions are met: 114s 114s * Redistributions of source code must retain the above copyright notice, this 114s list of conditions and the following disclaimer. 114s 114s * Redistributions in binary form must reproduce the above copyright notice, 114s this list of conditions and the following disclaimer in the documentation 114s and/or other materials provided with the distribution. 114s 114s * Neither the name of the developer nor the names of its contributors may be 114s used to endorse or promote products derived from this software without 114s specific prior written permission. 114s 114s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 114s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 114s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 114s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 114s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 114s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 114s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 114s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 114s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 114s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 114s ---------------------------------------------------------------------- 114s APBS uses FETK (the Finite Element ToolKit) to solve the 114s Poisson-Boltzmann equation numerically. FETK is a portable collection 114s of finite element modeling class libraries developed by the Michael Holst 114s research group and written in an object-oriented form of C. FEtk is 114s designed to solve general coupled systems of nonlinear partial differential 114s equations using adaptive finite element methods, inexact Newton methods, 114s and algebraic multilevel methods. More information about FEtk may be found 114s at . 114s ---------------------------------------------------------------------- 114s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 114s Aqua is a modified form of the Holst group PMG library 114s which has been modified by Patrice Koehl 114s for improved efficiency and 114s memory usage when solving the Poisson-Boltzmann equation. 114s ---------------------------------------------------------------------- 114s Please cite your use of APBS as: 114s 114s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 114s nanosystems: application to microtubules and the ribosome. Proc. 114s Natl. Acad. Sci. USA 98, 10037-10041 2001. 114s 114s 114s This executable compiled on Jan 3 2025 at 11:01:42 114s 114s Parsing input file apbs-smol-parallel-PE3.in... 114s rank 0 size 1... 114s Parsed input file. 114s Got paths for 1 molecules 114s Reading PQR-format atom data from ion.pqr. 114s 1 atoms 114s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 114s Net charge 1.00e+00 e 114s Preparing to run 6 PBE calculations. 114s ---------------------------------------- 114s CALCULATION #1 (solvated): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.280 MB total, 61.280 MB high water 114s Using cubic spline charge discretization. 114s Partition overlap fraction = 0.1 114s Processor array = 2 x 2 x 1 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.781 x 0.781 x 0.781 114s Grid lengths: 50.000 x 50.000 x 50.000 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Multiple Debye-Huckel sphere boundary conditions 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 78.540 114s Using "molecular" surface definition;harmonic average smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 2.383232191909E+02 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s CALCULATION #2 (solvated): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.280 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Partition overlap fraction = 0.1 114s Processor array = 2 x 2 x 1 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.296 x 0.296 x 0.383 114s Grid lengths: 18.944 x 18.944 x 24.495 114s Grid center: (2.411, 2.411, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 78.540 114s Using "molecular" surface definition;harmonic average smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 8.145419900310E+02 kJ/mol 114s Calculating forces... 114s [focusFillBound()]: WARNING: 114s Unusually large potential values 114s detected on the focusing boundary! 114s Convergence not guaranteed for NPBE/NRPBE calculations! 114s 114s ---------------------------------------- 114s CALCULATION #3 (solvated): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.280 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Partition overlap fraction = 0.1 114s Processor array = 2 x 2 x 1 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.112 x 0.112 x 0.188 114s Grid lengths: 7.178 x 7.178 x 12.000 114s Grid center: (2.411, 2.411, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 78.540 114s Using "molecular" surface definition;harmonic average smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 1.485529328301E+03 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s CALCULATION #4 (reference): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.207 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Partition overlap fraction = 0.1 114s Processor array = 2 x 2 x 1 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.781 x 0.781 x 0.781 114s Grid lengths: 50.000 x 50.000 x 50.000 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Multiple Debye-Huckel sphere boundary conditions 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 1.000 114s Using "molecular" surface definition;harmonic average smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 2.977178707146E+02 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s CALCULATION #5 (reference): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.207 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Partition overlap fraction = 0.1 114s Processor array = 2 x 2 x 1 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.296 x 0.296 x 0.383 114s Grid lengths: 18.944 x 18.944 x 24.495 114s Grid center: (2.411, 2.411, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 1.000 114s Using "molecular" surface definition;harmonic average smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 8.799304557596E+02 kJ/mol 114s Calculating forces... 114s [focusFillBound()]: WARNING: 114s Unusually large potential values 114s detected on the focusing boundary! 114s Convergence not guaranteed for NPBE/NRPBE calculations! 114s 114s ---------------------------------------- 114s CALCULATION #6 (reference): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.207 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Partition overlap fraction = 0.1 114s Processor array = 2 x 2 x 1 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.112 x 0.112 x 0.188 114s Grid lengths: 7.178 x 7.178 x 12.000 114s Grid center: (2.411, 2.411, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 1.000 114s Using "molecular" surface definition;harmonic average smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 1.542873949141E+03 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s PRINT STATEMENTS 114s 114s print energy 1 (solvated) - 2 (reference) end 114s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 114s Global net ELEC energy = -5.734462084052E+01 kJ/mol 114s ---------------------------------------- 114s CLEANING UP AND SHUTTING DOWN... 114s Destroying force arrays. 114s No energy arrays to destroy. 114s Destroying multigrid structures. 114s Destroying finite element structures. 114s Destroying 1 molecules 114s Final memory usage: 0.001 MB total, 122.102 MB high water 114s 114s 114s Thanks for using APBS! 114s 114s Processor 3 results: 114s 2.383232191909e+02 114s 8.145419900310e+02 114s 1.485529328301e+03 114s 2.977178707146e+02 114s 8.799304557596e+02 114s 1.542873949141e+03 114s -5.734462084052e+01 114s 114s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 114s *** PASSED *** 114s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 114s *** PASSED *** 114s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 114s *** PASSED *** 114s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 114s *** PASSED *** 114s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 114s *** PASSED *** 114s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 114s *** PASSED *** 114s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 114s *** PASSED *** 114s Elapsed time: 6.078418 seconds 114s -------------------------------------------------------------------------------- 114s Total elapsed time: 14.846938 seconds 114s Test results have been logged 114s -------------------------------------------------------------------------------- 114s -------------------------------------------------------------------------------- 114s Testing input file apbs-mol-auto.in 114s 175s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 175s EXPECTED COMPUTED: 7 175s EXPECTED EXPECTED: 7 175s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 175s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 175s COMPUTED RESULT 953.292876745 175s COMPUTED RESULT 3258.1578983732998 175s COMPUTED RESULT 5942.108652589999 175s COMPUTED RESULT 1190.8714828309999 175s COMPUTED RESULT 3519.7218230368003 175s COMPUTED RESULT 6171.495796544 175s COMPUTED RESULT -229.38714395599 175s Running tests for actin-dimer-auto section 175s BINARY: /usr/bin/apbs 175s INPUT: apbs-mol-auto.in 175s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 175s asc_getToken: Error occurred (bailing out). 175s Vio_scanf: Format problem with input. 175s 175s 175s ---------------------------------------------------------------------- 175s APBS -- Adaptive Poisson-Boltzmann Solver 175s Version APBS 3.4.1 175s 175s Nathan A. Baker (nathan.baker@pnnl.gov) 175s Pacific Northwest National Laboratory 175s 175s Additional contributing authors listed in the code documentation. 175s 175s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 175s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 175s Northwest Division for the U.S. Department of Energy. 175s 175s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 175s Portions Copyright (c) 2002-2020, Nathan A. Baker. 175s Portions Copyright (c) 1999-2002, The Regents of the University of California. 175s Portions Copyright (c) 1995, Michael Holst. 175s All rights reserved. 175s 175s Redistribution and use in source and binary forms, with or without 175s modification, are permitted provided that the following conditions are met: 175s 175s * Redistributions of source code must retain the above copyright notice, this 175s list of conditions and the following disclaimer. 175s 175s * Redistributions in binary form must reproduce the above copyright notice, 175s this list of conditions and the following disclaimer in the documentation 175s and/or other materials provided with the distribution. 175s 175s * Neither the name of the developer nor the names of its contributors may be 175s used to endorse or promote products derived from this software without 175s specific prior written permission. 175s 175s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 175s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 175s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 175s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 175s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 175s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 175s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 175s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 175s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 175s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 175s ---------------------------------------------------------------------- 175s APBS uses FETK (the Finite Element ToolKit) to solve the 175s Poisson-Boltzmann equation numerically. FETK is a portable collection 175s of finite element modeling class libraries developed by the Michael Holst 175s research group and written in an object-oriented form of C. FEtk is 175s designed to solve general coupled systems of nonlinear partial differential 175s equations using adaptive finite element methods, inexact Newton methods, 175s and algebraic multilevel methods. More information about FEtk may be found 175s at . 175s ---------------------------------------------------------------------- 175s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 175s Aqua is a modified form of the Holst group PMG library 175s which has been modified by Patrice Koehl 175s for improved efficiency and 175s memory usage when solving the Poisson-Boltzmann equation. 175s ---------------------------------------------------------------------- 175s Please cite your use of APBS as: 175s 175s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 175s nanosystems: application to microtubules and the ribosome. Proc. 175s Natl. Acad. Sci. USA 98, 10037-10041 2001. 175s 175s 175s This executable compiled on Jan 3 2025 at 11:01:42 175s 175s Parsing input file apbs-mol-auto.in... 175s rank 0 size 1... 175s Parsed input file. 175s Got paths for 3 molecules 175s Reading PQR-format atom data from mol1.pqr. 175s asc_getToken: Error occurred (bailing out). 175s Vio_scanf: Format problem with input. 175s 5877 atoms 175s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 175s Net charge -1.20e+01 e 175s Reading PQR-format atom data from mol2.pqr. 175s asc_getToken: Error occurred (bailing out). 175s Vio_scanf: Format problem with input. 175s 5877 atoms 175s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 175s Net charge -1.20e+01 e 175s Reading PQR-format atom data from complex.pqr. 175s 11754 atoms 175s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 175s Net charge -2.40e+01 e 175s Preparing to run 6 PBE calculations. 175s ---------------------------------------- 175s CALCULATION #1 (mol1): MULTIGRID 175s Setting up problem... 175s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 175s Debye length: 13.5959 A 175s Current memory usage: 1028.322 MB total, 1028.322 MB high water 175s Using linear spline charge discretization. 175s Grid dimensions: 161 x 161 x 161 175s Grid spacings: 0.975 x 0.756 x 1.012 175s Grid lengths: 156.000 x 121.000 x 162.000 175s Grid center: (2.518, -2.465, 16.742) 175s Multigrid levels: 4 175s Molecule ID: 1 175s Nonlinear traditional PBE 175s Single Debye-Huckel sphere boundary conditions 175s 2 ion species (0.050 M ionic strength): 175s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 175s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 175s Solute dielectric: 2.000 175s Solvent dielectric: 78.400 175s Using "molecular" surface definition; no smoothing 175s Solvent probe radius: 1.400 A 175s Temperature: 298.150 K 175s Electrostatic energies will be calculated 175s Total electrostatic energy = 1.527617850342E+05 kJ/mol 175s Calculating forces... 175s ---------------------------------------- 175s CALCULATION #2 (mol1): MULTIGRID 175s Setting up problem... 175s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 175s Debye length: 13.5959 A 175s Current memory usage: 1028.322 MB total, 2042.113 MB high water 175s Using linear spline charge discretization. 175s Grid dimensions: 161 x 161 x 161 175s Grid spacings: 0.700 x 0.569 x 0.725 175s Grid lengths: 112.000 x 91.000 x 116.000 175s Grid center: (2.518, -2.465, 16.742) 175s Multigrid levels: 4 175s Molecule ID: 1 175s Nonlinear traditional PBE 175s Boundary conditions from focusing 175s 2 ion species (0.050 M ionic strength): 175s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 175s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 175s Solute dielectric: 2.000 175s Solvent dielectric: 78.400 175s Using "molecular" surface definition; no smoothing 175s Solvent probe radius: 1.400 A 175s Temperature: 298.150 K 175s Electrostatic energies will be calculated 175s Total electrostatic energy = 2.919510754196E+05 kJ/mol 175s Calculating forces... 175s ---------------------------------------- 175s CALCULATION #3 (mol2): MULTIGRID 175s Setting up problem... 175s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 175s Debye length: 13.5959 A 175s Current memory usage: 1030.291 MB total, 2042.113 MB high water 175s Using linear spline charge discretization. 175s Grid dimensions: 161 x 161 x 161 175s Grid spacings: 0.975 x 0.756 x 1.012 175s Grid lengths: 156.000 x 121.000 x 162.000 175s Grid center: (2.518, -2.465, 16.742) 175s Multigrid levels: 4 175s Molecule ID: 2 175s Nonlinear traditional PBE 175s Single Debye-Huckel sphere boundary conditions 175s 2 ion species (0.050 M ionic strength): 175s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 175s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 175s Solute dielectric: 2.000 175s Solvent dielectric: 78.400 175s Using "molecular" surface definition; no smoothing 175s Solvent probe radius: 1.400 A 175s Temperature: 298.150 K 175s Electrostatic energies will be calculated 175s Total electrostatic energy = 1.527671844880E+05 kJ/mol 175s Calculating forces... 175s ---------------------------------------- 175s CALCULATION #4 (mol2): MULTIGRID 175s Setting up problem... 175s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 175s Debye length: 13.5959 A 175s Current memory usage: 1030.291 MB total, 2046.048 MB high water 175s Using linear spline charge discretization. 175s Grid dimensions: 161 x 161 x 161 175s Grid spacings: 0.700 x 0.569 x 0.725 175s Grid lengths: 112.000 x 91.000 x 116.000 175s Grid center: (2.518, -2.465, 16.742) 175s Multigrid levels: 4 175s Molecule ID: 2 175s Nonlinear traditional PBE 175s Boundary conditions from focusing 175s 2 ion species (0.050 M ionic strength): 175s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 175s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 175s Solute dielectric: 2.000 175s Solvent dielectric: 78.400 175s Using "molecular" surface definition; no smoothing 175s Solvent probe radius: 1.400 A 175s Temperature: 298.150 K 175s Electrostatic energies will be calculated 175s Total electrostatic energy = 2.915468859278E+05 kJ/mol 175s Calculating forces... 175s ---------------------------------------- 175s CALCULATION #5 (complex): MULTIGRID 175s Setting up problem... 175s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 175s Debye length: 13.5959 A 175s Current memory usage: 1046.446 MB total, 2046.048 MB high water 175s Using linear spline charge discretization. 175s Grid dimensions: 161 x 161 x 161 175s Grid spacings: 0.975 x 0.756 x 1.012 175s Grid lengths: 156.000 x 121.000 x 162.000 175s Grid center: (2.518, -2.465, 16.742) 175s Multigrid levels: 4 175s Molecule ID: 3 175s Nonlinear traditional PBE 175s Single Debye-Huckel sphere boundary conditions 175s 2 ion species (0.050 M ionic strength): 175s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 175s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 175s Solute dielectric: 2.000 175s Solvent dielectric: 78.400 175s Using "molecular" surface definition; no smoothing 175s Solvent probe radius: 1.400 A 175s Temperature: 298.150 K 175s Electrostatic energies will be calculated 175s Total electrostatic energy = 3.056317807611E+05 kJ/mol 175s Calculating forces... 175s ---------------------------------------- 175s CALCULATION #6 (complex): MULTIGRID 175s Setting up problem... 175s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 175s Debye length: 13.5959 A 175s Current memory usage: 1046.446 MB total, 2069.492 MB high water 175s Using linear spline charge discretization. 175s Grid dimensions: 161 x 161 x 161 175s Grid spacings: 0.700 x 0.569 x 0.725 175s Grid lengths: 112.000 x 91.000 x 116.000 175s Grid center: (2.518, -2.465, 16.742) 175s Multigrid levels: 4 175s Molecule ID: 3 175s Nonlinear traditional PBE 175s Boundary conditions from focusing 175s 2 ion species (0.050 M ionic strength): 175s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 175s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 175s Solute dielectric: 2.000 175s Solvent dielectric: 78.400 175s Using "molecular" surface definition; no smoothing 175s Solvent probe radius: 1.400 A 175s Temperature: 298.150 K 175s Electrostatic energies will be calculated 175s Total electrostatic energy = 5.836028296532E+05 kJ/mol 175s Calculating forces... 175s ---------------------------------------- 175s PRINT STATEMENTS 175s 175s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 175s Local net energy (PE 0) = 1.048683058621E+02 kJ/mol 175s Global net ELEC energy = 1.048683058621E+02 kJ/mol 175s ---------------------------------------- 175s CLEANING UP AND SHUTTING DOWN... 175s Destroying force arrays. 175s No energy arrays to destroy. 175s Destroying multigrid structures. 175s Destroying finite element structures. 175s Destroying 3 molecules 175s Final memory usage: 0.001 MB total, 2069.492 MB high water 175s 175s 175s Thanks for using APBS! 175s 175s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 175s *** PASSED *** 175s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 175s *** PASSED *** 175s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 175s *** PASSED *** 175s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 175s *** PASSED *** 175s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 175s *** PASSED *** 175s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 175s *** PASSED *** 175s Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) 175s *** PASSED *** 175s Elapsed time: 61.073492 seconds 175s -------------------------------------------------------------------------------- 175s -------------------------------------------------------------------------------- 175s Testing input file apbs-smol-auto.in 175s 221s Checking for intermediate energies in input file apbs-mol-auto.out 221s EXPECTED COMPUTED: 7 221s EXPECTED EXPECTED: 7 221s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] 221s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 221s COMPUTED RESULT 152761.7850342 221s COMPUTED RESULT 291951.0754196 221s COMPUTED RESULT 152767.184488 221s COMPUTED RESULT 291546.8859278 221s COMPUTED RESULT 305631.7807611 221s COMPUTED RESULT 583602.8296532 221s COMPUTED RESULT 104.8683058621 221s BINARY: /usr/bin/apbs 221s INPUT: apbs-smol-auto.in 221s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 221s asc_getToken: Error occurred (bailing out). 221s Vio_scanf: Format problem with input. 221s 221s 221s ---------------------------------------------------------------------- 221s APBS -- Adaptive Poisson-Boltzmann Solver 221s Version APBS 3.4.1 221s 221s Nathan A. Baker (nathan.baker@pnnl.gov) 221s Pacific Northwest National Laboratory 221s 221s Additional contributing authors listed in the code documentation. 221s 221s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 221s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 221s Northwest Division for the U.S. Department of Energy. 221s 221s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 221s Portions Copyright (c) 2002-2020, Nathan A. Baker. 221s Portions Copyright (c) 1999-2002, The Regents of the University of California. 221s Portions Copyright (c) 1995, Michael Holst. 221s All rights reserved. 221s 221s Redistribution and use in source and binary forms, with or without 221s modification, are permitted provided that the following conditions are met: 221s 221s * Redistributions of source code must retain the above copyright notice, this 221s list of conditions and the following disclaimer. 221s 221s * Redistributions in binary form must reproduce the above copyright notice, 221s this list of conditions and the following disclaimer in the documentation 221s and/or other materials provided with the distribution. 221s 221s * Neither the name of the developer nor the names of its contributors may be 221s used to endorse or promote products derived from this software without 221s specific prior written permission. 221s 221s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 221s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 221s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 221s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 221s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 221s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 221s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 221s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 221s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 221s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 221s ---------------------------------------------------------------------- 221s APBS uses FETK (the Finite Element ToolKit) to solve the 221s Poisson-Boltzmann equation numerically. FETK is a portable collection 221s of finite element modeling class libraries developed by the Michael Holst 221s research group and written in an object-oriented form of C. FEtk is 221s designed to solve general coupled systems of nonlinear partial differential 221s equations using adaptive finite element methods, inexact Newton methods, 221s and algebraic multilevel methods. More information about FEtk may be found 221s at . 221s ---------------------------------------------------------------------- 221s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 221s Aqua is a modified form of the Holst group PMG library 221s which has been modified by Patrice Koehl 221s for improved efficiency and 221s memory usage when solving the Poisson-Boltzmann equation. 221s ---------------------------------------------------------------------- 221s Please cite your use of APBS as: 221s 221s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 221s nanosystems: application to microtubules and the ribosome. Proc. 221s Natl. Acad. Sci. USA 98, 10037-10041 2001. 221s 221s 221s This executable compiled on Jan 3 2025 at 11:01:42 221s 221s Parsing input file apbs-smol-auto.in... 221s rank 0 size 1... 221s Parsed input file. 221s Got paths for 3 molecules 221s Reading PQR-format atom data from mol1.pqr. 221s asc_getToken: Error occurred (bailing out). 221s Vio_scanf: Format problem with input. 221s 5877 atoms 221s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 221s Net charge -1.20e+01 e 221s Reading PQR-format atom data from mol2.pqr. 221s asc_getToken: Error occurred (bailing out). 221s Vio_scanf: Format problem with input. 221s 5877 atoms 221s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 221s Net charge -1.20e+01 e 221s Reading PQR-format atom data from complex.pqr. 221s 11754 atoms 221s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 221s Net charge -2.40e+01 e 221s Preparing to run 6 PBE calculations. 221s ---------------------------------------- 221s CALCULATION #1 (mol1): MULTIGRID 221s Setting up problem... 221s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 221s Debye length: 13.5959 A 221s Current memory usage: 1028.322 MB total, 1028.322 MB high water 221s Using linear spline charge discretization. 221s Grid dimensions: 161 x 161 x 161 221s Grid spacings: 0.975 x 0.756 x 1.012 221s Grid lengths: 156.000 x 121.000 x 162.000 221s Grid center: (2.518, -2.465, 16.742) 221s Multigrid levels: 4 221s Molecule ID: 1 221s Nonlinear traditional PBE 221s Single Debye-Huckel sphere boundary conditions 221s 2 ion species (0.050 M ionic strength): 221s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 221s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 221s Solute dielectric: 2.000 221s Solvent dielectric: 78.400 221s Using "molecular" surface definition;harmonic average smoothing 221s Solvent probe radius: 1.400 A 221s Temperature: 298.150 K 221s Electrostatic energies will be calculated 221s Total electrostatic energy = 1.528632421825E+05 kJ/mol 221s Calculating forces... 221s ---------------------------------------- 221s CALCULATION #2 (mol1): MULTIGRID 221s Setting up problem... 221s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 221s Debye length: 13.5959 A 221s Current memory usage: 1028.322 MB total, 2042.113 MB high water 221s Using linear spline charge discretization. 221s Grid dimensions: 161 x 161 x 161 221s Grid spacings: 0.700 x 0.569 x 0.725 221s Grid lengths: 112.000 x 91.000 x 116.000 221s Grid center: (2.518, -2.465, 16.742) 221s Multigrid levels: 4 221s Molecule ID: 1 221s Nonlinear traditional PBE 221s Boundary conditions from focusing 221s 2 ion species (0.050 M ionic strength): 221s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 221s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 221s Solute dielectric: 2.000 221s Solvent dielectric: 78.400 221s Using "molecular" surface definition;harmonic average smoothing 221s Solvent probe radius: 1.400 A 221s Temperature: 298.150 K 221s Electrostatic energies will be calculated 221s Total electrostatic energy = 2.920618662320E+05 kJ/mol 221s Calculating forces... 221s ---------------------------------------- 221s CALCULATION #3 (mol2): MULTIGRID 221s Setting up problem... 221s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 221s Debye length: 13.5959 A 221s Current memory usage: 1030.291 MB total, 2042.113 MB high water 221s Using linear spline charge discretization. 221s Grid dimensions: 161 x 161 x 161 221s Grid spacings: 0.975 x 0.756 x 1.012 221s Grid lengths: 156.000 x 121.000 x 162.000 221s Grid center: (2.518, -2.465, 16.742) 221s Multigrid levels: 4 221s Molecule ID: 2 221s Nonlinear traditional PBE 221s Single Debye-Huckel sphere boundary conditions 221s 2 ion species (0.050 M ionic strength): 221s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 221s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 221s Solute dielectric: 2.000 221s Solvent dielectric: 78.400 221s Using "molecular" surface definition;harmonic average smoothing 221s Solvent probe radius: 1.400 A 221s Temperature: 298.150 K 221s Electrostatic energies will be calculated 221s Total electrostatic energy = 1.529297900572E+05 kJ/mol 221s Calculating forces... 221s ---------------------------------------- 221s CALCULATION #4 (mol2): MULTIGRID 221s Setting up problem... 221s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 221s Debye length: 13.5959 A 221s Current memory usage: 1030.291 MB total, 2046.048 MB high water 221s Using linear spline charge discretization. 221s Grid dimensions: 161 x 161 x 161 221s Grid spacings: 0.700 x 0.569 x 0.725 221s Grid lengths: 112.000 x 91.000 x 116.000 221s Grid center: (2.518, -2.465, 16.742) 221s Multigrid levels: 4 221s Molecule ID: 2 221s Nonlinear traditional PBE 221s Boundary conditions from focusing 221s 2 ion species (0.050 M ionic strength): 221s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 221s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 221s Solute dielectric: 2.000 221s Solvent dielectric: 78.400 221s Using "molecular" surface definition;harmonic average smoothing 221s Solvent probe radius: 1.400 A 221s Temperature: 298.150 K 221s Electrostatic energies will be calculated 221s Total electrostatic energy = 2.916592202835E+05 kJ/mol 221s Calculating forces... 221s ---------------------------------------- 221s CALCULATION #5 (complex): MULTIGRID 221s Setting up problem... 221s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 221s Debye length: 13.5959 A 221s Current memory usage: 1046.446 MB total, 2046.048 MB high water 221s Using linear spline charge discretization. 221s Grid dimensions: 161 x 161 x 161 221s Grid spacings: 0.975 x 0.756 x 1.012 221s Grid lengths: 156.000 x 121.000 x 162.000 221s Grid center: (2.518, -2.465, 16.742) 221s Multigrid levels: 4 221s Molecule ID: 3 221s Nonlinear traditional PBE 221s Single Debye-Huckel sphere boundary conditions 221s 2 ion species (0.050 M ionic strength): 221s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 221s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 221s Solute dielectric: 2.000 221s Solvent dielectric: 78.400 221s Using "molecular" surface definition;harmonic average smoothing 221s Solvent probe radius: 1.400 A 221s Temperature: 298.150 K 221s Electrostatic energies will be calculated 221s Total electrostatic energy = 3.059244262535E+05 kJ/mol 221s Calculating forces... 221s ---------------------------------------- 221s CALCULATION #6 (complex): MULTIGRID 221s Setting up problem... 221s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 221s Debye length: 13.5959 A 221s Current memory usage: 1046.446 MB total, 2069.492 MB high water 221s Using linear spline charge discretization. 221s Grid dimensions: 161 x 161 x 161 221s Grid spacings: 0.700 x 0.569 x 0.725 221s Grid lengths: 112.000 x 91.000 x 116.000 221s Grid center: (2.518, -2.465, 16.742) 221s Multigrid levels: 4 221s Molecule ID: 3 221s Nonlinear traditional PBE 221s Boundary conditions from focusing 221s 2 ion species (0.050 M ionic strength): 221s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 221s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 221s Solute dielectric: 2.000 221s Solvent dielectric: 78.400 221s Using "molecular" surface definition;harmonic average smoothing 221s Solvent probe radius: 1.400 A 221s Temperature: 298.150 K 221s Electrostatic energies will be calculated 221s Total electrostatic energy = 5.838306706232E+05 kJ/mol 221s Calculating forces... 221s ---------------------------------------- 221s PRINT STATEMENTS 221s 221s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 221s Local net energy (PE 0) = 1.095841077688E+02 kJ/mol 221s Global net ELEC energy = 1.095841077688E+02 kJ/mol 221s ---------------------------------------- 221s CLEANING UP AND SHUTTING DOWN... 221s Destroying force arrays. 221s No energy arrays to destroy. 221s Destroying multigrid structures. 221s Destroying finite element structures. 221s Destroying 3 molecules 221s Final memory usage: 0.001 MB total, 2069.492 MB high water 221s 221s 221s Thanks for using APBS! 221s 221s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 221s *** PASSED *** 221s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 221s *** PASSED *** 221s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 221s *** PASSED *** 221s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 221s *** PASSED *** 221s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 221s *** PASSED *** 221s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 221s *** PASSED *** 221s Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) 221s *** PASSED *** 221s Elapsed time: 45.40873 seconds 221s -------------------------------------------------------------------------------- 221s Total elapsed time: 106.482222 seconds 221s Test results have been logged 221s -------------------------------------------------------------------------------- 221s -------------------------------------------------------------------------------- 221s Testing input file alkanes.in 221s 234s Checking for intermediate energies in input file apbs-smol-auto.out 234s EXPECTED COMPUTED: 7 234s EXPECTED EXPECTED: 7 234s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] 234s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 234s COMPUTED RESULT 152863.2421825 234s COMPUTED RESULT 292061.866232 234s COMPUTED RESULT 152929.7900572 234s COMPUTED RESULT 291659.2202835 234s COMPUTED RESULT 305924.4262535 234s COMPUTED RESULT 583830.6706232 234s COMPUTED RESULT 109.5841077688 234s Running tests for alkanes section 234s BINARY: /usr/bin/apbs 234s INPUT: alkanes.in 234s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 234s 234s ---------------------------------------------------------------------- 234s APBS -- Adaptive Poisson-Boltzmann Solver 234s Version APBS 3.4.1 234s 234s Nathan A. Baker (nathan.baker@pnnl.gov) 234s Pacific Northwest National Laboratory 234s 234s Additional contributing authors listed in the code documentation. 234s 234s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 234s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 234s Northwest Division for the U.S. Department of Energy. 234s 234s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 234s Portions Copyright (c) 2002-2020, Nathan A. Baker. 234s Portions Copyright (c) 1999-2002, The Regents of the University of California. 234s Portions Copyright (c) 1995, Michael Holst. 234s All rights reserved. 234s 234s Redistribution and use in source and binary forms, with or without 234s modification, are permitted provided that the following conditions are met: 234s 234s * Redistributions of source code must retain the above copyright notice, this 234s list of conditions and the following disclaimer. 234s 234s * Redistributions in binary form must reproduce the above copyright notice, 234s this list of conditions and the following disclaimer in the documentation 234s and/or other materials provided with the distribution. 234s 234s * Neither the name of the developer nor the names of its contributors may be 234s used to endorse or promote products derived from this software without 234s specific prior written permission. 234s 234s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 234s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 234s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 234s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 234s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 234s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 234s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 234s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 234s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 234s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 234s ---------------------------------------------------------------------- 234s APBS uses FETK (the Finite Element ToolKit) to solve the 234s Poisson-Boltzmann equation numerically. FETK is a portable collection 234s of finite element modeling class libraries developed by the Michael Holst 234s research group and written in an object-oriented form of C. FEtk is 234s designed to solve general coupled systems of nonlinear partial differential 234s equations using adaptive finite element methods, inexact Newton methods, 234s and algebraic multilevel methods. More information about FEtk may be found 234s at . 234s ---------------------------------------------------------------------- 234s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 234s Aqua is a modified form of the Holst group PMG library 234s which has been modified by Patrice Koehl 234s for improved efficiency and 234s memory usage when solving the Poisson-Boltzmann equation. 234s ---------------------------------------------------------------------- 234s Please cite your use of APBS as: 234s 234s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 234s nanosystems: application to microtubules and the ribosome. Proc. 234s Natl. Acad. Sci. USA 98, 10037-10041 2001. 234s 234s 234s This executable compiled on Jan 3 2025 at 11:01:42 234s 234s Parsing input file alkanes.in... 234s rank 0 size 1... 234s Parsed input file. 234s Reading parameter data from parm.dat. 234s Got paths for 11 molecules 234s Reading PDB-format atom data from 2-methylbutane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 17 atoms 234s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 234s Net charge 4.33e+00 e 234s Reading PDB-format atom data from butane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 14 atoms 234s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 234s Net charge 3.51e+00 e 234s Reading PDB-format atom data from cyclohexane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 18 atoms 234s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 234s Net charge 4.93e+00 e 234s Reading PDB-format atom data from cyclopentane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 13 atoms 234s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 234s Net charge 3.88e+00 e 234s Reading PDB-format atom data from ethane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 8 atoms 234s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 234s Net charge 1.87e+00 e 234s Reading PDB-format atom data from hexane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 20 atoms 234s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 234s Net charge 5.16e+00 e 234s Reading PDB-format atom data from isobutane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 14 atoms 234s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 234s Net charge 3.51e+00 e 234s Reading PDB-format atom data from methane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 5 atoms 234s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 234s Net charge 1.05e+00 e 234s Reading PDB-format atom data from neopentane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 17 atoms 234s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 234s Net charge 4.33e+00 e 234s Reading PDB-format atom data from pentane.pdb. 234s asc_getToken: Error occurred (bailing out). 234s Vio_scanf: Format problem with input. 234s 17 atoms 234s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 234s Net charge 4.33e+00 e 234s Reading PDB-format atom data from propane.pdb. 234s 11 atoms 234s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 234s Net charge 2.69e+00 e 234s Preparing to run 11 PBE calculations. 234s ---------------------------------------- 234s CALCULATION #1 (solvated-2-methylbutane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 3.815624614267E+00 234s SASA for atom 1: 0.000000000000E+00 234s SASA for atom 2: 6.122920124655E-01 234s SASA for atom 3: 3.957497153740E+00 234s SASA for atom 4: 4.308445014544E+00 234s SASA for atom 5: 1.843264951960E+01 234s SASA for atom 6: 1.837011296483E+01 234s SASA for atom 7: 1.666599184724E+01 234s SASA for atom 8: 1.480031796315E+01 234s SASA for atom 9: 1.603020354037E+01 234s SASA for atom 10: 1.473778140838E+01 234s SASA for atom 11: 1.611879699297E+01 234s SASA for atom 12: 1.810954398660E+01 234s SASA for atom 13: 1.420100931324E+01 234s SASA for atom 14: 1.437298483886E+01 234s SASA for atom 15: 1.814081226399E+01 234s SASA for atom 16: 2.152820898091E+01 234s 234s Total solvent accessible surface area: 214.202 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 3.243280922127E-02 234s Surface tension*area energy for atom 1: 0.000000000000E+00 234s Surface tension*area energy for atom 2: 5.204482105957E-03 234s Surface tension*area energy for atom 3: 3.363872580679E-02 234s Surface tension*area energy for atom 4: 3.662178262362E-02 234s Surface tension*area energy for atom 5: 1.566775209166E-01 234s Surface tension*area energy for atom 6: 1.561459602010E-01 234s Surface tension*area energy for atom 7: 1.416609307015E-01 234s Surface tension*area energy for atom 8: 1.258027026868E-01 234s Surface tension*area energy for atom 9: 1.362567300932E-01 234s Surface tension*area energy for atom 10: 1.252711419712E-01 234s Surface tension*area energy for atom 11: 1.370097744402E-01 234s Surface tension*area energy for atom 12: 1.539311238861E-01 234s Surface tension*area energy for atom 13: 1.207085791625E-01 234s Surface tension*area energy for atom 14: 1.221703711303E-01 234s Surface tension*area energy for atom 15: 1.541969042439E-01 234s Surface tension*area energy for atom 16: 1.829897763377E-01 234s 234s Total surface tension energy: 1.82072 kJ/mol 234s 234s Total solvent accessible volume: 253.665 A^3 234s 234s Total pressure*volume energy: 60.7274 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.271287875274E+00 234s WCA energy for atom 1: -5.600872869478E+00 234s WCA energy for atom 2: -5.773775123943E+00 234s WCA energy for atom 3: -6.072801488986E+00 234s WCA energy for atom 4: -6.378470721845E+00 234s WCA energy for atom 5: -1.573474558351E+00 234s WCA energy for atom 6: -1.582338715648E+00 234s WCA energy for atom 7: -1.504044838266E+00 234s WCA energy for atom 8: -1.351002262819E+00 234s WCA energy for atom 9: -1.437367175239E+00 234s WCA energy for atom 10: -1.384626257493E+00 234s WCA energy for atom 11: -1.468867560891E+00 234s WCA energy for atom 12: -1.557005662832E+00 234s WCA energy for atom 13: -1.473759654043E+00 234s WCA energy for atom 14: -1.502261431335E+00 234s WCA energy for atom 15: -1.550940901474E+00 234s WCA energy for atom 16: -1.667828659696E+00 234s 234s Total WCA energy: -48.1507 kJ/mol 234s 234s Total non-polar energy = 1.439739455792E+01 kJ/mol 234s ---------------------------------------- 234s CALCULATION #2 (solvated-butane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 4.405515699447E+00 234s SASA for atom 1: 8.213673337951E-01 234s SASA for atom 2: 8.064333822716E-01 234s SASA for atom 3: 4.375647796400E+00 234s SASA for atom 4: 1.855251124959E+01 234s SASA for atom 5: 2.147609518526E+01 234s SASA for atom 6: 1.852645435176E+01 234s SASA for atom 7: 1.660345529247E+01 234s SASA for atom 8: 1.658782115377E+01 234s SASA for atom 9: 1.658260977421E+01 234s SASA for atom 10: 1.658260977421E+01 234s SASA for atom 11: 2.145003828744E+01 234s SASA for atom 12: 1.852124297220E+01 234s SASA for atom 13: 1.856293400871E+01 234s 234s Total solvent accessible surface area: 193.855 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 3.744688344530E-02 234s Surface tension*area energy for atom 1: 6.981622337259E-03 234s Surface tension*area energy for atom 2: 6.854683749309E-03 234s Surface tension*area energy for atom 3: 3.719300626940E-02 234s Surface tension*area energy for atom 4: 1.576963456215E-01 234s Surface tension*area energy for atom 5: 1.825468090747E-01 234s Surface tension*area energy for atom 6: 1.574748619900E-01 234s Surface tension*area energy for atom 7: 1.411293699860E-01 234s Surface tension*area energy for atom 8: 1.409964798071E-01 234s Surface tension*area energy for atom 9: 1.409521830808E-01 234s Surface tension*area energy for atom 10: 1.409521830808E-01 234s Surface tension*area energy for atom 11: 1.823253254433E-01 234s Surface tension*area energy for atom 12: 1.574305652637E-01 234s Surface tension*area energy for atom 13: 1.577849390741E-01 234s 234s Total surface tension energy: 1.64777 kJ/mol 234s 234s Total solvent accessible volume: 217.863 A^3 234s 234s Total pressure*volume energy: 52.1564 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.728858147814E+00 234s WCA energy for atom 1: -6.204037472587E+00 234s WCA energy for atom 2: -6.202937735018E+00 234s WCA energy for atom 3: -6.728762249931E+00 234s WCA energy for atom 4: -1.623549989062E+00 234s WCA energy for atom 5: -1.709092300778E+00 234s WCA energy for atom 6: -1.625196457114E+00 234s WCA energy for atom 7: -1.484289341167E+00 234s WCA energy for atom 8: -1.485410538626E+00 234s WCA energy for atom 9: -1.485593139015E+00 234s WCA energy for atom 10: -1.484878734279E+00 234s WCA energy for atom 11: -1.708585062695E+00 234s WCA energy for atom 12: -1.625094916482E+00 234s WCA energy for atom 13: -1.624416805392E+00 234s 234s Total WCA energy: -41.7207 kJ/mol 234s 234s Total non-polar energy = 1.208346456826E+01 kJ/mol 234s ---------------------------------------- 234s CALCULATION #3 (solvated-cyclohexane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 7.840324549863E-01 234s SASA for atom 1: 8.064333822716E-01 234s SASA for atom 2: 8.288343095569E-01 234s SASA for atom 3: 7.840324549863E-01 234s SASA for atom 4: 7.989664065098E-01 234s SASA for atom 5: 8.363012853187E-01 234s SASA for atom 6: 2.001169752764E+01 234s SASA for atom 7: 1.616048802948E+01 234s SASA for atom 8: 2.001169752764E+01 234s SASA for atom 9: 1.619175630687E+01 234s SASA for atom 10: 1.616048802948E+01 234s SASA for atom 11: 1.993352683418E+01 234s SASA for atom 12: 2.001169752764E+01 234s SASA for atom 13: 1.618133354774E+01 234s SASA for atom 14: 1.617091078861E+01 234s SASA for atom 15: 2.001690890721E+01 234s SASA for atom 16: 1.993873821374E+01 234s SASA for atom 17: 1.617091078861E+01 234s 234s Total solvent accessible surface area: 221.799 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 6.664275867383E-03 234s Surface tension*area energy for atom 1: 6.854683749309E-03 234s Surface tension*area energy for atom 2: 7.045091631234E-03 234s Surface tension*area energy for atom 3: 6.664275867383E-03 234s Surface tension*area energy for atom 4: 6.791214455333E-03 234s Surface tension*area energy for atom 5: 7.108560925209E-03 234s Surface tension*area energy for atom 6: 1.700994289850E-01 234s Surface tension*area energy for atom 7: 1.373641482506E-01 234s Surface tension*area energy for atom 8: 1.700994289850E-01 234s Surface tension*area energy for atom 9: 1.376299286084E-01 234s Surface tension*area energy for atom 10: 1.373641482506E-01 234s Surface tension*area energy for atom 11: 1.694349780905E-01 234s Surface tension*area energy for atom 12: 1.700994289850E-01 234s Surface tension*area energy for atom 13: 1.375413351558E-01 234s Surface tension*area energy for atom 14: 1.374527417032E-01 234s Surface tension*area energy for atom 15: 1.701437257113E-01 234s Surface tension*area energy for atom 16: 1.694792748168E-01 234s Surface tension*area energy for atom 17: 1.374527417032E-01 234s 234s Total surface tension energy: 1.88529 kJ/mol 234s 234s Total solvent accessible volume: 267.435 A^3 234s 234s Total pressure*volume energy: 64.0239 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -5.793234697241E+00 234s WCA energy for atom 1: -5.784370526583E+00 234s WCA energy for atom 2: -5.791799130412E+00 234s WCA energy for atom 3: -5.788504399087E+00 234s WCA energy for atom 4: -5.797319672490E+00 234s WCA energy for atom 5: -5.787358035342E+00 234s WCA energy for atom 6: -1.523887929614E+00 234s WCA energy for atom 7: -1.413678912317E+00 234s WCA energy for atom 8: -1.521751604392E+00 234s WCA energy for atom 9: -1.414741802525E+00 234s WCA energy for atom 10: -1.413367854344E+00 234s WCA energy for atom 11: -1.523407238081E+00 234s WCA energy for atom 12: -1.523000623583E+00 234s WCA energy for atom 13: -1.413922068538E+00 234s WCA energy for atom 14: -1.416316744211E+00 234s WCA energy for atom 15: -1.524577474659E+00 234s WCA energy for atom 16: -1.523300410052E+00 234s WCA energy for atom 17: -1.414522566061E+00 234s 234s Total WCA energy: -52.3691 kJ/mol 234s 234s Total non-polar energy = 1.354016672221E+01 kJ/mol 234s ---------------------------------------- 234s CALCULATION #4 (solvated-cyclopentane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 9.490526193215E+00 234s SASA for atom 1: 9.512927120500E+00 234s SASA for atom 2: 2.299828534626E+00 234s SASA for atom 3: 1.919012770776E+00 234s SASA for atom 4: 2.307295510388E+00 234s SASA for atom 5: 2.325838699632E+01 234s SASA for atom 6: 2.325838699632E+01 234s SASA for atom 7: 2.045987617019E+01 234s SASA for atom 8: 2.067875411190E+01 234s SASA for atom 9: 2.028790064456E+01 234s SASA for atom 10: 1.897463299431E+01 234s SASA for atom 11: 2.048593306801E+01 234s SASA for atom 12: 2.070481100972E+01 234s 234s Total solvent accessible surface area: 193.638 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 8.066947264233E-02 234s Surface tension*area energy for atom 1: 8.085988052425E-02 234s Surface tension*area energy for atom 2: 1.954854254432E-02 234s Surface tension*area energy for atom 3: 1.631160855160E-02 234s Surface tension*area energy for atom 4: 1.961201183830E-02 234s Surface tension*area energy for atom 5: 1.976962894687E-01 234s Surface tension*area energy for atom 6: 1.976962894687E-01 234s Surface tension*area energy for atom 7: 1.739089474466E-01 234s Surface tension*area energy for atom 8: 1.757694099511E-01 234s Surface tension*area energy for atom 9: 1.724471554788E-01 234s Surface tension*area energy for atom 10: 1.612843804516E-01 234s Surface tension*area energy for atom 11: 1.741304310781E-01 234s Surface tension*area energy for atom 12: 1.759908935826E-01 234s 234s Total surface tension energy: 1.64593 kJ/mol 234s 234s Total solvent accessible volume: 217.998 A^3 234s 234s Total pressure*volume energy: 52.1887 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.343496616804E+00 234s WCA energy for atom 1: -6.327869601807E+00 234s WCA energy for atom 2: -6.334858040579E+00 234s WCA energy for atom 3: -6.296075406417E+00 234s WCA energy for atom 4: -6.345600816761E+00 234s WCA energy for atom 5: -1.663697465126E+00 234s WCA energy for atom 6: -1.662444032853E+00 234s WCA energy for atom 7: -1.572325104493E+00 234s WCA energy for atom 8: -1.604626551065E+00 234s WCA energy for atom 9: -1.586431484963E+00 234s WCA energy for atom 10: -1.554291291374E+00 234s WCA energy for atom 11: -1.574315220751E+00 234s WCA energy for atom 12: -1.604941679892E+00 234s 234s Total WCA energy: -44.471 kJ/mol 234s 234s Total non-polar energy = 9.363673200142E+00 kJ/mol 234s ---------------------------------------- 234s CALCULATION #5 (solvated-ethane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 5.995981536705E+00 234s SASA for atom 1: 5.966113633657E+00 234s SASA for atom 2: 2.121552620704E+01 234s SASA for atom 3: 2.124158310486E+01 234s SASA for atom 4: 2.125200586399E+01 234s SASA for atom 5: 2.123116034573E+01 234s SASA for atom 6: 2.125200586399E+01 234s SASA for atom 7: 2.127285138225E+01 234s 234s Total solvent accessible surface area: 139.427 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 5.096584306199E-02 234s Surface tension*area energy for atom 1: 5.071196588609E-02 234s Surface tension*area energy for atom 2: 1.803319727598E-01 234s Surface tension*area energy for atom 3: 1.805534563913E-01 234s Surface tension*area energy for atom 4: 1.806420498439E-01 234s Surface tension*area energy for atom 5: 1.804648629387E-01 234s Surface tension*area energy for atom 6: 1.806420498439E-01 234s Surface tension*area energy for atom 7: 1.808192367491E-01 234s 234s Total surface tension energy: 1.18513 kJ/mol 234s 234s Total solvent accessible volume: 140.346 A^3 234s 234s Total pressure*volume energy: 33.5988 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -7.360066353115E+00 234s WCA energy for atom 1: -7.355483516201E+00 234s WCA energy for atom 2: -1.776106201066E+00 234s WCA energy for atom 3: -1.773973940651E+00 234s WCA energy for atom 4: -1.775401936843E+00 234s WCA energy for atom 5: -1.773464835521E+00 234s WCA energy for atom 6: -1.774382856097E+00 234s WCA energy for atom 7: -1.772366599434E+00 234s 234s Total WCA energy: -25.3612 kJ/mol 234s 234s Total non-polar energy = 9.422717598546E+00 kJ/mol 234s ---------------------------------------- 234s CALCULATION #6 (solvated-hexane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 4.405515699447E+00 234s SASA for atom 1: 8.213673337951E-01 234s SASA for atom 2: 3.285469335181E-01 234s SASA for atom 3: 2.986790304710E-01 234s SASA for atom 4: 1.855251124959E+01 234s SASA for atom 5: 2.147609518526E+01 234s SASA for atom 6: 1.852645435176E+01 234s SASA for atom 7: 1.655655287639E+01 234s SASA for atom 8: 1.655134149682E+01 234s SASA for atom 9: 1.360170066332E+01 234s SASA for atom 10: 1.357043238593E+01 234s SASA for atom 11: 1.381536722546E+01 234s SASA for atom 12: 1.384142412329E+01 234s SASA for atom 13: 7.765654792245E-01 234s SASA for atom 14: 1.684839013200E+01 234s SASA for atom 15: 1.682233323417E+01 234s SASA for atom 16: 4.166572475070E+00 234s SASA for atom 17: 2.179398933870E+01 234s SASA for atom 18: 1.877660057086E+01 234s SASA for atom 19: 1.876096643216E+01 234s 234s Total solvent accessible surface area: 250.291 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 3.744688344530E-02 234s Surface tension*area energy for atom 1: 6.981622337259E-03 234s Surface tension*area energy for atom 2: 2.792648934903E-03 234s Surface tension*area energy for atom 3: 2.538771759003E-03 234s Surface tension*area energy for atom 4: 1.576963456215E-01 234s Surface tension*area energy for atom 5: 1.825468090747E-01 234s Surface tension*area energy for atom 6: 1.574748619900E-01 234s Surface tension*area energy for atom 7: 1.407306994493E-01 234s Surface tension*area energy for atom 8: 1.406864027230E-01 234s Surface tension*area energy for atom 9: 1.156144556382E-01 234s Surface tension*area energy for atom 10: 1.153486752804E-01 234s Surface tension*area energy for atom 11: 1.174306214164E-01 234s Surface tension*area energy for atom 12: 1.176521050479E-01 234s Surface tension*area energy for atom 13: 6.600806573408E-03 234s Surface tension*area energy for atom 14: 1.432113161220E-01 234s Surface tension*area energy for atom 15: 1.429898324905E-01 234s Surface tension*area energy for atom 16: 3.541586603809E-02 234s Surface tension*area energy for atom 17: 1.852489093789E-01 234s Surface tension*area energy for atom 18: 1.596011048523E-01 234s Surface tension*area energy for atom 19: 1.594682146734E-01 234s 234s Total surface tension energy: 2.12748 kJ/mol 234s 234s Total solvent accessible volume: 298.053 A^3 234s 234s Total pressure*volume energy: 71.3539 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.635406071935E+00 234s WCA energy for atom 1: -5.957247427848E+00 234s WCA energy for atom 2: -5.524801144538E+00 234s WCA energy for atom 3: -5.522294168859E+00 234s WCA energy for atom 4: -1.605314409440E+00 234s WCA energy for atom 5: -1.701051761776E+00 234s WCA energy for atom 6: -1.606669162773E+00 234s WCA energy for atom 7: -1.442505934938E+00 234s WCA energy for atom 8: -1.443059002759E+00 234s WCA energy for atom 9: -1.328947132810E+00 234s WCA energy for atom 10: -1.328906972440E+00 234s WCA energy for atom 11: -1.331566344214E+00 234s WCA energy for atom 12: -1.328041776815E+00 234s WCA energy for atom 13: -5.937562025661E+00 234s WCA energy for atom 14: -1.442277774427E+00 234s WCA energy for atom 15: -1.442777091510E+00 234s WCA energy for atom 16: -6.602262542378E+00 234s WCA energy for atom 17: -1.698172146664E+00 234s WCA energy for atom 18: -1.600970858835E+00 234s WCA energy for atom 19: -1.600841970217E+00 234s 234s Total WCA energy: -57.0807 kJ/mol 234s 234s Total non-polar energy = 1.640068943201E+01 kJ/mol 234s ---------------------------------------- 234s CALCULATION #7 (solvated-isobutane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 3.464676753463E+00 234s SASA for atom 1: 1.984493338158E+01 234s SASA for atom 2: 1.778643845361E+01 234s SASA for atom 3: 1.671289426332E+01 234s SASA for atom 4: 0.000000000000E+00 234s SASA for atom 5: 3.531879535319E+00 234s SASA for atom 6: 1.673895116114E+01 234s SASA for atom 7: 1.793756846098E+01 234s SASA for atom 8: 1.973549441072E+01 234s SASA for atom 9: 1.710895911022E+01 234s SASA for atom 10: 4.599657069253E+00 234s SASA for atom 11: 1.937069784121E+01 234s SASA for atom 12: 1.654613011726E+01 234s SASA for atom 13: 1.936548646165E+01 234s 234s Total solvent accessible surface area: 192.744 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 2.944975240444E-02 234s Surface tension*area energy for atom 1: 1.686819337434E-01 234s Surface tension*area energy for atom 2: 1.511847268556E-01 234s Surface tension*area energy for atom 3: 1.420596012382E-01 234s Surface tension*area energy for atom 4: 0.000000000000E+00 234s Surface tension*area energy for atom 5: 3.002097605021E-02 234s Surface tension*area energy for atom 6: 1.422810848697E-01 234s Surface tension*area energy for atom 7: 1.524693319183E-01 234s Surface tension*area energy for atom 8: 1.677517024912E-01 234s Surface tension*area energy for atom 9: 1.454261524369E-01 234s Surface tension*area energy for atom 10: 3.909708508865E-02 234s Surface tension*area energy for atom 11: 1.646509316503E-01 234s Surface tension*area energy for atom 12: 1.406421059967E-01 234s Surface tension*area energy for atom 13: 1.646066349240E-01 234s 234s Total surface tension energy: 1.63832 kJ/mol 234s 234s Total solvent accessible volume: 218.943 A^3 234s 234s Total pressure*volume energy: 52.415 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.381016335247E+00 234s WCA energy for atom 1: -1.612317964554E+00 234s WCA energy for atom 2: -1.588013719598E+00 234s WCA energy for atom 3: -1.532162371190E+00 234s WCA energy for atom 4: -5.987950445279E+00 234s WCA energy for atom 5: -6.393089030861E+00 234s WCA energy for atom 6: -1.533454887042E+00 234s WCA energy for atom 7: -1.587650918485E+00 234s WCA energy for atom 8: -1.614083521570E+00 234s WCA energy for atom 9: -1.442402031577E+00 234s WCA energy for atom 10: -6.408813541353E+00 234s WCA energy for atom 11: -1.605830214390E+00 234s WCA energy for atom 12: -1.529385873788E+00 234s WCA energy for atom 13: -1.605662490385E+00 234s 234s Total WCA energy: -40.8218 kJ/mol 234s 234s Total non-polar energy = 1.323144287435E+01 kJ/mol 234s ---------------------------------------- 234s CALCULATION #8 (solvated-methane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 1.231304303117E+01 234s SASA for atom 1: 2.323233009850E+01 234s SASA for atom 2: 2.345641941977E+01 234s SASA for atom 3: 2.377431357320E+01 234s SASA for atom 4: 2.264344420771E+01 234s 234s Total solvent accessible surface area: 105.42 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 1.046608657649E-01 234s Surface tension*area energy for atom 1: 1.974748058372E-01 234s Surface tension*area energy for atom 2: 1.993795650680E-01 234s Surface tension*area energy for atom 3: 2.020816653722E-01 234s Surface tension*area energy for atom 4: 1.924692757655E-01 234s 234s Total surface tension energy: 0.896066 kJ/mol 234s 234s Total solvent accessible volume: 95.985 A^3 234s 234s Total pressure*volume energy: 22.9788 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -8.133807570805E+00 234s WCA energy for atom 1: -1.962181541765E+00 234s WCA energy for atom 2: -1.964078319162E+00 234s WCA energy for atom 3: -1.963015006647E+00 234s WCA energy for atom 4: -1.957425549100E+00 234s 234s Total WCA energy: -15.9805 kJ/mol 234s 234s Total non-polar energy = 7.894367190329E+00 kJ/mol 234s ---------------------------------------- 234s CALCULATION #9 (solvated-neopentane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 2.441701074100E+00 234s SASA for atom 1: 1.663993494942E+01 234s SASA for atom 2: 1.715586152630E+01 234s SASA for atom 3: 1.645753666466E+01 234s SASA for atom 4: 0.000000000000E+00 234s SASA for atom 5: 2.389432243768E+00 234s SASA for atom 6: 1.638457735076E+01 234s SASA for atom 7: 1.667641460637E+01 234s SASA for atom 8: 1.721839808108E+01 234s SASA for atom 9: 2.419300146815E+00 234s SASA for atom 10: 1.640021148945E+01 234s SASA for atom 11: 1.666599184724E+01 234s SASA for atom 12: 1.719234118325E+01 234s SASA for atom 13: 2.449168049862E+00 234s SASA for atom 14: 1.723403221977E+01 234s SASA for atom 15: 1.639500010989E+01 234s SASA for atom 16: 1.663472356985E+01 234s 234s Total solvent accessible surface area: 210.755 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 2.075445912985E-02 234s Surface tension*area energy for atom 1: 1.414394470700E-01 234s Surface tension*area energy for atom 2: 1.458248229736E-01 234s Surface tension*area energy for atom 3: 1.398890616496E-01 234s Surface tension*area energy for atom 4: 0.000000000000E+00 234s Surface tension*area energy for atom 5: 2.031017407203E-02 234s Surface tension*area energy for atom 6: 1.392689074814E-01 234s Surface tension*area energy for atom 7: 1.417495241541E-01 234s Surface tension*area energy for atom 8: 1.463563836891E-01 234s Surface tension*area energy for atom 9: 2.056405124793E-02 234s Surface tension*area energy for atom 10: 1.394017976603E-01 234s Surface tension*area energy for atom 11: 1.416609307015E-01 234s Surface tension*area energy for atom 12: 1.461349000577E-01 234s Surface tension*area energy for atom 13: 2.081792842383E-02 234s Surface tension*area energy for atom 14: 1.464892738680E-01 234s Surface tension*area energy for atom 15: 1.393575009340E-01 234s Surface tension*area energy for atom 16: 1.413951503437E-01 234s 234s Total surface tension energy: 1.79141 kJ/mol 234s 234s Total solvent accessible volume: 251.127 A^3 234s 234s Total pressure*volume energy: 60.1198 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.011082520236E+00 234s WCA energy for atom 1: -1.497367782613E+00 234s WCA energy for atom 2: -1.498546483218E+00 234s WCA energy for atom 3: -1.492562171495E+00 234s WCA energy for atom 4: -5.447325863939E+00 234s WCA energy for atom 5: -6.004516149175E+00 234s WCA energy for atom 6: -1.492776531092E+00 234s WCA energy for atom 7: -1.496078170066E+00 234s WCA energy for atom 8: -1.501529655270E+00 234s WCA energy for atom 9: -5.996267554365E+00 234s WCA energy for atom 10: -1.492194267752E+00 234s WCA energy for atom 11: -1.496027211216E+00 234s WCA energy for atom 12: -1.500561393960E+00 234s WCA energy for atom 13: -6.000218612907E+00 234s WCA energy for atom 14: -1.500859921426E+00 234s WCA energy for atom 15: -1.492908499790E+00 234s WCA energy for atom 16: -1.494057174414E+00 234s 234s Total WCA energy: -47.4149 kJ/mol 234s 234s Total non-polar energy = 1.449633815052E+01 kJ/mol 234s ---------------------------------------- 234s CALCULATION #10 (solvated-pentane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 4.405515699447E+00 234s SASA for atom 1: 8.213673337951E-01 234s SASA for atom 2: 3.285469335181E-01 234s SASA for atom 3: 7.466975761774E-01 234s SASA for atom 4: 1.855251124959E+01 234s SASA for atom 5: 2.147609518526E+01 234s SASA for atom 6: 1.852645435176E+01 234s SASA for atom 7: 1.655655287639E+01 234s SASA for atom 8: 1.655134149682E+01 234s SASA for atom 9: 1.360170066332E+01 234s SASA for atom 10: 1.357043238593E+01 234s SASA for atom 11: 1.685881289113E+01 234s SASA for atom 12: 1.687444702982E+01 234s SASA for atom 13: 4.196440378117E+00 234s SASA for atom 14: 1.881308022781E+01 234s SASA for atom 15: 1.882350298694E+01 234s SASA for atom 16: 2.182004623652E+01 234s 234s Total solvent accessible surface area: 222.524 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 3.744688344530E-02 234s Surface tension*area energy for atom 1: 6.981622337259E-03 234s Surface tension*area energy for atom 2: 2.792648934903E-03 234s Surface tension*area energy for atom 3: 6.346929397508E-03 234s Surface tension*area energy for atom 4: 1.576963456215E-01 234s Surface tension*area energy for atom 5: 1.825468090747E-01 234s Surface tension*area energy for atom 6: 1.574748619900E-01 234s Surface tension*area energy for atom 7: 1.407306994493E-01 234s Surface tension*area energy for atom 8: 1.406864027230E-01 234s Surface tension*area energy for atom 9: 1.156144556382E-01 234s Surface tension*area energy for atom 10: 1.153486752804E-01 234s Surface tension*area energy for atom 11: 1.432999095746E-01 234s Surface tension*area energy for atom 12: 1.434327997535E-01 234s Surface tension*area energy for atom 13: 3.566974321399E-02 234s Surface tension*area energy for atom 14: 1.599111819364E-01 234s Surface tension*area energy for atom 15: 1.599997753890E-01 234s Surface tension*area energy for atom 16: 1.854703930104E-01 234s 234s Total surface tension energy: 1.89145 kJ/mol 234s 234s Total solvent accessible volume: 258.93 A^3 234s 234s Total pressure*volume energy: 61.9878 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.655804319869E+00 234s WCA energy for atom 1: -6.027315962813E+00 234s WCA energy for atom 2: -5.696430965386E+00 234s WCA energy for atom 3: -6.016749084714E+00 234s WCA energy for atom 4: -1.608595384643E+00 234s WCA energy for atom 5: -1.703300955380E+00 234s WCA energy for atom 6: -1.609931495887E+00 234s WCA energy for atom 7: -1.457107525189E+00 234s WCA energy for atom 8: -1.457741620594E+00 234s WCA energy for atom 9: -1.354235498709E+00 234s WCA energy for atom 10: -1.354106470090E+00 234s WCA energy for atom 11: -1.456736412636E+00 234s WCA energy for atom 12: -1.455995435596E+00 234s WCA energy for atom 13: -6.633650611186E+00 234s WCA energy for atom 14: -1.605996088477E+00 234s WCA energy for atom 15: -1.606549890103E+00 234s WCA energy for atom 16: -1.700042300035E+00 234s 234s Total WCA energy: -49.4003 kJ/mol 234s 234s Total non-polar energy = 1.447900211546E+01 kJ/mol 234s ---------------------------------------- 234s CALCULATION #11 (solvated-propane): APOLAR 234s 234s Solvent Accessible Surface Area (SASA) for each atom: 234s SASA for atom 0: 3.173464698754E+00 234s SASA for atom 1: 1.931858404557E+01 234s SASA for atom 2: 2.014198201675E+01 234s SASA for atom 3: 2.149694070352E+01 234s SASA for atom 4: 1.904078819252E+00 234s SASA for atom 5: 2.067354273233E+01 234s SASA for atom 6: 1.937590922077E+01 234s SASA for atom 7: 3.098794941136E+00 234s SASA for atom 8: 1.942802301642E+01 234s SASA for atom 9: 1.973028303116E+01 234s SASA for atom 10: 2.204934693736E+01 234s 234s Total solvent accessible surface area: 170.391 A^2 234s 234s Surface tension*area energies (gamma * SASA) for each atom: 234s Surface tension*area energy for atom 0: 2.697444993941E-02 234s Surface tension*area energy for atom 1: 1.642079643873E-01 234s Surface tension*area energy for atom 2: 1.712068471424E-01 234s Surface tension*area energy for atom 3: 1.827239959799E-01 234s Surface tension*area energy for atom 4: 1.618466996365E-02 234s Surface tension*area energy for atom 5: 1.757251132248E-01 234s Surface tension*area energy for atom 6: 1.646952283766E-01 234s Surface tension*area energy for atom 7: 2.633975699966E-02 234s Surface tension*area energy for atom 8: 1.651381956396E-01 234s Surface tension*area energy for atom 9: 1.677074057649E-01 234s Surface tension*area energy for atom 10: 1.874194489675E-01 234s 234s Total surface tension energy: 1.44832 kJ/mol 234s 234s Total solvent accessible volume: 183.573 A^3 234s 234s Total pressure*volume energy: 43.9474 kJ/mol 234s 234s WCA dispersion Energies for each atom: 234s WCA energy for atom 0: -6.818670105515E+00 234s WCA energy for atom 1: -1.641297645338E+00 234s WCA energy for atom 2: -1.649584120441E+00 234s WCA energy for atom 3: -1.711408141255E+00 234s WCA energy for atom 4: -6.624720142882E+00 234s WCA energy for atom 5: -1.610117050515E+00 234s WCA energy for atom 6: -1.596858009746E+00 234s WCA energy for atom 7: -6.816460624835E+00 234s WCA energy for atom 8: -1.642782751806E+00 234s WCA energy for atom 9: -1.645779566650E+00 234s WCA energy for atom 10: -1.714436154542E+00 234s 234s Total WCA energy: -33.4721 kJ/mol 234s 234s Total non-polar energy = 1.192358496286E+01 kJ/mol 234s ---------------------------------------- 234s PRINT STATEMENTS 234s 234s print APOL energy 1 (solvated-2-methylbutane) end 234s Global net APOL energy = 1.439739455792E+01 kJ/mol 234s 234s print APOL energy 2 (solvated-butane) end 234s Global net APOL energy = 1.208346456826E+01 kJ/mol 234s 234s print APOL energy 3 (solvated-cyclohexane) end 234s Global net APOL energy = 1.354016672221E+01 kJ/mol 234s 234s print APOL energy 4 (solvated-cyclopentane) end 234s Global net APOL energy = 9.363673200142E+00 kJ/mol 234s 234s print APOL energy 5 (solvated-ethane) end 234s Global net APOL energy = 9.422717598546E+00 kJ/mol 234s 234s print APOL energy 6 (solvated-hexane) end 234s Global net APOL energy = 1.640068943201E+01 kJ/mol 234s 234s print APOL energy 7 (solvated-isobutane) end 234s Global net APOL energy = 1.323144287435E+01 kJ/mol 234s 234s print APOL energy 8 (solvated-methane) end 234s Global net APOL energy = 7.894367190329E+00 kJ/mol 234s 234s print APOL energy 9 (solvated-neopentane) end 234s Global net APOL energy = 1.449633815052E+01 kJ/mol 234s 234s print APOL energy 10 (solvated-pentane) end 234s Global net APOL energy = 1.447900211546E+01 kJ/mol 234s 234s print APOL energy 11 (solvated-propane) end 234s Global net APOL energy = 1.192358496286E+01 kJ/mol 234s ---------------------------------------- 234s CLEANING UP AND SHUTTING DOWN... 234s Destroying force arrays. 234s No energy arrays to destroy. 234s Destroying multigrid structures. 234s Destroying finite element structures. 234s Destroying 11 molecules 234s Final memory usage: 0.001 MB total, 2.267 MB high water 234s 234s 234s Thanks for using APBS! 234s 234s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 234s *** PASSED *** 234s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 234s *** PASSED *** 234s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 234s *** PASSED *** 234s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 234s *** PASSED *** 234s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 234s *** PASSED *** 234s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 234s *** PASSED *** 234s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 234s *** PASSED *** 234s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 234s *** PASSED *** 234s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 234s *** PASSED *** 234s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 234s *** PASSED *** 234s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 234s *** PASSED *** 234s Elapsed time: 13.210823 seconds 234s -------------------------------------------------------------------------------- 234s Total elapsed time: 13.210823 seconds 234s Test results have been logged 234s -------------------------------------------------------------------------------- 234s -------------------------------------------------------------------------------- 234s Testing input file 1d7h-dmso-mol.in 234s 243s Checking for intermediate energies in input file alkanes.out 243s EXPECTED COMPUTED: 11 243s EXPECTED EXPECTED: 11 243s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 243s 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'] 243s COMPUTED RESULT 14.39739455792 243s COMPUTED RESULT 12.08346456826 243s COMPUTED RESULT 13.54016672221 243s COMPUTED RESULT 9.363673200142 243s COMPUTED RESULT 9.422717598546 243s COMPUTED RESULT 16.40068943201 243s COMPUTED RESULT 13.23144287435 243s COMPUTED RESULT 7.894367190329 243s COMPUTED RESULT 14.49633815052 243s COMPUTED RESULT 14.47900211546 243s COMPUTED RESULT 11.92358496286 243s Running tests for FKBP section 243s BINARY: /usr/bin/apbs 243s INPUT: 1d7h-dmso-mol.in 243s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 243s asc_getToken: Error occurred (bailing out). 243s Vio_scanf: Format problem with input. 243s 243s 243s ---------------------------------------------------------------------- 243s APBS -- Adaptive Poisson-Boltzmann Solver 243s Version APBS 3.4.1 243s 243s Nathan A. Baker (nathan.baker@pnnl.gov) 243s Pacific Northwest National Laboratory 243s 243s Additional contributing authors listed in the code documentation. 243s 243s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 243s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 243s Northwest Division for the U.S. Department of Energy. 243s 243s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 243s Portions Copyright (c) 2002-2020, Nathan A. Baker. 243s Portions Copyright (c) 1999-2002, The Regents of the University of California. 243s Portions Copyright (c) 1995, Michael Holst. 243s All rights reserved. 243s 243s Redistribution and use in source and binary forms, with or without 243s modification, are permitted provided that the following conditions are met: 243s 243s * Redistributions of source code must retain the above copyright notice, this 243s list of conditions and the following disclaimer. 243s 243s * Redistributions in binary form must reproduce the above copyright notice, 243s this list of conditions and the following disclaimer in the documentation 243s and/or other materials provided with the distribution. 243s 243s * Neither the name of the developer nor the names of its contributors may be 243s used to endorse or promote products derived from this software without 243s specific prior written permission. 243s 243s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 243s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 243s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 243s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 243s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 243s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 243s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 243s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 243s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 243s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 243s ---------------------------------------------------------------------- 243s APBS uses FETK (the Finite Element ToolKit) to solve the 243s Poisson-Boltzmann equation numerically. FETK is a portable collection 243s of finite element modeling class libraries developed by the Michael Holst 243s research group and written in an object-oriented form of C. FEtk is 243s designed to solve general coupled systems of nonlinear partial differential 243s equations using adaptive finite element methods, inexact Newton methods, 243s and algebraic multilevel methods. More information about FEtk may be found 243s at . 243s ---------------------------------------------------------------------- 243s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 243s Aqua is a modified form of the Holst group PMG library 243s which has been modified by Patrice Koehl 243s for improved efficiency and 243s memory usage when solving the Poisson-Boltzmann equation. 243s ---------------------------------------------------------------------- 243s Please cite your use of APBS as: 243s 243s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 243s nanosystems: application to microtubules and the ribosome. Proc. 243s Natl. Acad. Sci. USA 98, 10037-10041 2001. 243s 243s 243s This executable compiled on Jan 3 2025 at 11:01:42 243s 243s Parsing input file 1d7h-dmso-mol.in... 243s rank 0 size 1... 243s Parsed input file. 243s Got paths for 3 molecules 243s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 243s asc_getToken: Error occurred (bailing out). 243s Vio_scanf: Format problem with input. 243s 1673 atoms 243s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 243s Net charge 9.91e-01 e 243s Reading PQR-format atom data from dmso-min.pqr. 243s asc_getToken: Error occurred (bailing out). 243s Vio_scanf: Format problem with input. 243s 10 atoms 243s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 243s Net charge 2.78e-17 e 243s Reading PQR-format atom data from 1d7h-min.pqr. 243s 1663 atoms 243s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 243s Net charge 9.91e-01 e 243s Preparing to run 12 PBE calculations. 243s ---------------------------------------- 243s CALCULATION #1 (complex-solv-coarse): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 30.4176 A 243s Current memory usage: 122.059 MB total, 122.059 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 1.500 x 1.500 x 1.500 243s Grid lengths: 96.000 x 96.000 x 96.000 243s Grid center: (25.875, 18.349, 19.112) 243s Multigrid levels: 5 243s Molecule ID: 1 243s Linearized traditional PBE 243s Multiple Debye-Huckel sphere boundary conditions 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 78.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 1.060899690259E+04 kJ/mol 243s Calculating forces... 243s [focusFillBound()]: WARNING: 243s Unusually large potential values 243s detected on the focusing boundary! 243s Convergence not guaranteed for NPBE/NRPBE calculations! 243s 243s ---------------------------------------- 243s CALCULATION #2 (complex-solv-fine): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 30.4176 A 243s Current memory usage: 122.059 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 0.225 x 0.225 x 0.225 243s Grid lengths: 14.400 x 14.400 x 14.400 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 1 243s Linearized traditional PBE 243s Boundary conditions from focusing 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 78.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 4.276523673491E+04 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s CALCULATION #3 (complex-ref-coarse): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 4.87072 A 243s Current memory usage: 122.059 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 1.500 x 1.500 x 1.500 243s Grid lengths: 96.000 x 96.000 x 96.000 243s Grid center: (25.875, 18.349, 19.112) 243s Multigrid levels: 5 243s Molecule ID: 1 243s Linearized traditional PBE 243s Multiple Debye-Huckel sphere boundary conditions 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 2.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 1.399234956777E+04 kJ/mol 243s Calculating forces... 243s [focusFillBound()]: WARNING: 243s Unusually large potential values 243s detected on the focusing boundary! 243s Convergence not guaranteed for NPBE/NRPBE calculations! 243s 243s ---------------------------------------- 243s CALCULATION #4 (complex-ref-fine): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 4.87072 A 243s Current memory usage: 122.059 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 0.225 x 0.225 x 0.225 243s Grid lengths: 14.400 x 14.400 x 14.400 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 1 243s Linearized traditional PBE 243s Boundary conditions from focusing 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 2.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 4.610066575192E+04 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 30.4176 A 243s Current memory usage: 62.428 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 1.500 x 1.500 x 1.500 243s Grid lengths: 96.000 x 96.000 x 96.000 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 2 243s Linearized traditional PBE 243s Multiple Debye-Huckel sphere boundary conditions 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 78.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 3.961107503213E+01 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s CALCULATION #6 (dmso-solv-fine): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 30.4176 A 243s Current memory usage: 62.428 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 0.225 x 0.225 x 0.225 243s Grid lengths: 14.400 x 14.400 x 14.400 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 2 243s Linearized traditional PBE 243s Boundary conditions from focusing 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 78.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 7.121048606059E+02 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 4.87072 A 243s Current memory usage: 62.428 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 1.500 x 1.500 x 1.500 243s Grid lengths: 96.000 x 96.000 x 96.000 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 2 243s Linearized traditional PBE 243s Multiple Debye-Huckel sphere boundary conditions 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 2.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 6.751571424823E+01 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s CALCULATION #8 (dmso-ref-fine): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 4.87072 A 243s Current memory usage: 62.428 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 0.225 x 0.225 x 0.225 243s Grid lengths: 14.400 x 14.400 x 14.400 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 2 243s Linearized traditional PBE 243s Boundary conditions from focusing 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 2.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 7.339101343121E+02 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 30.4176 A 243s Current memory usage: 121.736 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 1.500 x 1.500 x 1.500 243s Grid lengths: 96.000 x 96.000 x 96.000 243s Grid center: (25.875, 18.349, 19.112) 243s Multigrid levels: 5 243s Molecule ID: 3 243s Linearized traditional PBE 243s Multiple Debye-Huckel sphere boundary conditions 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 78.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 1.058410584089E+04 kJ/mol 243s Calculating forces... 243s [focusFillBound()]: WARNING: 243s Unusually large potential values 243s detected on the focusing boundary! 243s Convergence not guaranteed for NPBE/NRPBE calculations! 243s 243s ---------------------------------------- 243s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 30.4176 A 243s Current memory usage: 121.736 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 0.225 x 0.225 x 0.225 243s Grid lengths: 14.400 x 14.400 x 14.400 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 3 243s Linearized traditional PBE 243s Boundary conditions from focusing 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 78.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 4.205385249581E+04 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 4.87072 A 243s Current memory usage: 121.736 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 1.500 x 1.500 x 1.500 243s Grid lengths: 96.000 x 96.000 x 96.000 243s Grid center: (25.875, 18.349, 19.112) 243s Multigrid levels: 5 243s Molecule ID: 3 243s Linearized traditional PBE 243s Multiple Debye-Huckel sphere boundary conditions 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 2.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 1.395961902233E+04 kJ/mol 243s Calculating forces... 243s [focusFillBound()]: WARNING: 243s Unusually large potential values 243s detected on the focusing boundary! 243s Convergence not guaranteed for NPBE/NRPBE calculations! 243s 243s ---------------------------------------- 243s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 243s Setting up problem... 243s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 243s Debye length: 4.87072 A 243s Current memory usage: 121.736 MB total, 221.696 MB high water 243s Using linear spline charge discretization. 243s Grid dimensions: 65 x 65 x 65 243s Grid spacings: 0.225 x 0.225 x 0.225 243s Grid lengths: 14.400 x 14.400 x 14.400 243s Grid center: (17.751, 17.770, 20.492) 243s Multigrid levels: 5 243s Molecule ID: 3 243s Linearized traditional PBE 243s Boundary conditions from focusing 243s 2 ion species (0.010 M ionic strength): 243s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 243s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 243s Solute dielectric: 2.000 243s Solvent dielectric: 2.000 243s Using "molecular" surface definition; no smoothing 243s Solvent probe radius: 0.000 A 243s Temperature: 300.000 K 243s Electrostatic energies will be calculated 243s Total electrostatic energy = 4.538248433997E+04 kJ/mol 243s Calculating forces... 243s ---------------------------------------- 243s PRINT STATEMENTS 243s 243s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 243s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 243s Global net ELEC energy = -3.335429017008E+03 kJ/mol 243s 243s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 243s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 243s Global net ELEC energy = -2.180527370616E+01 kJ/mol 243s 243s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 243s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 243s Global net ELEC energy = -3.328631844166E+03 kJ/mol 243s 243s 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 243s Local net energy (PE 0) = 1.500810086373E+01 kJ/mol 243s Global net ELEC energy = 1.500810086373E+01 kJ/mol 243s ---------------------------------------- 243s CLEANING UP AND SHUTTING DOWN... 243s Destroying force arrays. 243s No energy arrays to destroy. 243s Destroying multigrid structures. 243s Destroying finite element structures. 243s Destroying 3 molecules 243s Final memory usage: 0.001 MB total, 221.696 MB high water 243s 243s 243s Thanks for using APBS! 243s 243s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 243s *** PASSED *** 243s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 243s *** PASSED *** 243s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 243s *** PASSED *** 243s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 243s *** PASSED *** 243s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 243s *** PASSED *** 243s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 243s *** PASSED *** 243s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 243s *** PASSED *** 243s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 243s *** PASSED *** 243s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 243s *** PASSED *** 243s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 243s *** PASSED *** 243s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 243s *** PASSED *** 243s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 243s *** PASSED *** 243s Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) 243s *** PASSED *** 243s Elapsed time: 9.04493 seconds 243s -------------------------------------------------------------------------------- 243s -------------------------------------------------------------------------------- 243s Testing input file 1d7h-dmso-smol.in 243s 251s Checking for intermediate energies in input file 1d7h-dmso-mol.out 251s EXPECTED COMPUTED: 16 251s EXPECTED EXPECTED: 16 251s COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086373] 251s 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'] 251s COMPUTED RESULT 10608.99690259 251s COMPUTED RESULT 42765.23673491 251s COMPUTED RESULT 13992.34956777 251s COMPUTED RESULT 46100.66575192 251s COMPUTED RESULT 39.61107503213 251s COMPUTED RESULT 712.1048606059 251s COMPUTED RESULT 67.51571424823 251s COMPUTED RESULT 733.9101343121 251s COMPUTED RESULT 10584.10584089 251s COMPUTED RESULT 42053.85249581 251s COMPUTED RESULT 13959.61902233 251s COMPUTED RESULT 45382.48433997 251s COMPUTED RESULT -3335.429017008 251s COMPUTED RESULT -21.80527370616 251s COMPUTED RESULT -3328.631844166 251s COMPUTED RESULT 15.00810086373 251s BINARY: /usr/bin/apbs 251s INPUT: 1d7h-dmso-smol.in 251s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 251s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 251s *** PASSED *** 251s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 251s *** PASSED *** 251s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 251s *** PASSED *** 251s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 251s *** PASSED *** 251s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 251s *** PASSED *** 251s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 251s *** PASSED *** 251s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 251s *** PASSED *** 251s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 251s *** PASSED *** 251s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 251s *** PASSED *** 251s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 251s *** PASSED *** 251s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 251s *** PASSED *** 251s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 251s *** PASSED *** 251s Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) 251s *** PASSED *** 251s Elapsed time: 8.343939 seconds 251s -------------------------------------------------------------------------------- 251s -------------------------------------------------------------------------------- 251s Testing input file 1d7i-dss-mol.in 251s 251s asc_getToken: Error occurred (bailing out). 251s Vio_scanf: Format problem with input. 251s 251s 251s ---------------------------------------------------------------------- 251s APBS -- Adaptive Poisson-Boltzmann Solver 251s Version APBS 3.4.1 251s 251s Nathan A. Baker (nathan.baker@pnnl.gov) 251s Pacific Northwest National Laboratory 251s 251s Additional contributing authors listed in the code documentation. 251s 251s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 251s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 251s Northwest Division for the U.S. Department of Energy. 251s 251s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 251s Portions Copyright (c) 2002-2020, Nathan A. Baker. 251s Portions Copyright (c) 1999-2002, The Regents of the University of California. 251s Portions Copyright (c) 1995, Michael Holst. 251s All rights reserved. 251s 251s Redistribution and use in source and binary forms, with or without 251s modification, are permitted provided that the following conditions are met: 251s 251s * Redistributions of source code must retain the above copyright notice, this 251s list of conditions and the following disclaimer. 251s 251s * Redistributions in binary form must reproduce the above copyright notice, 251s this list of conditions and the following disclaimer in the documentation 251s and/or other materials provided with the distribution. 251s 251s * Neither the name of the developer nor the names of its contributors may be 251s used to endorse or promote products derived from this software without 251s specific prior written permission. 251s 251s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 251s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 251s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 251s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 251s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 251s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 251s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 251s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 251s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 251s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 251s ---------------------------------------------------------------------- 251s APBS uses FETK (the Finite Element ToolKit) to solve the 251s Poisson-Boltzmann equation numerically. FETK is a portable collection 251s of finite element modeling class libraries developed by the Michael Holst 251s research group and written in an object-oriented form of C. FEtk is 251s designed to solve general coupled systems of nonlinear partial differential 251s equations using adaptive finite element methods, inexact Newton methods, 251s and algebraic multilevel methods. More information about FEtk may be found 251s at . 251s ---------------------------------------------------------------------- 251s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 251s Aqua is a modified form of the Holst group PMG library 251s which has been modified by Patrice Koehl 251s for improved efficiency and 251s memory usage when solving the Poisson-Boltzmann equation. 251s ---------------------------------------------------------------------- 251s Please cite your use of APBS as: 251s 251s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 251s nanosystems: application to microtubules and the ribosome. Proc. 251s Natl. Acad. Sci. USA 98, 10037-10041 2001. 251s 251s 251s This executable compiled on Jan 3 2025 at 11:01:42 251s 251s Parsing input file 1d7h-dmso-smol.in... 251s rank 0 size 1... 251s Parsed input file. 251s Got paths for 3 molecules 251s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 251s asc_getToken: Error occurred (bailing out). 251s Vio_scanf: Format problem with input. 251s 1673 atoms 251s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 251s Net charge 9.91e-01 e 251s Reading PQR-format atom data from dmso-min.pqr. 251s asc_getToken: Error occurred (bailing out). 251s Vio_scanf: Format problem with input. 251s 10 atoms 251s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 251s Net charge 2.78e-17 e 251s Reading PQR-format atom data from 1d7h-min.pqr. 251s 1663 atoms 251s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 251s Net charge 9.91e-01 e 251s Preparing to run 12 PBE calculations. 251s ---------------------------------------- 251s CALCULATION #1 (complex-solv-coarse): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 30.4176 A 251s Current memory usage: 122.059 MB total, 122.059 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 1.500 x 1.500 x 1.500 251s Grid lengths: 96.000 x 96.000 x 96.000 251s Grid center: (25.875, 18.349, 19.112) 251s Multigrid levels: 5 251s Molecule ID: 1 251s Linearized traditional PBE 251s Multiple Debye-Huckel sphere boundary conditions 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 78.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 1.074948704824E+04 kJ/mol 251s Calculating forces... 251s [focusFillBound()]: WARNING: 251s Unusually large potential values 251s detected on the focusing boundary! 251s Convergence not guaranteed for NPBE/NRPBE calculations! 251s 251s ---------------------------------------- 251s CALCULATION #2 (complex-solv-fine): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 30.4176 A 251s Current memory usage: 122.059 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 0.225 x 0.225 x 0.225 251s Grid lengths: 14.400 x 14.400 x 14.400 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 1 251s Linearized traditional PBE 251s Boundary conditions from focusing 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 78.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 4.289487256481E+04 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s CALCULATION #3 (complex-ref-coarse): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 4.87072 A 251s Current memory usage: 122.059 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 1.500 x 1.500 x 1.500 251s Grid lengths: 96.000 x 96.000 x 96.000 251s Grid center: (25.875, 18.349, 19.112) 251s Multigrid levels: 5 251s Molecule ID: 1 251s Linearized traditional PBE 251s Multiple Debye-Huckel sphere boundary conditions 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 2.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 1.399234956777E+04 kJ/mol 251s Calculating forces... 251s [focusFillBound()]: WARNING: 251s Unusually large potential values 251s detected on the focusing boundary! 251s Convergence not guaranteed for NPBE/NRPBE calculations! 251s 251s ---------------------------------------- 251s CALCULATION #4 (complex-ref-fine): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 4.87072 A 251s Current memory usage: 122.059 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 0.225 x 0.225 x 0.225 251s Grid lengths: 14.400 x 14.400 x 14.400 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 1 251s Linearized traditional PBE 251s Boundary conditions from focusing 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 2.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 4.610066575192E+04 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 30.4176 A 251s Current memory usage: 62.428 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 1.500 x 1.500 x 1.500 251s Grid lengths: 96.000 x 96.000 x 96.000 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 2 251s Linearized traditional PBE 251s Multiple Debye-Huckel sphere boundary conditions 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 78.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 3.719709905887E+01 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s CALCULATION #6 (dmso-solv-fine): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 30.4176 A 251s Current memory usage: 62.428 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 0.225 x 0.225 x 0.225 251s Grid lengths: 14.400 x 14.400 x 14.400 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 2 251s Linearized traditional PBE 251s Boundary conditions from focusing 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 78.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 7.125747080979E+02 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 4.87072 A 251s Current memory usage: 62.428 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 1.500 x 1.500 x 1.500 251s Grid lengths: 96.000 x 96.000 x 96.000 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 2 251s Linearized traditional PBE 251s Multiple Debye-Huckel sphere boundary conditions 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 2.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 6.751571424823E+01 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s CALCULATION #8 (dmso-ref-fine): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 4.87072 A 251s Current memory usage: 62.428 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 0.225 x 0.225 x 0.225 251s Grid lengths: 14.400 x 14.400 x 14.400 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 2 251s Linearized traditional PBE 251s Boundary conditions from focusing 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 2.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 7.339101343121E+02 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 30.4176 A 251s Current memory usage: 121.736 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 1.500 x 1.500 x 1.500 251s Grid lengths: 96.000 x 96.000 x 96.000 251s Grid center: (25.875, 18.349, 19.112) 251s Multigrid levels: 5 251s Molecule ID: 3 251s Linearized traditional PBE 251s Multiple Debye-Huckel sphere boundary conditions 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 78.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 1.071654753674E+04 kJ/mol 251s Calculating forces... 251s [focusFillBound()]: WARNING: 251s Unusually large potential values 251s detected on the focusing boundary! 251s Convergence not guaranteed for NPBE/NRPBE calculations! 251s 251s ---------------------------------------- 251s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 30.4176 A 251s Current memory usage: 121.736 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 0.225 x 0.225 x 0.225 251s Grid lengths: 14.400 x 14.400 x 14.400 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 3 251s Linearized traditional PBE 251s Boundary conditions from focusing 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 78.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 4.218178203716E+04 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 4.87072 A 251s Current memory usage: 121.736 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 1.500 x 1.500 x 1.500 251s Grid lengths: 96.000 x 96.000 x 96.000 251s Grid center: (25.875, 18.349, 19.112) 251s Multigrid levels: 5 251s Molecule ID: 3 251s Linearized traditional PBE 251s Multiple Debye-Huckel sphere boundary conditions 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 2.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 1.395961902233E+04 kJ/mol 251s Calculating forces... 251s [focusFillBound()]: WARNING: 251s Unusually large potential values 251s detected on the focusing boundary! 251s Convergence not guaranteed for NPBE/NRPBE calculations! 251s 251s ---------------------------------------- 251s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 251s Setting up problem... 251s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 251s Debye length: 4.87072 A 251s Current memory usage: 121.736 MB total, 221.696 MB high water 251s Using linear spline charge discretization. 251s Grid dimensions: 65 x 65 x 65 251s Grid spacings: 0.225 x 0.225 x 0.225 251s Grid lengths: 14.400 x 14.400 x 14.400 251s Grid center: (17.751, 17.770, 20.492) 251s Multigrid levels: 5 251s Molecule ID: 3 251s Linearized traditional PBE 251s Boundary conditions from focusing 251s 2 ion species (0.010 M ionic strength): 251s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 251s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 251s Solute dielectric: 2.000 251s Solvent dielectric: 2.000 251s Using "molecular" surface definition;harmonic average smoothing 251s Solvent probe radius: 0.000 A 251s Temperature: 300.000 K 251s Electrostatic energies will be calculated 251s Total electrostatic energy = 4.538248433997E+04 kJ/mol 251s Calculating forces... 251s ---------------------------------------- 251s PRINT STATEMENTS 251s 251s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 251s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 251s Global net ELEC energy = -3.205793187109E+03 kJ/mol 251s 251s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 251s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 251s Global net ELEC energy = -2.133542621421E+01 kJ/mol 251s 251s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 251s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 251s Global net ELEC energy = -3.200702302816E+03 kJ/mol 251s 251s 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 251s Local net energy (PE 0) = 1.624454192074E+01 kJ/mol 251s Global net ELEC energy = 1.624454192074E+01 kJ/mol 251s ---------------------------------------- 251s CLEANING UP AND SHUTTING DOWN... 251s Destroying force arrays. 251s No energy arrays to destroy. 251s Destroying multigrid structures. 251s Destroying finite element structures. 251s Destroying 3 molecules 251s Final memory usage: 0.001 MB total, 221.696 MB high water 251s 251s 251s Thanks for using APBS! 251s 260s Checking for intermediate energies in input file 1d7h-dmso-smol.out 260s EXPECTED COMPUTED: 16 260s EXPECTED EXPECTED: 16 260s COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192074] 260s 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'] 260s COMPUTED RESULT 10749.48704824 260s COMPUTED RESULT 42894.87256481 260s COMPUTED RESULT 13992.34956777 260s COMPUTED RESULT 46100.66575192 260s COMPUTED RESULT 37.19709905887 260s COMPUTED RESULT 712.5747080979 260s COMPUTED RESULT 67.51571424823 260s COMPUTED RESULT 733.9101343121 260s COMPUTED RESULT 10716.54753674 260s COMPUTED RESULT 42181.78203716 260s COMPUTED RESULT 13959.61902233 260s COMPUTED RESULT 45382.48433997 260s COMPUTED RESULT -3205.793187109 260s COMPUTED RESULT -21.33542621421 260s COMPUTED RESULT -3200.702302816 260s COMPUTED RESULT 16.24454192074 260s BINARY: /usr/bin/apbs 260s INPUT: 1d7i-dss-mol.in 260s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 260s asc_getToken: Error occurred (bailing out). 260s Vio_scanf: Format problem with input. 260s 260s 260s ---------------------------------------------------------------------- 260s APBS -- Adaptive Poisson-Boltzmann Solver 260s Version APBS 3.4.1 260s 260s Nathan A. Baker (nathan.baker@pnnl.gov) 260s Pacific Northwest National Laboratory 260s 260s Additional contributing authors listed in the code documentation. 260s 260s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 260s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 260s Northwest Division for the U.S. Department of Energy. 260s 260s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 260s Portions Copyright (c) 2002-2020, Nathan A. Baker. 260s Portions Copyright (c) 1999-2002, The Regents of the University of California. 260s Portions Copyright (c) 1995, Michael Holst. 260s All rights reserved. 260s 260s Redistribution and use in source and binary forms, with or without 260s modification, are permitted provided that the following conditions are met: 260s 260s * Redistributions of source code must retain the above copyright notice, this 260s list of conditions and the following disclaimer. 260s 260s * Redistributions in binary form must reproduce the above copyright notice, 260s this list of conditions and the following disclaimer in the documentation 260s and/or other materials provided with the distribution. 260s 260s * Neither the name of the developer nor the names of its contributors may be 260s used to endorse or promote products derived from this software without 260s specific prior written permission. 260s 260s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 260s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 260s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 260s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 260s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 260s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 260s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 260s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 260s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 260s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 260s ---------------------------------------------------------------------- 260s APBS uses FETK (the Finite Element ToolKit) to solve the 260s Poisson-Boltzmann equation numerically. FETK is a portable collection 260s of finite element modeling class libraries developed by the Michael Holst 260s research group and written in an object-oriented form of C. FEtk is 260s designed to solve general coupled systems of nonlinear partial differential 260s equations using adaptive finite element methods, inexact Newton methods, 260s and algebraic multilevel methods. More information about FEtk may be found 260s at . 260s ---------------------------------------------------------------------- 260s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 260s Aqua is a modified form of the Holst group PMG library 260s which has been modified by Patrice Koehl 260s for improved efficiency and 260s memory usage when solving the Poisson-Boltzmann equation. 260s ---------------------------------------------------------------------- 260s Please cite your use of APBS as: 260s 260s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 260s nanosystems: application to microtubules and the ribosome. Proc. 260s Natl. Acad. Sci. USA 98, 10037-10041 2001. 260s 260s 260s This executable compiled on Jan 3 2025 at 11:01:42 260s 260s Parsing input file 1d7i-dss-mol.in... 260s rank 0 size 1... 260s Parsed input file. 260s Got paths for 3 molecules 260s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 260s asc_getToken: Error occurred (bailing out). 260s Vio_scanf: Format problem with input. 260s 1677 atoms 260s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 260s Net charge 9.91e-01 e 260s Reading PQR-format atom data from dss-min.pqr. 260s asc_getToken: Error occurred (bailing out). 260s Vio_scanf: Format problem with input. 260s 14 atoms 260s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 260s Net charge -8.33e-17 e 260s Reading PQR-format atom data from 1d7i-min.pqr. 260s 1663 atoms 260s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 260s Net charge 9.91e-01 e 260s Preparing to run 12 PBE calculations. 260s ---------------------------------------- 260s CALCULATION #1 (complex-solv-coarse): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 30.4176 A 260s Current memory usage: 122.425 MB total, 122.425 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 1.500 x 1.500 x 1.500 260s Grid lengths: 96.000 x 96.000 x 96.000 260s Grid center: (25.264, 18.988, 19.122) 260s Multigrid levels: 5 260s Molecule ID: 1 260s Linearized traditional PBE 260s Multiple Debye-Huckel sphere boundary conditions 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 78.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 9.160578033846E+03 kJ/mol 260s Calculating forces... 260s [focusFillBound()]: WARNING: 260s Unusually large potential values 260s detected on the focusing boundary! 260s Convergence not guaranteed for NPBE/NRPBE calculations! 260s 260s ---------------------------------------- 260s CALCULATION #2 (complex-solv-fine): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 30.4176 A 260s Current memory usage: 122.425 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 0.225 x 0.225 x 0.225 260s Grid lengths: 14.400 x 14.400 x 14.400 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 1 260s Linearized traditional PBE 260s Boundary conditions from focusing 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 78.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 3.955701871716E+04 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s CALCULATION #3 (complex-ref-coarse): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 4.87072 A 260s Current memory usage: 122.425 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 1.500 x 1.500 x 1.500 260s Grid lengths: 96.000 x 96.000 x 96.000 260s Grid center: (25.264, 18.988, 19.122) 260s Multigrid levels: 5 260s Molecule ID: 1 260s Linearized traditional PBE 260s Multiple Debye-Huckel sphere boundary conditions 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 2.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 1.264965939588E+04 kJ/mol 260s Calculating forces... 260s [focusFillBound()]: WARNING: 260s Unusually large potential values 260s detected on the focusing boundary! 260s Convergence not guaranteed for NPBE/NRPBE calculations! 260s 260s ---------------------------------------- 260s CALCULATION #4 (complex-ref-fine): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 4.87072 A 260s Current memory usage: 122.425 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 0.225 x 0.225 x 0.225 260s Grid lengths: 14.400 x 14.400 x 14.400 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 1 260s Linearized traditional PBE 260s Boundary conditions from focusing 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 2.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 4.301801664829E+04 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s CALCULATION #5 (dss-solv-coarse): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 30.4176 A 260s Current memory usage: 62.528 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 1.500 x 1.500 x 1.500 260s Grid lengths: 96.000 x 96.000 x 96.000 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 2 260s Linearized traditional PBE 260s Multiple Debye-Huckel sphere boundary conditions 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 78.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 9.431133325426E+01 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s CALCULATION #6 (dss-solv-fine): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 30.4176 A 260s Current memory usage: 62.528 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 0.225 x 0.225 x 0.225 260s Grid lengths: 14.400 x 14.400 x 14.400 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 2 260s Linearized traditional PBE 260s Boundary conditions from focusing 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 78.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 1.677348113184E+03 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s CALCULATION #7 (dss-ref-coarse): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 4.87072 A 260s Current memory usage: 62.528 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 1.500 x 1.500 x 1.500 260s Grid lengths: 96.000 x 96.000 x 96.000 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 2 260s Linearized traditional PBE 260s Multiple Debye-Huckel sphere boundary conditions 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 2.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 1.171079106781E+02 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s CALCULATION #8 (dss-ref-fine): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 4.87072 A 260s Current memory usage: 62.528 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 0.225 x 0.225 x 0.225 260s Grid lengths: 14.400 x 14.400 x 14.400 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 2 260s Linearized traditional PBE 260s Boundary conditions from focusing 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 2.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 1.697869784185E+03 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 30.4176 A 260s Current memory usage: 121.977 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 1.500 x 1.500 x 1.500 260s Grid lengths: 96.000 x 96.000 x 96.000 260s Grid center: (25.264, 18.988, 19.122) 260s Multigrid levels: 5 260s Molecule ID: 3 260s Linearized traditional PBE 260s Multiple Debye-Huckel sphere boundary conditions 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 78.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 9.040108332204E+03 kJ/mol 260s Calculating forces... 260s [focusFillBound()]: WARNING: 260s Unusually large potential values 260s detected on the focusing boundary! 260s Convergence not guaranteed for NPBE/NRPBE calculations! 260s 260s ---------------------------------------- 260s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 30.4176 A 260s Current memory usage: 121.977 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 0.225 x 0.225 x 0.225 260s Grid lengths: 14.400 x 14.400 x 14.400 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 3 260s Linearized traditional PBE 260s Boundary conditions from focusing 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 78.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 3.787747796627E+04 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 4.87072 A 260s Current memory usage: 121.977 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 1.500 x 1.500 x 1.500 260s Grid lengths: 96.000 x 96.000 x 96.000 260s Grid center: (25.264, 18.988, 19.122) 260s Multigrid levels: 5 260s Molecule ID: 3 260s Linearized traditional PBE 260s Multiple Debye-Huckel sphere boundary conditions 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 2.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 1.252495566243E+04 kJ/mol 260s Calculating forces... 260s [focusFillBound()]: WARNING: 260s Unusually large potential values 260s detected on the focusing boundary! 260s Convergence not guaranteed for NPBE/NRPBE calculations! 260s 260s ---------------------------------------- 260s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 260s Setting up problem... 260s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 260s Debye length: 4.87072 A 260s Current memory usage: 121.977 MB total, 222.305 MB high water 260s Using linear spline charge discretization. 260s Grid dimensions: 65 x 65 x 65 260s Grid spacings: 0.225 x 0.225 x 0.225 260s Grid lengths: 14.400 x 14.400 x 14.400 260s Grid center: (17.340, 19.211, 20.503) 260s Multigrid levels: 5 260s Molecule ID: 3 260s Linearized traditional PBE 260s Boundary conditions from focusing 260s 2 ion species (0.010 M ionic strength): 260s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 260s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 260s Solute dielectric: 2.000 260s Solvent dielectric: 2.000 260s Using "molecular" surface definition; no smoothing 260s Solvent probe radius: 0.000 A 260s Temperature: 300.000 K 260s Electrostatic energies will be calculated 260s Total electrostatic energy = 4.133237922574E+04 kJ/mol 260s Calculating forces... 260s ---------------------------------------- 260s PRINT STATEMENTS 260s 260s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 260s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 260s Global net ELEC energy = -3.460997931137E+03 kJ/mol 260s 260s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 260s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 260s Global net ELEC energy = -2.052167100108E+01 kJ/mol 260s 260s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 260s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 260s Global net ELEC energy = -3.454901259473E+03 kJ/mol 260s 260s 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 260s Local net energy (PE 0) = 1.442499933664E+01 kJ/mol 260s Global net ELEC energy = 1.442499933664E+01 kJ/mol 260s ---------------------------------------- 260s CLEANING UP AND SHUTTING DOWN... 260s Destroying force arrays. 260s No energy arrays to destroy. 260s Destroying multigrid structures. 260s Destroying finite element structures. 260s Destroying 3 molecules 260s Final memory usage: 0.001 MB total, 222.305 MB high water 260s 260s 260s Thanks for using APBS! 260s 260s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 260s *** PASSED *** 260s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 260s *** PASSED *** 260s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 260s *** PASSED *** 260s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 260s *** PASSED *** 260s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 260s *** PASSED *** 260s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 260s *** PASSED *** 260s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 260s *** PASSED *** 260s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 260s *** PASSED *** 260s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 260s *** PASSED *** 260s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 260s *** PASSED *** 260s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 260s *** PASSED *** 260s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 260s *** PASSED *** 260s Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) 260s *** PASSED *** 260s Elapsed time: 8.741097 seconds 260s -------------------------------------------------------------------------------- 260s -------------------------------------------------------------------------------- 260s Testing input file 1d7i-dss-smol.in 260s 268s Checking for intermediate energies in input file 1d7i-dss-mol.out 268s EXPECTED COMPUTED: 16 268s EXPECTED EXPECTED: 16 268s COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933664] 268s 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'] 268s COMPUTED RESULT 9160.578033846 268s COMPUTED RESULT 39557.01871716 268s COMPUTED RESULT 12649.65939588 268s COMPUTED RESULT 43018.01664829 268s COMPUTED RESULT 94.31133325426 268s COMPUTED RESULT 1677.348113184 268s COMPUTED RESULT 117.1079106781 268s COMPUTED RESULT 1697.869784185 268s COMPUTED RESULT 9040.108332204 268s COMPUTED RESULT 37877.47796627 268s COMPUTED RESULT 12524.95566243 268s COMPUTED RESULT 41332.37922574 268s COMPUTED RESULT -3460.997931137 268s COMPUTED RESULT -20.52167100108 268s COMPUTED RESULT -3454.901259473 268s COMPUTED RESULT 14.42499933664 268s BINARY: /usr/bin/apbs 268s INPUT: 1d7i-dss-smol.in 268s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 268s asc_getToken: Error occurred (bailing out). 268s Vio_scanf: Format problem with input. 268s 268s 268s ---------------------------------------------------------------------- 268s APBS -- Adaptive Poisson-Boltzmann Solver 268s Version APBS 3.4.1 268s 268s Nathan A. Baker (nathan.baker@pnnl.gov) 268s Pacific Northwest National Laboratory 268s 268s Additional contributing authors listed in the code documentation. 268s 268s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 268s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 268s Northwest Division for the U.S. Department of Energy. 268s 268s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 268s Portions Copyright (c) 2002-2020, Nathan A. Baker. 268s Portions Copyright (c) 1999-2002, The Regents of the University of California. 268s Portions Copyright (c) 1995, Michael Holst. 268s All rights reserved. 268s 268s Redistribution and use in source and binary forms, with or without 268s modification, are permitted provided that the following conditions are met: 268s 268s * Redistributions of source code must retain the above copyright notice, this 268s list of conditions and the following disclaimer. 268s 268s * Redistributions in binary form must reproduce the above copyright notice, 268s this list of conditions and the following disclaimer in the documentation 268s and/or other materials provided with the distribution. 268s 268s * Neither the name of the developer nor the names of its contributors may be 268s used to endorse or promote products derived from this software without 268s specific prior written permission. 268s 268s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 268s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 268s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 268s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 268s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 268s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 268s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 268s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 268s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 268s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 268s ---------------------------------------------------------------------- 268s APBS uses FETK (the Finite Element ToolKit) to solve the 268s Poisson-Boltzmann equation numerically. FETK is a portable collection 268s of finite element modeling class libraries developed by the Michael Holst 268s research group and written in an object-oriented form of C. FEtk is 268s designed to solve general coupled systems of nonlinear partial differential 268s equations using adaptive finite element methods, inexact Newton methods, 268s and algebraic multilevel methods. More information about FEtk may be found 268s at . 268s ---------------------------------------------------------------------- 268s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 268s Aqua is a modified form of the Holst group PMG library 268s which has been modified by Patrice Koehl 268s for improved efficiency and 268s memory usage when solving the Poisson-Boltzmann equation. 268s ---------------------------------------------------------------------- 268s Please cite your use of APBS as: 268s 268s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 268s nanosystems: application to microtubules and the ribosome. Proc. 268s Natl. Acad. Sci. USA 98, 10037-10041 2001. 268s 268s 268s This executable compiled on Jan 3 2025 at 11:01:42 268s 268s Parsing input file 1d7i-dss-smol.in... 268s rank 0 size 1... 268s Parsed input file. 268s Got paths for 3 molecules 268s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 268s asc_getToken: Error occurred (bailing out). 268s Vio_scanf: Format problem with input. 268s 1677 atoms 268s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 268s Net charge 9.91e-01 e 268s Reading PQR-format atom data from dss-min.pqr. 268s asc_getToken: Error occurred (bailing out). 268s Vio_scanf: Format problem with input. 268s 14 atoms 268s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 268s Net charge -8.33e-17 e 268s Reading PQR-format atom data from 1d7i-min.pqr. 268s 1663 atoms 268s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 268s Net charge 9.91e-01 e 268s Preparing to run 12 PBE calculations. 268s ---------------------------------------- 268s CALCULATION #1 (complex-solv-coarse): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 30.4176 A 268s Current memory usage: 122.425 MB total, 122.425 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 1.500 x 1.500 x 1.500 268s Grid lengths: 96.000 x 96.000 x 96.000 268s Grid center: (25.264, 18.988, 19.122) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 9.634884642408E+03 kJ/mol 268s Calculating forces... 268s [focusFillBound()]: WARNING: 268s Unusually large potential values 268s detected on the focusing boundary! 268s Convergence not guaranteed for NPBE/NRPBE calculations! 268s 268s ---------------------------------------- 268s CALCULATION #2 (complex-solv-fine): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 30.4176 A 268s Current memory usage: 122.425 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.225 x 0.225 x 0.225 268s Grid lengths: 14.400 x 14.400 x 14.400 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 4.003177540425E+04 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #3 (complex-ref-coarse): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 4.87072 A 268s Current memory usage: 122.425 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 1.500 x 1.500 x 1.500 268s Grid lengths: 96.000 x 96.000 x 96.000 268s Grid center: (25.264, 18.988, 19.122) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 2.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.264965939588E+04 kJ/mol 268s Calculating forces... 268s [focusFillBound()]: WARNING: 268s Unusually large potential values 268s detected on the focusing boundary! 268s Convergence not guaranteed for NPBE/NRPBE calculations! 268s 268s ---------------------------------------- 268s CALCULATION #4 (complex-ref-fine): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 4.87072 A 268s Current memory usage: 122.425 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.225 x 0.225 x 0.225 268s Grid lengths: 14.400 x 14.400 x 14.400 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 1 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 2.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 4.301801664829E+04 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #5 (dss-solv-coarse): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 30.4176 A 268s Current memory usage: 62.528 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 1.500 x 1.500 x 1.500 268s Grid lengths: 96.000 x 96.000 x 96.000 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 2 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 7.942232645345E+01 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #6 (dss-solv-fine): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 30.4176 A 268s Current memory usage: 62.528 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.225 x 0.225 x 0.225 268s Grid lengths: 14.400 x 14.400 x 14.400 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 2 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.677798535473E+03 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #7 (dss-ref-coarse): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 4.87072 A 268s Current memory usage: 62.528 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 1.500 x 1.500 x 1.500 268s Grid lengths: 96.000 x 96.000 x 96.000 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 2 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 2.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.171079106781E+02 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #8 (dss-ref-fine): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 4.87072 A 268s Current memory usage: 62.528 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.225 x 0.225 x 0.225 268s Grid lengths: 14.400 x 14.400 x 14.400 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 2 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 2.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.697869784185E+03 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 30.4176 A 268s Current memory usage: 121.977 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 1.500 x 1.500 x 1.500 268s Grid lengths: 96.000 x 96.000 x 96.000 268s Grid center: (25.264, 18.988, 19.122) 268s Multigrid levels: 5 268s Molecule ID: 3 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 9.507068451372E+03 kJ/mol 268s Calculating forces... 268s [focusFillBound()]: WARNING: 268s Unusually large potential values 268s detected on the focusing boundary! 268s Convergence not guaranteed for NPBE/NRPBE calculations! 268s 268s ---------------------------------------- 268s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 30.4176 A 268s Current memory usage: 121.977 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.225 x 0.225 x 0.225 268s Grid lengths: 14.400 x 14.400 x 14.400 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 3 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 3.835075772299E+04 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 4.87072 A 268s Current memory usage: 121.977 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 1.500 x 1.500 x 1.500 268s Grid lengths: 96.000 x 96.000 x 96.000 268s Grid center: (25.264, 18.988, 19.122) 268s Multigrid levels: 5 268s Molecule ID: 3 268s Linearized traditional PBE 268s Multiple Debye-Huckel sphere boundary conditions 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 2.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.252495566243E+04 kJ/mol 268s Calculating forces... 268s [focusFillBound()]: WARNING: 268s Unusually large potential values 268s detected on the focusing boundary! 268s Convergence not guaranteed for NPBE/NRPBE calculations! 268s 268s ---------------------------------------- 268s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 4.87072 A 268s Current memory usage: 121.977 MB total, 222.305 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 65 x 65 x 65 268s Grid spacings: 0.225 x 0.225 x 0.225 268s Grid lengths: 14.400 x 14.400 x 14.400 268s Grid center: (17.340, 19.211, 20.503) 268s Multigrid levels: 5 268s Molecule ID: 3 268s Linearized traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.010 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 2.000 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 0.000 A 268s Temperature: 300.000 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 4.133237922574E+04 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s PRINT STATEMENTS 268s 268s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 268s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 268s Global net ELEC energy = -2.986241244040E+03 kJ/mol 268s 268s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 268s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 268s Global net ELEC energy = -2.007124871262E+01 kJ/mol 268s 268s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 268s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 268s Global net ELEC energy = -2.981621502756E+03 kJ/mol 268s 268s 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 268s Local net energy (PE 0) = 1.545150742843E+01 kJ/mol 268s Global net ELEC energy = 1.545150742843E+01 kJ/mol 268s ---------------------------------------- 268s CLEANING UP AND SHUTTING DOWN... 268s Destroying force arrays. 268s No energy arrays to destroy. 268s Destroying multigrid structures. 268s Destroying finite element structures. 268s Destroying 3 molecules 268s Final memory usage: 0.001 MB total, 222.305 MB high water 268s 268s 268s Thanks for using APBS! 268s 268s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 268s *** PASSED *** 268s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 268s *** PASSED *** 268s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 268s *** PASSED *** 268s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 268s *** PASSED *** 268s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 268s *** PASSED *** 268s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 268s *** PASSED *** 268s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 268s *** PASSED *** 268s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 268s *** PASSED *** 268s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 268s *** PASSED *** 268s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 268s *** PASSED *** 268s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 268s *** PASSED *** 268s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 268s *** PASSED *** 268s Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) 268s *** PASSED *** 268s Elapsed time: 8.378634 seconds 268s -------------------------------------------------------------------------------- 268s Total elapsed time: 34.5086 seconds 268s Test results have been logged 268s -------------------------------------------------------------------------------- 268s -------------------------------------------------------------------------------- 268s Testing input file apbs-mol.in 268s 276s Checking for intermediate energies in input file 1d7i-dss-smol.out 276s EXPECTED COMPUTED: 16 276s EXPECTED EXPECTED: 16 276s COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742843] 276s 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'] 276s COMPUTED RESULT 9634.884642408 276s COMPUTED RESULT 40031.77540425 276s COMPUTED RESULT 12649.65939588 276s COMPUTED RESULT 43018.01664829 276s COMPUTED RESULT 79.42232645345 276s COMPUTED RESULT 1677.798535473 276s COMPUTED RESULT 117.1079106781 276s COMPUTED RESULT 1697.869784185 276s COMPUTED RESULT 9507.068451372 276s COMPUTED RESULT 38350.75772299 276s COMPUTED RESULT 12524.95566243 276s COMPUTED RESULT 41332.37922574 276s COMPUTED RESULT -2986.24124404 276s COMPUTED RESULT -20.07124871262 276s COMPUTED RESULT -2981.621502756 276s COMPUTED RESULT 15.45150742843 276s Running tests for hca-bind section 276s BINARY: /usr/bin/apbs 276s INPUT: apbs-mol.in 276s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 276s asc_getToken: Error occurred (bailing out). 276s Vio_scanf: Format problem with input. 276s 276s 276s ---------------------------------------------------------------------- 276s APBS -- Adaptive Poisson-Boltzmann Solver 276s Version APBS 3.4.1 276s 276s Nathan A. Baker (nathan.baker@pnnl.gov) 276s Pacific Northwest National Laboratory 276s 276s Additional contributing authors listed in the code documentation. 276s 276s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 276s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 276s Northwest Division for the U.S. Department of Energy. 276s 276s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 276s Portions Copyright (c) 2002-2020, Nathan A. Baker. 276s Portions Copyright (c) 1999-2002, The Regents of the University of California. 276s Portions Copyright (c) 1995, Michael Holst. 276s All rights reserved. 276s 276s Redistribution and use in source and binary forms, with or without 276s modification, are permitted provided that the following conditions are met: 276s 276s * Redistributions of source code must retain the above copyright notice, this 276s list of conditions and the following disclaimer. 276s 276s * Redistributions in binary form must reproduce the above copyright notice, 276s this list of conditions and the following disclaimer in the documentation 276s and/or other materials provided with the distribution. 276s 276s * Neither the name of the developer nor the names of its contributors may be 276s used to endorse or promote products derived from this software without 276s specific prior written permission. 276s 276s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 276s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 276s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 276s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 276s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 276s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 276s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 276s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 276s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 276s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 276s ---------------------------------------------------------------------- 276s APBS uses FETK (the Finite Element ToolKit) to solve the 276s Poisson-Boltzmann equation numerically. FETK is a portable collection 276s of finite element modeling class libraries developed by the Michael Holst 276s research group and written in an object-oriented form of C. FEtk is 276s designed to solve general coupled systems of nonlinear partial differential 276s equations using adaptive finite element methods, inexact Newton methods, 276s and algebraic multilevel methods. More information about FEtk may be found 276s at . 276s ---------------------------------------------------------------------- 276s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 276s Aqua is a modified form of the Holst group PMG library 276s which has been modified by Patrice Koehl 276s for improved efficiency and 276s memory usage when solving the Poisson-Boltzmann equation. 276s ---------------------------------------------------------------------- 276s Please cite your use of APBS as: 276s 276s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 276s nanosystems: application to microtubules and the ribosome. Proc. 276s Natl. Acad. Sci. USA 98, 10037-10041 2001. 276s 276s 276s This executable compiled on Jan 3 2025 at 11:01:42 276s 276s Parsing input file apbs-mol.in... 276s rank 0 size 1... 276s Parsed input file. 276s Got paths for 3 molecules 276s Reading PQR-format atom data from acet.pqr. 276s asc_getToken: Error occurred (bailing out). 276s Vio_scanf: Format problem with input. 276s 18 atoms 276s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 276s Net charge -1.00e+00 e 276s Reading PQR-format atom data from hca.pqr. 276s asc_getToken: Error occurred (bailing out). 276s Vio_scanf: Format problem with input. 276s 2482 atoms 276s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 276s Net charge 1.00e+00 e 276s Reading PQR-format atom data from complex.pqr. 276s 2500 atoms 276s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 276s Net charge -1.02e-14 e 276s Preparing to run 9 PBE calculations. 276s ---------------------------------------- 276s CALCULATION #1 (acet): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 62.727 MB total, 62.727 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 1.500 x 1.500 x 1.500 276s Grid lengths: 96.000 x 96.000 x 96.000 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 1 276s Linearized traditional PBE 276s Single Debye-Huckel sphere boundary conditions 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 2.213600726771E+02 kJ/mol 276s Calculating forces... 276s ---------------------------------------- 276s CALCULATION #2 (acet): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 62.727 MB total, 123.701 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 0.581 x 0.581 x 0.581 276s Grid lengths: 37.181 x 37.181 x 37.181 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 1 276s Linearized traditional PBE 276s Boundary conditions from focusing 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 1.825764811255E+03 kJ/mol 276s Calculating forces... 276s ---------------------------------------- 276s CALCULATION #3 (acet): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 62.727 MB total, 123.701 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 0.225 x 0.225 x 0.225 276s Grid lengths: 14.400 x 14.400 x 14.400 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 1 276s Linearized traditional PBE 276s Boundary conditions from focusing 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 6.458471211905E+03 kJ/mol 276s Calculating forces... 276s ---------------------------------------- 276s CALCULATION #4 (hca): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 146.516 MB total, 146.516 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 1.500 x 1.500 x 1.500 276s Grid lengths: 96.000 x 96.000 x 96.000 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 2 276s Linearized traditional PBE 276s Single Debye-Huckel sphere boundary conditions 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 2.093606095527E+04 kJ/mol 276s Calculating forces... 276s [focusFillBound()]: WARNING: 276s Unusually large potential values 276s detected on the focusing boundary! 276s Convergence not guaranteed for NPBE/NRPBE calculations! 276s 276s ---------------------------------------- 276s CALCULATION #5 (hca): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 146.516 MB total, 245.092 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 0.581 x 0.581 x 0.581 276s Grid lengths: 37.181 x 37.181 x 37.181 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 2 276s Linearized traditional PBE 276s Boundary conditions from focusing 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 1.515433544464E+05 kJ/mol 276s Calculating forces... 276s [focusFillBound()]: WARNING: 276s Unusually large potential values 276s detected on the focusing boundary! 276s Convergence not guaranteed for NPBE/NRPBE calculations! 276s 276s ---------------------------------------- 276s CALCULATION #6 (hca): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 146.516 MB total, 245.092 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 0.225 x 0.225 x 0.225 276s Grid lengths: 14.400 x 14.400 x 14.400 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 2 276s Linearized traditional PBE 276s Boundary conditions from focusing 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 1.786369323561E+05 kJ/mol 276s Calculating forces... 276s ---------------------------------------- 276s CALCULATION #7 (complex): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 146.926 MB total, 245.092 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 1.500 x 1.500 x 1.500 276s Grid lengths: 96.000 x 96.000 x 96.000 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 3 276s Linearized traditional PBE 276s Single Debye-Huckel sphere boundary conditions 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 2.105322784838E+04 kJ/mol 276s Calculating forces... 276s [focusFillBound()]: WARNING: 276s Unusually large potential values 276s detected on the focusing boundary! 276s Convergence not guaranteed for NPBE/NRPBE calculations! 276s 276s ---------------------------------------- 276s CALCULATION #8 (complex): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 146.926 MB total, 245.725 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 0.581 x 0.581 x 0.581 276s Grid lengths: 37.181 x 37.181 x 37.181 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 3 276s Linearized traditional PBE 276s Boundary conditions from focusing 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 1.533304996252E+05 kJ/mol 276s Calculating forces... 276s [focusFillBound()]: WARNING: 276s Unusually large potential values 276s detected on the focusing boundary! 276s Convergence not guaranteed for NPBE/NRPBE calculations! 276s 276s ---------------------------------------- 276s CALCULATION #9 (complex): MULTIGRID 276s Setting up problem... 276s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 276s Debye length: 0 A 276s Current memory usage: 146.926 MB total, 245.725 MB high water 276s Using linear spline charge discretization. 276s Grid dimensions: 65 x 65 x 65 276s Grid spacings: 0.225 x 0.225 x 0.225 276s Grid lengths: 14.400 x 14.400 x 14.400 276s Grid center: (-6.028, 3.898, 15.179) 276s Multigrid levels: 5 276s Molecule ID: 3 276s Linearized traditional PBE 276s Boundary conditions from focusing 276s 2 ion species (0.000 M ionic strength): 276s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 276s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 276s Solute dielectric: 2.000 276s Solvent dielectric: 78.540 276s Using "molecular" surface definition; no smoothing 276s Solvent probe radius: 0.000 A 276s Temperature: 298.150 K 276s Electrostatic energies will be calculated 276s Total electrostatic energy = 1.850429388099E+05 kJ/mol 276s Calculating forces... 276s ---------------------------------------- 276s PRINT STATEMENTS 276s 276s print energy 3 (complex) - 1 (acet) - 2 (hca) end 276s Local net energy (PE 0) = -5.246475812684E+01 kJ/mol 276s Global net ELEC energy = -5.246475812684E+01 kJ/mol 276s ---------------------------------------- 276s CLEANING UP AND SHUTTING DOWN... 276s Destroying force arrays. 276s No energy arrays to destroy. 276s Destroying multigrid structures. 276s Destroying finite element structures. 276s Destroying 3 molecules 276s Final memory usage: 0.001 MB total, 245.725 MB high water 276s 276s 276s Thanks for using APBS! 276s 276s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 276s *** PASSED *** 276s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 276s *** PASSED *** 276s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 276s *** PASSED *** 276s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 276s *** PASSED *** 276s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 276s *** PASSED *** 276s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 276s *** PASSED *** 276s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 276s *** PASSED *** 276s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 276s *** PASSED *** 276s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 276s *** PASSED *** 276s Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) 276s *** PASSED *** 276s Elapsed time: 7.600938 seconds 276s -------------------------------------------------------------------------------- 276s -------------------------------------------------------------------------------- 276s Testing input file apbs-smol.in 276s 283s Checking for intermediate energies in input file apbs-mol.out 283s EXPECTED COMPUTED: 10 283s EXPECTED EXPECTED: 10 283s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] 283s 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'] 283s COMPUTED RESULT 221.3600726771 283s COMPUTED RESULT 1825.764811255 283s COMPUTED RESULT 6458.471211905 283s COMPUTED RESULT 20936.06095527 283s COMPUTED RESULT 151543.3544464 283s COMPUTED RESULT 178636.9323561 283s COMPUTED RESULT 21053.22784838 283s COMPUTED RESULT 153330.4996252 283s COMPUTED RESULT 185042.9388099 283s COMPUTED RESULT -52.46475812684 283s BINARY: /usr/bin/apbs 283s INPUT: apbs-smol.in 283s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 283s 283s ---------------------------------------------------------------------- 283s APBS -- Adaptive Poisson-Boltzmann Solver 283s Version APBS 3.4.1 283s 283s Nathan A. Baker (nathan.baker@pnnl.gov) 283s Pacific Northwest National Laboratory 283s 283s Additional contributing authors listed in the code documentation. 283s 283s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 283s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 283s Northwest Division for the U.S. Department of Energy. 283s 283s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 283s Portions Copyright (c) 2002-2020, Nathan A. Baker. 283s Portions Copyright (c) 1999-2002, The Regents of the University of California. 283s Portions Copyright (c) 1995, Michael Holst. 283s All rights reserved. 283s 283s Redistribution and use in source and binary forms, with or without 283s modification, are permitted provided that the following conditions are met: 283s 283s * Redistributions of source code must retain the above copyright notice, this 283s list of conditions and the following disclaimer. 283s 283s * Redistributions in binary form must reproduce the above copyright notice, 283s this list of conditions and the following disclaimer in the documentation 283s and/or other materials provided with the distribution. 283s 283s * Neither the name of the developer nor the names of its contributors may be 283s used to endorse or promote products derived from this software without 283s specific prior written permission. 283s 283s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 283s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 283s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 283s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 283s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 283s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 283s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 283s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 283s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 283s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 283s ---------------------------------------------------------------------- 283s APBS uses FETK (the Finite Element ToolKit) to solve the 283s Poisson-Boltzmann equation numerically. FETK is a portable collection 283s of finite element modeling class libraries developed by the Michael Holst 283s research group and written in an object-oriented form of C. FEtk is 283s designed to solve general coupled systems of nonlinear partial differential 283s equations using adaptive finite element methods, inexact Newton methods, 283s and algebraic multilevel methods. More information about FEtk may be found 283s at . 283s ---------------------------------------------------------------------- 283s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 283s Aqua is a modified form of the Holst group PMG library 283s which has been modified by Patrice Koehl 283s for improved efficiency and 283s memory usage when solving the Poisson-Boltzmann equation. 283s ---------------------------------------------------------------------- 283s Please cite your use of APBS as: 283s 283s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 283s nanosystems: application to microtubules and the ribosome. Proc. 283s Natl. Acad. Sci. USA 98, 10037-10041 2001. 283s 283s 283s This executable compiled on Jan 3 2025 at 11:01:42 283s 283s Parsing input file apbs-smol.in... 283s rank 0 size 1... 283s Parsed input file. 283s Got paths for 3 molecules 283s Reading PQR-format atom data from acet.pqr. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 18 atoms 283s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 283s Net charge -1.00e+00 e 283s Reading PQR-format atom data from hca.pqr. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 2482 atoms 283s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 283s Net charge 1.00e+00 e 283s Reading PQR-format atom data from complex.pqr. 283s 2500 atoms 283s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 283s Net charge -1.02e-14 e 283s Preparing to run 9 PBE calculations. 283s ---------------------------------------- 283s CALCULATION #1 (acet): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 62.727 MB total, 62.727 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 1.500 x 1.500 x 1.500 283s Grid lengths: 96.000 x 96.000 x 96.000 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 1 283s Linearized traditional PBE 283s Single Debye-Huckel sphere boundary conditions 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 1.884888131017E+02 kJ/mol 283s Calculating forces... 283s ---------------------------------------- 283s CALCULATION #2 (acet): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 62.727 MB total, 123.701 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 0.581 x 0.581 x 0.581 283s Grid lengths: 37.181 x 37.181 x 37.181 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 1 283s Linearized traditional PBE 283s Boundary conditions from focusing 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 1.820045922544E+03 kJ/mol 283s Calculating forces... 283s ---------------------------------------- 283s CALCULATION #3 (acet): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 62.727 MB total, 123.701 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 0.225 x 0.225 x 0.225 283s Grid lengths: 14.400 x 14.400 x 14.400 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 1 283s Linearized traditional PBE 283s Boundary conditions from focusing 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 6.460002606908E+03 kJ/mol 283s Calculating forces... 283s ---------------------------------------- 283s CALCULATION #4 (hca): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 146.516 MB total, 146.516 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 1.500 x 1.500 x 1.500 283s Grid lengths: 96.000 x 96.000 x 96.000 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 2 283s Linearized traditional PBE 283s Single Debye-Huckel sphere boundary conditions 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 2.189161497021E+04 kJ/mol 283s Calculating forces... 283s [focusFillBound()]: WARNING: 283s Unusually large potential values 283s detected on the focusing boundary! 283s Convergence not guaranteed for NPBE/NRPBE calculations! 283s 283s ---------------------------------------- 283s CALCULATION #5 (hca): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 146.516 MB total, 245.092 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 0.581 x 0.581 x 0.581 283s Grid lengths: 37.181 x 37.181 x 37.181 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 2 283s Linearized traditional PBE 283s Boundary conditions from focusing 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 1.520000494925E+05 kJ/mol 283s Calculating forces... 283s [focusFillBound()]: WARNING: 283s Unusually large potential values 283s detected on the focusing boundary! 283s Convergence not guaranteed for NPBE/NRPBE calculations! 283s 283s ---------------------------------------- 283s CALCULATION #6 (hca): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 146.516 MB total, 245.092 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 0.225 x 0.225 x 0.225 283s Grid lengths: 14.400 x 14.400 x 14.400 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 2 283s Linearized traditional PBE 283s Boundary conditions from focusing 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 1.790436191580E+05 kJ/mol 283s Calculating forces... 283s ---------------------------------------- 283s CALCULATION #7 (complex): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 146.926 MB total, 245.092 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 1.500 x 1.500 x 1.500 283s Grid lengths: 96.000 x 96.000 x 96.000 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 3 283s Linearized traditional PBE 283s Single Debye-Huckel sphere boundary conditions 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 2.195842512312E+04 kJ/mol 283s Calculating forces... 283s [focusFillBound()]: WARNING: 283s Unusually large potential values 283s detected on the focusing boundary! 283s Convergence not guaranteed for NPBE/NRPBE calculations! 283s 283s ---------------------------------------- 283s CALCULATION #8 (complex): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 146.926 MB total, 245.725 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 0.581 x 0.581 x 0.581 283s Grid lengths: 37.181 x 37.181 x 37.181 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 3 283s Linearized traditional PBE 283s Boundary conditions from focusing 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 1.537771604355E+05 kJ/mol 283s Calculating forces... 283s [focusFillBound()]: WARNING: 283s Unusually large potential values 283s detected on the focusing boundary! 283s Convergence not guaranteed for NPBE/NRPBE calculations! 283s 283s ---------------------------------------- 283s CALCULATION #9 (complex): MULTIGRID 283s Setting up problem... 283s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 283s Debye length: 0 A 283s Current memory usage: 146.926 MB total, 245.725 MB high water 283s Using linear spline charge discretization. 283s Grid dimensions: 65 x 65 x 65 283s Grid spacings: 0.225 x 0.225 x 0.225 283s Grid lengths: 14.400 x 14.400 x 14.400 283s Grid center: (-6.028, 3.898, 15.179) 283s Multigrid levels: 5 283s Molecule ID: 3 283s Linearized traditional PBE 283s Boundary conditions from focusing 283s 2 ion species (0.000 M ionic strength): 283s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 283s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 283s Solute dielectric: 2.000 283s Solvent dielectric: 78.540 283s Using "molecular" surface definition;harmonic average smoothing 283s Solvent probe radius: 0.000 A 283s Temperature: 298.150 K 283s Electrostatic energies will be calculated 283s Total electrostatic energy = 1.854495619747E+05 kJ/mol 283s Calculating forces... 283s ---------------------------------------- 283s PRINT STATEMENTS 283s 283s print energy 3 (complex) - 1 (acet) - 2 (hca) end 283s Local net energy (PE 0) = -5.405979017059E+01 kJ/mol 283s Global net ELEC energy = -5.405979017059E+01 kJ/mol 283s ---------------------------------------- 283s CLEANING UP AND SHUTTING DOWN... 283s Destroying force arrays. 283s No energy arrays to destroy. 283s Destroying multigrid structures. 283s Destroying finite element structures. 283s Destroying 3 molecules 283s Final memory usage: 0.001 MB total, 245.725 MB high water 283s 283s 283s Thanks for using APBS! 283s 283s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 283s *** PASSED *** 283s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 283s *** PASSED *** 283s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 283s *** PASSED *** 283s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 283s *** PASSED *** 283s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 283s *** PASSED *** 283s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 283s *** PASSED *** 283s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 283s *** PASSED *** 283s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 283s *** PASSED *** 283s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 283s *** PASSED *** 283s Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) 283s *** PASSED *** 283s Elapsed time: 6.989998 seconds 283s -------------------------------------------------------------------------------- 283s Total elapsed time: 14.590936 seconds 283s Test results have been logged 283s -------------------------------------------------------------------------------- 283s -------------------------------------------------------------------------------- 283s Testing input file apbs-mol.in 283s 285s Checking for intermediate energies in input file apbs-smol.out 285s EXPECTED COMPUTED: 10 285s EXPECTED EXPECTED: 10 285s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] 285s 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'] 285s COMPUTED RESULT 188.4888131017 285s COMPUTED RESULT 1820.045922544 285s COMPUTED RESULT 6460.002606908 285s COMPUTED RESULT 21891.61497021 285s COMPUTED RESULT 152000.0494925 285s COMPUTED RESULT 179043.619158 285s COMPUTED RESULT 21958.42512312 285s COMPUTED RESULT 153777.1604355 285s COMPUTED RESULT 185449.5619747 285s COMPUTED RESULT -54.05979017059 285s Running tests for ionize section 285s BINARY: /usr/bin/apbs 285s INPUT: apbs-mol.in 285s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 285s asc_getToken: Error occurred (bailing out). 285s Vio_scanf: Format problem with input. 285s 285s 285s ---------------------------------------------------------------------- 285s APBS -- Adaptive Poisson-Boltzmann Solver 285s Version APBS 3.4.1 285s 285s Nathan A. Baker (nathan.baker@pnnl.gov) 285s Pacific Northwest National Laboratory 285s 285s Additional contributing authors listed in the code documentation. 285s 285s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 285s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 285s Northwest Division for the U.S. Department of Energy. 285s 285s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 285s Portions Copyright (c) 2002-2020, Nathan A. Baker. 285s Portions Copyright (c) 1999-2002, The Regents of the University of California. 285s Portions Copyright (c) 1995, Michael Holst. 285s All rights reserved. 285s 285s Redistribution and use in source and binary forms, with or without 285s modification, are permitted provided that the following conditions are met: 285s 285s * Redistributions of source code must retain the above copyright notice, this 285s list of conditions and the following disclaimer. 285s 285s * Redistributions in binary form must reproduce the above copyright notice, 285s this list of conditions and the following disclaimer in the documentation 285s and/or other materials provided with the distribution. 285s 285s * Neither the name of the developer nor the names of its contributors may be 285s used to endorse or promote products derived from this software without 285s specific prior written permission. 285s 285s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 285s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 285s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 285s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 285s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 285s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 285s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 285s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 285s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 285s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 285s ---------------------------------------------------------------------- 285s APBS uses FETK (the Finite Element ToolKit) to solve the 285s Poisson-Boltzmann equation numerically. FETK is a portable collection 285s of finite element modeling class libraries developed by the Michael Holst 285s research group and written in an object-oriented form of C. FEtk is 285s designed to solve general coupled systems of nonlinear partial differential 285s equations using adaptive finite element methods, inexact Newton methods, 285s and algebraic multilevel methods. More information about FEtk may be found 285s at . 285s ---------------------------------------------------------------------- 285s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 285s Aqua is a modified form of the Holst group PMG library 285s which has been modified by Patrice Koehl 285s for improved efficiency and 285s memory usage when solving the Poisson-Boltzmann equation. 285s ---------------------------------------------------------------------- 285s Please cite your use of APBS as: 285s 285s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 285s nanosystems: application to microtubules and the ribosome. Proc. 285s Natl. Acad. Sci. USA 98, 10037-10041 2001. 285s 285s 285s This executable compiled on Jan 3 2025 at 11:01:42 285s 285s Parsing input file apbs-mol.in... 285s rank 0 size 1... 285s Parsed input file. 285s Got paths for 3 molecules 285s Reading PQR-format atom data from acetic-acid.pqr. 285s asc_getToken: Error occurred (bailing out). 285s Vio_scanf: Format problem with input. 285s 8 atoms 285s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 285s Net charge -1.67e-16 e 285s Reading PQR-format atom data from acetate.pqr. 285s asc_getToken: Error occurred (bailing out). 285s Vio_scanf: Format problem with input. 285s 8 atoms 285s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 285s Net charge -1.00e+00 e 285s Reading PQR-format atom data from proton.pqr. 285s 1 atoms 285s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 285s Net charge 1.00e+00 e 285s Preparing to run 12 PBE calculations. 285s ---------------------------------------- 285s CALCULATION #1 (acetic-solv): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 7.76163 A 285s Current memory usage: 61.598 MB total, 61.598 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.188 x 0.188 x 0.188 285s Grid lengths: 12.000 x 12.000 x 12.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 1 285s Linearized traditional PBE 285s Multiple Debye-Huckel sphere boundary conditions 285s 2 ion species (0.150 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 78.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 5.823898055191E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #2 (acetic-solv): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 7.76163 A 285s Current memory usage: 61.598 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.094 x 0.094 x 0.094 285s Grid lengths: 6.000 x 6.000 x 6.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 1 285s Linearized traditional PBE 285s Boundary conditions from focusing 285s 2 ion species (0.150 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 78.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 9.793274462353E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #3 (acetic-ref): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 0 A 285s Current memory usage: 61.422 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.188 x 0.188 x 0.188 285s Grid lengths: 12.000 x 12.000 x 12.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 1 285s Linearized traditional PBE 285s Multiple Debye-Huckel sphere boundary conditions 285s 2 ion species (0.000 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 285s 2.000 A-radius, -1.000 e-Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 285s *** PASSED *** 285s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 285s *** PASSED *** 285s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 285s *** PASSED *** 285s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 285s *** PASSED *** 285s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 285s *** PASSED *** 285s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 285s *** PASSED *** 285s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 285s *** PASSED *** 285s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 285s *** PASSED *** 285s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 285s *** PASSED *** 285s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 285s *** PASSED *** 285s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 285s *** PASSED *** 285s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 285s *** PASSED *** 285s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 285s *** PASSED *** 285s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 285s *** PASSED *** 285s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 285s *** PASSED *** 285s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 285s *** PASSED *** 285s Elapsed time: 1.72109 seconds 285s -------------------------------------------------------------------------------- 285s -------------------------------------------------------------------------------- 285s Testing input file apbs-smol.in 285s 285s charge, 0.000 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 2.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 5.846917564309E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #4 (acetic-ref): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 0 A 285s Current memory usage: 61.422 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.094 x 0.094 x 0.094 285s Grid lengths: 6.000 x 6.000 x 6.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 1 285s Linearized traditional PBE 285s Boundary conditions from focusing 285s 2 ion species (0.000 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 2.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 9.815953282539E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #5 (acetate-solv): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 7.76163 A 285s Current memory usage: 61.598 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.188 x 0.188 x 0.188 285s Grid lengths: 12.000 x 12.000 x 12.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 2 285s Linearized traditional PBE 285s Multiple Debye-Huckel sphere boundary conditions 285s 2 ion species (0.150 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 78.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 8.219846763777E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #6 (acetate-solv): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 7.76163 A 285s Current memory usage: 61.598 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.094 x 0.094 x 0.094 285s Grid lengths: 6.000 x 6.000 x 6.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 2 285s Linearized traditional PBE 285s Boundary conditions from focusing 285s 2 ion species (0.150 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 78.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 1.392741988698E+04 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #7 (acetate-ref): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 0 A 285s Current memory usage: 61.422 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.188 x 0.188 x 0.188 285s Grid lengths: 12.000 x 12.000 x 12.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 2 285s Linearized traditional PBE 285s Multiple Debye-Huckel sphere boundary conditions 285s 2 ion species (0.000 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 2.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 8.420373979905E+03 kJ/mol 285s Calculating forces... 285s [focusFillBound()]: WARNING: 285s Unusually large potential values 285s detected on the focusing boundary! 285s Convergence not guaranteed for NPBE/NRPBE calculations! 285s 285s ---------------------------------------- 285s CALCULATION #8 (acetate-ref): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 0 A 285s Current memory usage: 61.422 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.094 x 0.094 x 0.094 285s Grid lengths: 6.000 x 6.000 x 6.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 2 285s Linearized traditional PBE 285s Boundary conditions from focusing 285s 2 ion species (0.000 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 2.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 1.412716615065E+04 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #9 (proton-solv): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 7.76163 A 285s Current memory usage: 61.412 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.188 x 0.188 x 0.188 285s Grid lengths: 12.000 x 12.000 x 12.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 3 285s Linearized traditional PBE 285s Multiple Debye-Huckel sphere boundary conditions 285s 2 ion species (0.150 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 78.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 3.862359524598E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #10 (proton-solv): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 7.76163 A 285s Current memory usage: 61.412 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.094 x 0.094 x 0.094 285s Grid lengths: 6.000 x 6.000 x 6.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 3 285s Linearized traditional PBE 285s Boundary conditions from focusing 285s 2 ion species (0.150 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 78.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 6.288156251610E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s CALCULATION #11 (proton-ref): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 0 A 285s Current memory usage: 61.373 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.188 x 0.188 x 0.188 285s Grid lengths: 12.000 x 12.000 x 12.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 3 285s Linearized traditional PBE 285s Multiple Debye-Huckel sphere boundary conditions 285s 2 ion species (0.000 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 2.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 4.162533113906E+03 kJ/mol 285s Calculating forces... 285s [focusFillBound()]: WARNING: 285s Unusually large potential values 285s detected on the focusing boundary! 285s Convergence not guaranteed for NPBE/NRPBE calculations! 285s 285s ---------------------------------------- 285s CALCULATION #12 (proton-ref): MULTIGRID 285s Setting up problem... 285s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 285s Debye length: 0 A 285s Current memory usage: 61.373 MB total, 122.404 MB high water 285s Using linear spline charge discretization. 285s Grid dimensions: 65 x 65 x 65 285s Grid spacings: 0.094 x 0.094 x 0.094 285s Grid lengths: 6.000 x 6.000 x 6.000 285s Grid center: (0.000, -0.154, 1.287) 285s Multigrid levels: 5 285s Molecule ID: 3 285s Linearized traditional PBE 285s Boundary conditions from focusing 285s 2 ion species (0.000 M ionic strength): 285s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 285s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 285s Solute dielectric: 2.000 285s Solvent dielectric: 2.000 285s Using "molecular" surface definition; no smoothing 285s Solvent probe radius: 0.000 A 285s Temperature: 293.000 K 285s Electrostatic energies will be calculated 285s Total electrostatic energy = 6.585616091973E+03 kJ/mol 285s Calculating forces... 285s ---------------------------------------- 285s PRINT STATEMENTS 285s 285s print energy 1 (acetic-solv) - 2 (acetic-ref) end 285s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 285s Global net ELEC energy = -2.267882018629E+01 kJ/mol 285s 285s print energy 3 (acetate-solv) - 4 (acetate-ref) end 285s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 285s Global net ELEC energy = -1.997462636633E+02 kJ/mol 285s 285s print energy 5 (proton-solv) - 6 (proton-ref) end 285s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 285s Global net ELEC energy = -2.974598403628E+02 kJ/mol 285s 285s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 285s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 285s Global net ELEC energy = -4.745272838398E+02 kJ/mol 285s ---------------------------------------- 285s CLEANING UP AND SHUTTING DOWN... 285s Destroying force arrays. 285s No energy arrays to destroy. 285s Destroying multigrid structures. 285s Destroying finite element structures. 285s Destroying 3 molecules 285s Final memory usage: 0.001 MB total, 122.404 MB high water 285s 285s 285s Thanks for using APBS! 285s 286s Checking for intermediate energies in input file apbs-mol.out 286s EXPECTED COMPUTED: 16 286s EXPECTED EXPECTED: 16 286s 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] 286s 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'] 286s COMPUTED RESULT 5823.898055191 286s COMPUTED RESULT 9793.274462353 286s COMPUTED RESULT 5846.917564309 286s COMPUTED RESULT 9815.953282539 286s COMPUTED RESULT 8219.846763777 286s COMPUTED RESULT 13927.41988698 286s COMPUTED RESULT 8420.373979905 286s COMPUTED RESULT 14127.16615065 286s COMPUTED RESULT 3862.359524598 286s COMPUTED RESULT 6288.15625161 286s COMPUTED RESULT 4162.533113906 286s COMPUTED RESULT 6585.616091973 286s COMPUTED RESULT -22.67882018629 286s COMPUTED RESULT -199.7462636633 286s COMPUTED RESULT -297.4598403628 286s COMPUTED RESULT -474.5272838398 286s BINARY: /usr/bin/apbs 286s INPUT: apbs-smol.in 286s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 286s Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 286s *** PASSED *** 286s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 286s *** PASSED *** 286s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 286s *** PASSED *** 286s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 286s *** PASSED *** 286s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 286s *** PASSED *** 286s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 286s *** PASSED *** 286s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 286s *** PASSED *** 286s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 286s *** PASSED *** 286s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 286s *** PASSED *** 286s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 286s *** PASSED *** 286s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 286s *** PASSED *** 286s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 286s *** PASSED *** 286s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 286s *** PASSED *** 286s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 286s *** PASSED *** 286s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 286s *** PASSED *** 286s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 286s *** PASSED *** 286s Elapsed time: 1.572842 seconds 286s -------------------------------------------------------------------------------- 286s Total elapsed time: 3.293932 seconds 286s Test results have been logged 286s -------------------------------------------------------------------------------- 286s -------------------------------------------------------------------------------- 286s Testing input file ion-pmf.in 286s 286s asc_getToken: Error occurred (bailing out). 286s Vio_scanf: Format problem with input. 286s 286s 286s ---------------------------------------------------------------------- 286s APBS -- Adaptive Poisson-Boltzmann Solver 286s Version APBS 3.4.1 286s 286s Nathan A. Baker (nathan.baker@pnnl.gov) 286s Pacific Northwest National Laboratory 286s 286s Additional contributing authors listed in the code documentation. 286s 286s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 286s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 286s Northwest Division for the U.S. Department of Energy. 286s 286s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 286s Portions Copyright (c) 2002-2020, Nathan A. Baker. 286s Portions Copyright (c) 1999-2002, The Regents of the University of California. 286s Portions Copyright (c) 1995, Michael Holst. 286s All rights reserved. 286s 286s Redistribution and use in source and binary forms, with or without 286s modification, are permitted provided that the following conditions are met: 286s 286s * Redistributions of source code must retain the above copyright notice, this 286s list of conditions and the following disclaimer. 286s 286s * Redistributions in binary form must reproduce the above copyright notice, 286s this list of conditions and the following disclaimer in the documentation 286s and/or other materials provided with the distribution. 286s 286s * Neither the name of the developer nor the names of its contributors may be 286s used to endorse or promote products derived from this software without 286s specific prior written permission. 286s 286s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 286s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 286s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 286s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 286s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 286s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 286s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 286s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 286s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 286s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 286s ---------------------------------------------------------------------- 286s APBS uses FETK (the Finite Element ToolKit) to solve the 286s Poisson-Boltzmann equation numerically. FETK is a portable collection 286s of finite element modeling class libraries developed by the Michael Holst 286s research group and written in an object-oriented form of C. FEtk is 286s designed to solve general coupled systems of nonlinear partial differential 286s equations using adaptive finite element methods, inexact Newton methods, 286s and algebraic multilevel methods. More information about FEtk may be found 286s at . 286s ---------------------------------------------------------------------- 286s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 286s Aqua is a modified form of the Holst group PMG library 286s which has been modified by Patrice Koehl 286s for improved efficiency and 286s memory usage when solving the Poisson-Boltzmann equation. 286s ---------------------------------------------------------------------- 286s Please cite your use of APBS as: 286s 286s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 286s nanosystems: application to microtubules and the ribosome. Proc. 286s Natl. Acad. Sci. USA 98, 10037-10041 2001. 286s 286s 286s This executable compiled on Jan 3 2025 at 11:01:42 286s 286s Parsing input file apbs-smol.in... 286s rank 0 size 1... 286s Parsed input file. 286s Got paths for 3 molecules 286s Reading PQR-format atom data from acetic-acid.pqr. 286s asc_getToken: Error occurred (bailing out). 286s Vio_scanf: Format problem with input. 286s 8 atoms 286s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 286s Net charge -1.67e-16 e 286s Reading PQR-format atom data from acetate.pqr. 286s asc_getToken: Error occurred (bailing out). 286s Vio_scanf: Format problem with input. 286s 8 atoms 286s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 286s Net charge -1.00e+00 e 286s Reading PQR-format atom data from proton.pqr. 286s 1 atoms 286s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 286s Net charge 1.00e+00 e 286s Preparing to run 12 PBE calculations. 286s ---------------------------------------- 286s CALCULATION #1 (acetic-solv): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 7.76163 A 286s Current memory usage: 61.598 MB total, 61.598 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.188 x 0.188 x 0.188 286s Grid lengths: 12.000 x 12.000 x 12.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 2 ion species (0.150 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 5.824172730822E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #2 (acetic-solv): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 7.76163 A 286s Current memory usage: 61.598 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.094 x 0.094 x 0.094 286s Grid lengths: 6.000 x 6.000 x 6.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.150 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 9.793622759239E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #3 (acetic-ref): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.422 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.188 x 0.188 x 0.188 286s Grid lengths: 12.000 x 12.000 x 12.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 2.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 5.846917564309E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #4 (acetic-ref): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.422 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.094 x 0.094 x 0.094 286s Grid lengths: 6.000 x 6.000 x 6.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 2.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 9.815953282539E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #5 (acetate-solv): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 7.76163 A 286s Current memory usage: 61.598 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.188 x 0.188 x 0.188 286s Grid lengths: 12.000 x 12.000 x 12.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 2 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 2 ion species (0.150 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 8.221328580569E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #6 (acetate-solv): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 7.76163 A 286s Current memory usage: 61.598 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.094 x 0.094 x 0.094 286s Grid lengths: 6.000 x 6.000 x 6.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 2 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.150 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.392867783119E+04 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #7 (acetate-ref): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.422 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.188 x 0.188 x 0.188 286s Grid lengths: 12.000 x 12.000 x 12.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 2 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 2.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 8.420373979905E+03 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #8 (acetate-ref): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.422 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.094 x 0.094 x 0.094 286s Grid lengths: 6.000 x 6.000 x 6.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 2 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 2.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.412716615065E+04 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #9 (proton-solv): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 7.76163 A 286s Current memory usage: 61.412 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.188 x 0.188 x 0.188 286s Grid lengths: 12.000 x 12.000 x 12.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 3 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 2 ion species (0.150 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 3.863066835285E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #10 (proton-solv): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 7.76163 A 286s Current memory usage: 61.412 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.094 x 0.094 x 0.094 286s Grid lengths: 6.000 x 6.000 x 6.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 3 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.150 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 6.289649216644E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #11 (proton-ref): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.373 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.188 x 0.188 x 0.188 286s Grid lengths: 12.000 x 12.000 x 12.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 3 286s Linearized traditional PBE 286s Multiple Debye-Huckel sphere boundary conditions 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 2.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 4.162533113906E+03 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #12 (proton-ref): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 61.373 MB total, 122.404 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.094 x 0.094 x 0.094 286s Grid lengths: 6.000 x 6.000 x 6.000 286s Grid center: (0.000, -0.154, 1.287) 286s Multigrid levels: 5 286s Molecule ID: 3 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 2.000 286s Using "molecular" surface definition;harmonic average smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 293.000 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 6.585616091973E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s PRINT STATEMENTS 286s 286s print energy 1 (acetic-solv) - 2 (acetic-ref) end 286s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 286s Global net ELEC energy = -2.233052329981E+01 kJ/mol 286s 286s print energy 3 (acetate-solv) - 4 (acetate-ref) end 286s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 286s Global net ELEC energy = -1.984883194538E+02 kJ/mol 286s 286s print energy 5 (proton-solv) - 6 (proton-ref) end 286s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 286s Global net ELEC energy = -2.959668753288E+02 kJ/mol 286s 286s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 286s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 286s Global net ELEC energy = -4.721246714828E+02 kJ/mol 286s ---------------------------------------- 286s CLEANING UP AND SHUTTING DOWN... 286s Destroying force arrays. 286s No energy arrays to destroy. 286s Destroying multigrid structures. 286s Destroying finite element structures. 286s Destroying 3 molecules 286s Final memory usage: 0.001 MB total, 122.404 MB high water 286s 286s 286s Thanks for using APBS! 286s 294s Checking for intermediate energies in input file apbs-smol.out 294s EXPECTED COMPUTED: 16 294s EXPECTED EXPECTED: 16 294s 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] 294s 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'] 294s COMPUTED RESULT 5824.172730822 294s COMPUTED RESULT 9793.622759239 294s COMPUTED RESULT 5846.917564309 294s COMPUTED RESULT 9815.953282539 294s COMPUTED RESULT 8221.328580569 294s COMPUTED RESULT 13928.67783119 294s COMPUTED RESULT 8420.373979905 294s COMPUTED RESULT 14127.16615065 294s COMPUTED RESULT 3863.066835285 294s COMPUTED RESULT 6289.649216644 294s COMPUTED RESULT 4162.533113906 294s COMPUTED RESULT 6585.616091973 294s COMPUTED RESULT -22.33052329981 294s COMPUTED RESULT -198.4883194538 294s COMPUTED RESULT -295.9668753288 294s COMPUTED RESULT -472.1246714828 294s Running tests for ion-pmf section 294s BINARY: /usr/bin/apbs 294s INPUT: ion-pmf.in 294s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 294s asc_getToken: Error occurred (bailing out). 294s Vio_scanf: Format problem with input. 294s asc_getToken: Error occurred (bailing out). 294s Vio_scanf: Format problem with input. 294s 294s 294s ---------------------------------------------------------------------- 294s APBS -- Adaptive Poisson-Boltzmann Solver 294s Version APBS 3.4.1 294s 294s Nathan A. Baker (nathan.baker@pnnl.gov) 294s Pacific Northwest National Laboratory 294s 294s Additional contributing authors listed in the code documentation. 294s 294s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 294s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 294s Northwest Division for the U.S. Department of Energy. 294s 294s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 294s Portions Copyright (c) 2002-2020, Nathan A. Baker. 294s Portions Copyright (c) 1999-2002, The Regents of the University of California. 294s Portions Copyright (c) 1995, Michael Holst. 294s All rights reserved. 294s 294s Redistribution and use in source and binary forms, with or without 294s modification, are permitted provided that the following conditions are met: 294s 294s * Redistributions of source code must retain the above copyright notice, this 294s list of conditions and the following disclaimer. 294s 294s * Redistributions in binary form must reproduce the above copyright notice, 294s this list of conditions and the following disclaimer in the documentation 294s and/or other materials provided with the distribution. 294s 294s * Neither the name of the developer nor the names of its contributors may be 294s used to endorse or promote products derived from this software without 294s specific prior written permission. 294s 294s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 294s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 294s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 294s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 294s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 294s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 294s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 294s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 294s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 294s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 294s ---------------------------------------------------------------------- 294s APBS uses FETK (the Finite Element ToolKit) to solve the 294s Poisson-Boltzmann equation numerically. FETK is a portable collection 294s of finite element modeling class libraries developed by the Michael Holst 294s research group and written in an object-oriented form of C. FEtk is 294s designed to solve general coupled systems of nonlinear partial differential 294s equations using adaptive finite element methods, inexact Newton methods, 294s and algebraic multilevel methods. More information about FEtk may be found 294s at . 294s ---------------------------------------------------------------------- 294s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 294s Aqua is a modified form of the Holst group PMG library 294s which has been modified by Patrice Koehl 294s for improved efficiency and 294s memory usage when solving the Poisson-Boltzmann equation. 294s ---------------------------------------------------------------------- 294s Please cite your use of APBS as: 294s 294s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 294s nanosystems: application to microtubules and the ribosome. Proc. 294s Natl. Acad. Sci. USA 98, 10037-10041 2001. 294s 294s 294s This executable compiled on Jan 3 2025 at 11:01:42 294s 294s Parsing input file ion-pmf.in... 294s rank 0 size 1... 294s Parsed input file. 294s Reading parameter data from parm.dat. 294s Got paths for 1 molecules 294s Reading PDB-format atom data from ion-pmf.pdb. 294s Vpmg_ibForce: No force for zero ionic strength! 294s Vpmg_ibForce: No force for zero ionic strength! 294s 2 atoms 294s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 294s Net charge 2.00e+00 e 294s Preparing to run 3 PBE calculations. 294s ---------------------------------------- 294s CALCULATION #1 (solv): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.106 MB total, 61.106 MB high water 294s Using cubic spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.210 x 0.210 x 0.210 294s Grid lengths: 13.440 x 13.440 x 13.440 294s Grid center: (0.000, 0.000, 0.000) 294s Multigrid levels: 5 294s Molecule ID: 1 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 0 ion species (0.000 M ionic strength): 294s Solute dielectric: 1.000 294s Solvent dielectric: 78.540 294s Using spline-based surface definition;window = 0.300 294s Temperature: 298.150 K 294s Electrostatic energies will be calculated 294s All-atom solvent forces will be calculated 294s Total electrostatic energy = 7.839535983197E+03 kJ/mol 294s Calculating forces... 294s Printing per-atom forces for molecule 1 (kJ/mol/A) 294s Legend: 294s tot n -- total force for atom n 294s qf n -- fixed charge force for atom n 294s db n -- dielectric boundary force for atom n 294s ib n -- ionic boundary force for atom n 294s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 294s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 294s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 294s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 294s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 294s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 294s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 294s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 294s Vpmg_ibForce: No force for zero ionic strength! 294s Vpmg_ibForce: No force for zero ionic strength! 294s ---------------------------------------- 294s CALCULATION #2 (ref): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.106 MB total, 61.155 MB high water 294s Using cubic spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.210 x 0.210 x 0.210 294s Grid lengths: 13.440 x 13.440 x 13.440 294s Grid center: (0.000, 0.000, 0.000) 294s Multigrid levels: 5 294s Molecule ID: 1 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 0 ion species (0.000 M ionic strength): 294s Solute dielectric: 1.000 294s Solvent dielectric: 1.000 294s Using spline-based surface definition;window = 0.300 294s Temperature: 298.150 K 294s Electrostatic energies will be calculated 294s All-atom solvent forces will be calculated 294s Total electrostatic energy = 8.964727588811E+03 kJ/mol 294s Calculating forces... 294s Printing per-atom forces for molecule 1 (kJ/mol/A) 294s Legend: 294s tot n -- total force for atom n 294s qf n -- fixed charge force for atom n 294s db n -- dielectric boundary force for atom n 294s ib n -- ionic boundary force for atom n 294s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 294s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 294s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 294s mgF db 0 0.000e+00 0.000e+00 0.000e+00 294s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 294s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 294s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 294s mgF db 1 0.000e+00 0.000e+00 0.000e+00 294s ---------------------------------------- 294s CALCULATION #3 (asolv): APOLAR 294s Printing per atom forces (kJ/mol/A) 294s Legend: 294s tot n -- Total force for atom n 294s sasa n -- SASA force for atom n 294s sav n -- SAV force for atom n 294s wca n -- WCA force for atom n 294s 294s gamma 0.000720 294s pressure 0.000000 294s bconc 0.033000 294s 294s tot 0 2.715e-02 9.130e-07 9.128e-07 294s sasa 0 -1.100e+01 0.000e+00 0.000e+00 294s sav 0 0.000e+00 0.000e+00 0.000e+00 294s wca 0 -5.827e-01 -2.767e-05 -2.766e-05 294s tot 1 -2.723e-02 9.131e-07 9.134e-07 294s sasa 1 1.112e+01 0.000e+00 0.000e+00 294s sav 1 0.000e+00 0.000e+00 0.000e+00 294s wca 1 5.827e-01 -2.767e-05 -2.768e-05 294s 294s 294s Solvent Accessible Surface Area (SASA) for each atom: 294s SASA for atom 0: 1.153275282828E+02 294s SASA for atom 1: 1.153114143344E+02 294s 294s Total solvent accessible surface area: 230.639 A^2 294s 294s Surface tension*area energies (gamma * SASA) for each atom: 294s Surface tension*area energy for atom 0: 8.303582036361E-02 294s Surface tension*area energy for atom 1: 8.302421832080E-02 294s 294s Total surface tension energy: 0.16606 kJ/mol 294s 294s Total solvent accessible volume: 0 A^3 294s 294s Total pressure*volume energy: 0 kJ/mol 294s 294s WCA dispersion Energies for each atom: 294s WCA energy for atom 0: -6.909718345777E+00 294s WCA energy for atom 1: -6.909411348230E+00 294s 294s Total WCA energy: -13.8191 kJ/mol 294s 294s Total non-polar energy = -1.365306965532E+01 kJ/mol 294s ---------------------------------------- 294s PRINT STATEMENTS 294s 294s print energy 1 (solv) - 2 (ref) end 294s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 294s Global net ELEC energy = -1.125191605614E+03 kJ/mol 294s print force 1 (solv) - 2 (ref) end 294s Printing per-atom forces (kJ/mol/A). 294s Legend: 294s tot n -- Total force for atom n 294s qf n -- Fixed charge force for atom n 294s db n -- Dielectric boundary force for atom n 294s ib n -- Ionic boundary force for atom n 294s tot all -- Total force for system 294s qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 294s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 294s db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 294s tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 294s qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 294s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 294s db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 294s tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 294s tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 294s 294s print APOL energy 1 (asolv) end 294s Global net APOL energy = -1.365306965532E+01 kJ/mol 294s 294s print APOL force 1 (asolv) end 294s Printing per atom forces (kJ/mol/A) 294s Legend: 294s tot n -- Total force for atom n 294s sasa n -- SASA force for atom n 294s sav n -- SAV force for atom n 294s wca n -- WCA force for atom n 294s tot all -- Total force for system 294s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 294s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 294s wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 294s tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 294s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 294s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 294s wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 294s tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 294s tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 294s ---------------------------------------- 294s CLEANING UP AND SHUTTING DOWN... 294s Destroying force arrays. 294s No energy arrays to destroy. 294s Destroying multigrid structures. 294s Destroying finite element structures. 294s Destroying 1 molecules 294s Final memory usage: 60.711 MB total, 62.250 MB high water 294s 294s 294s Thanks for using APBS! 294s 294s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 294s *** PASSED *** 294s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 294s *** PASSED *** 294s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 294s *** PASSED *** 294s Elapsed time: 7.572684 seconds 294s -------------------------------------------------------------------------------- 294s Total elapsed time: 7.572684 seconds 294s Test results have been logged 294s -------------------------------------------------------------------------------- 294s -------------------------------------------------------------------------------- 294s Testing input file apbs-mol-vdw.in 294s 304s Checking for intermediate energies in input file ion-pmf.out 304s EXPECTED COMPUTED: 4 304s EXPECTED EXPECTED: 4 304s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] 304s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 304s COMPUTED RESULT 7839.535983197 304s COMPUTED RESULT 8964.727588811 304s COMPUTED RESULT -1125.191605614 304s COMPUTED RESULT -13.65306965532 304s Running tests for pka-lig section 304s BINARY: /usr/bin/apbs 304s INPUT: apbs-mol-vdw.in 304s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 304s asc_getToken: Error occurred (bailing out). 304s Vio_scanf: Format problem with input. 304s 304s 304s ---------------------------------------------------------------------- 304s APBS -- Adaptive Poisson-Boltzmann Solver 304s Version APBS 3.4.1 304s 304s Nathan A. Baker (nathan.baker@pnnl.gov) 304s Pacific Northwest National Laboratory 304s 304s Additional contributing authors listed in the code documentation. 304s 304s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 304s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 304s Northwest Division for the U.S. Department of Energy. 304s 304s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 304s Portions Copyright (c) 2002-2020, Nathan A. Baker. 304s Portions Copyright (c) 1999-2002, The Regents of the University of California. 304s Portions Copyright (c) 1995, Michael Holst. 304s All rights reserved. 304s 304s Redistribution and use in source and binary forms, with or without 304s modification, are permitted provided that the following conditions are met: 304s 304s * Redistributions of source code must retain the above copyright notice, this 304s list of conditions and the following disclaimer. 304s 304s * Redistributions in binary form must reproduce the above copyright notice, 304s this list of conditions and the following disclaimer in the documentation 304s and/or other materials provided with the distribution. 304s 304s * Neither the name of the developer nor the names of its contributors may be 304s used to endorse or promote products derived from this software without 304s specific prior written permission. 304s 304s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 304s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 304s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 304s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 304s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 304s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 304s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 304s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 304s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 304s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 304s ---------------------------------------------------------------------- 304s APBS uses FETK (the Finite Element ToolKit) to solve the 304s Poisson-Boltzmann equation numerically. FETK is a portable collection 304s of finite element modeling class libraries developed by the Michael Holst 304s research group and written in an object-oriented form of C. FEtk is 304s designed to solve general coupled systems of nonlinear partial differential 304s equations using adaptive finite element methods, inexact Newton methods, 304s and algebraic multilevel methods. More information about FEtk may be found 304s at . 304s ---------------------------------------------------------------------- 304s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 304s Aqua is a modified form of the Holst group PMG library 304s which has been modified by Patrice Koehl 304s for improved efficiency and 304s memory usage when solving the Poisson-Boltzmann equation. 304s ---------------------------------------------------------------------- 304s Please cite your use of APBS as: 304s 304s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 304s nanosystems: application to microtubules and the ribosome. Proc. 304s Natl. Acad. Sci. USA 98, 10037-10041 2001. 304s 304s 304s This executable compiled on Jan 3 2025 at 11:01:42 304s 304s Parsing input file apbs-mol-vdw.in... 304s rank 0 size 1... 304s Parsed input file. 304s Got paths for 3 molecules 304s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 304s asc_getToken: Error occurred (bailing out). 304s Vio_scanf: Format problem with input. 304s 47 atoms 304s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 304s Net charge 1.11e-16 e 304s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 304s asc_getToken: Error occurred (bailing out). 304s Vio_scanf: Format problem with input. 304s 3423 atoms 304s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 304s Net charge 1.00e+00 e 304s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 304s 3470 atoms 304s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 304s Net charge 1.00e+00 e 304s Preparing to run 6 PBE calculations. 304s ---------------------------------------- 304s CALCULATION #1 (lig-coarse): MULTIGRID 304s Setting up problem... 304s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 304s Debye length: 0 A 304s Current memory usage: 204.292 MB total, 204.292 MB high water 304s Using linear spline charge discretization. 304s Grid dimensions: 97 x 97 x 97 304s Grid spacings: 0.729 x 0.729 x 0.729 304s Grid lengths: 70.000 x 70.000 x 70.000 304s Grid center: (28.969, -32.507, 27.022) 304s Multigrid levels: 4 304s Molecule ID: 1 304s Linearized traditional PBE 304s Single Debye-Huckel sphere boundary conditions 304s 2 ion species (0.000 M ionic strength): 304s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 304s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 304s Solute dielectric: 2.000 304s Solvent dielectric: 78.000 304s Using "molecular" surface definition; no smoothing 304s Solvent probe radius: 0.000 A 304s Temperature: 298.150 K 304s Electrostatic energies will be calculated 304s Total electrostatic energy = 2.224988750664E+03 kJ/mol 304s Calculating forces... 304s ---------------------------------------- 304s CALCULATION #2 (lig-fine): MULTIGRID 304s Setting up problem... 304s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 304s Debye length: 0 A 304s Current memory usage: 204.292 MB total, 406.001 MB high water 304s Using linear spline charge discretization. 304s Grid dimensions: 97 x 97 x 97 304s Grid spacings: 0.250 x 0.250 x 0.250 304s Grid lengths: 24.000 x 24.000 x 24.000 304s Grid center: (24.822, -33.153, 21.545) 304s Multigrid levels: 4 304s Molecule ID: 1 304s Linearized traditional PBE 304s Boundary conditions from focusing 304s 2 ion species (0.000 M ionic strength): 304s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 304s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 304s Solute dielectric: 2.000 304s Solvent dielectric: 78.000 304s Using "molecular" surface definition; no smoothing 304s Solvent probe radius: 0.000 A 304s Temperature: 298.150 K 304s Electrostatic energies will be calculated 304s Total electrostatic energy = 1.049695084686E+04 kJ/mol 304s Calculating forces... 304s ---------------------------------------- 304s CALCULATION #3 (pka-coarse): MULTIGRID 304s Setting up problem... 304s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 304s Debye length: 0 A 304s Current memory usage: 291.151 MB total, 406.001 MB high water 304s Using linear spline charge discretization. 304s Grid dimensions: 97 x 97 x 97 304s Grid spacings: 0.729 x 0.729 x 0.729 304s Grid lengths: 70.000 x 70.000 x 70.000 304s Grid center: (28.969, -32.507, 27.022) 304s Multigrid levels: 4 304s Molecule ID: 2 304s Linearized traditional PBE 304s Single Debye-Huckel sphere boundary conditions 304s 2 ion species (0.000 M ionic strength): 304s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 304s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 304s Solute dielectric: 2.000 304s Solvent dielectric: 78.000 304s Using "molecular" surface definition; no smoothing 304s Solvent probe radius: 0.000 A 304s Temperature: 298.150 K 304s Electrostatic energies will be calculated 304s Total electrostatic energy = 1.818450789522E+05 kJ/mol 304s Calculating forces... 304s [focusFillBound()]: WARNING: 304s Unusually large potential values 304s detected on the focusing boundary! 304s Convergence not guaranteed for NPBE/NRPBE calculations! 304s 304s ---------------------------------------- 304s CALCULATION #4 (pka-fine): MULTIGRID 304s Setting up problem... 304s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 304s Debye length: 0 A 304s Current memory usage: 291.151 MB total, 533.426 MB high water 304s Using linear spline charge discretization. 304s Grid dimensions: 97 x 97 x 97 304s Grid spacings: 0.250 x 0.250 x 0.250 304s Grid lengths: 24.000 x 24.000 x 24.000 304s Grid center: (24.822, -33.153, 21.545) 304s Multigrid levels: 4 304s Molecule ID: 2 304s Linearized traditional PBE 304s Boundary conditions from focusing 304s 2 ion species (0.000 M ionic strength): 304s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 304s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 304s Solute dielectric: 2.000 304s Solvent dielectric: 78.000 304s Using "molecular" surface definition; no smoothing 304s Solvent probe radius: 0.000 A 304s Temperature: 298.150 K 304s Electrostatic energies will be calculated 304s Total electrostatic energy = 3.008254338259E+05 kJ/mol 304s Calculating forces... 304s ---------------------------------------- 304s CALCULATION #5 (complex-coarse): MULTIGRID 304s Setting up problem... 304s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 304s Debye length: 0 A 304s Current memory usage: 292.063 MB total, 533.426 MB high water 304s Using linear spline charge discretization. 304s Grid dimensions: 97 x 97 x 97 304s Grid spacings: 0.729 x 0.729 x 0.729 304s Grid lengths: 70.000 x 70.000 x 70.000 304s Grid center: (28.969, -32.507, 27.022) 304s Multigrid levels: 4 304s Molecule ID: 3 304s Linearized traditional PBE 304s Single Debye-Huckel sphere boundary conditions 304s 2 ion species (0.000 M ionic strength): 304s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 304s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 304s Solute dielectric: 2.000 304s Solvent dielectric: 78.000 304s Using "molecular" surface definition; no smoothing 304s Solvent probe radius: 0.000 A 304s Temperature: 298.150 K 304s Electrostatic energies will be calculated 304s Total electrostatic energy = 1.840918409896E+05 kJ/mol 304s Calculating forces... 304s [focusFillBound()]: WARNING: 304s Unusually large potential values 304s detected on the focusing boundary! 304s Convergence not guaranteed for NPBE/NRPBE calculations! 304s 304s ---------------------------------------- 304s CALCULATION #6 (complex-fine): MULTIGRID 304s Setting up problem... 304s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 304s Debye length: 0 A 304s Current memory usage: 292.063 MB total, 534.806 MB high water 304s Using linear spline charge discretization. 304s Grid dimensions: 97 x 97 x 97 304s Grid spacings: 0.250 x 0.250 x 0.250 304s Grid lengths: 24.000 x 24.000 x 24.000 304s Grid center: (24.822, -33.153, 21.545) 304s Multigrid levels: 4 304s Molecule ID: 3 304s Linearized traditional PBE 304s Boundary conditions from focusing 304s 2 ion species (0.000 M ionic strength): 304s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 304s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 304s Solute dielectric: 2.000 304s Solvent dielectric: 78.000 304s Using "molecular" surface definition; no smoothing 304s Solvent probe radius: 0.000 A 304s Temperature: 298.150 K 304s Electrostatic energies will be calculated 304s Total electrostatic energy = 3.113304681884E+05 kJ/mol 304s Calculating forces... 304s ---------------------------------------- 304s PRINT STATEMENTS 304s 304s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 304s Local net energy (PE 0) = 8.083515648803E+00 kJ/mol 304s Global net ELEC energy = 8.083515648803E+00 kJ/mol 304s ---------------------------------------- 304s CLEANING UP AND SHUTTING DOWN... 304s Destroying force arrays. 304s No energy arrays to destroy. 304s Destroying multigrid structures. 304s Destroying finite element structures. 304s Destroying 3 molecules 304s Final memory usage: 0.001 MB total, 534.806 MB high water 304s 304s 304s Thanks for using APBS! 304s 304s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 304s *** PASSED *** 304s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 304s *** PASSED *** 304s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 304s *** PASSED *** 304s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 304s *** PASSED *** 304s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 304s *** PASSED *** 304s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 304s *** PASSED *** 304s Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) 304s *** PASSED *** 304s Elapsed time: 9.822923 seconds 304s -------------------------------------------------------------------------------- 304s -------------------------------------------------------------------------------- 304s Testing input file apbs-smol-vdw.in 304s 312s Checking for intermediate energies in input file apbs-mol-vdw.out 312s EXPECTED COMPUTED: 7 312s EXPECTED EXPECTED: 7 312s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] 312s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 312s COMPUTED RESULT 2224.988750664 312s COMPUTED RESULT 10496.95084686 312s COMPUTED RESULT 181845.0789522 312s COMPUTED RESULT 300825.4338259 312s COMPUTED RESULT 184091.8409896 312s COMPUTED RESULT 311330.4681884 312s COMPUTED RESULT 8.083515648803 312s BINARY: /usr/bin/apbs 312s INPUT: apbs-smol-vdw.in 312s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 312s asc_getToken: Error occurred (bailing out). 312s Vio_scanf: Format problem with input. 312s 312s 312s ---------------------------------------------------------------------- 312s APBS -- Adaptive Poisson-Boltzmann Solver 312s Version APBS 3.4.1 312s 312s Nathan A. Baker (nathan.baker@pnnl.gov) 312s Pacific Northwest National Laboratory 312s 312s Additional contributing authors listed in the code documentation. 312s 312s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 312s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 312s Northwest Division for the U.S. Department of Energy. 312s 312s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 312s Portions Copyright (c) 2002-2020, Nathan A. Baker. 312s Portions Copyright (c) 1999-2002, The Regents of the University of California. 312s Portions Copyright (c) 1995, Michael Holst. 312s All rights reserved. 312s 312s Redistribution and use in source and binary forms, with or without 312s modification, are permitted provided that the following conditions are met: 312s 312s * Redistributions of source code must retain the above copyright notice, this 312s list of conditions and the following disclaimer. 312s 312s * Redistributions in binary form must reproduce the above copyright notice, 312s this list of conditions and the following disclaimer in the documentation 312s and/or other materials provided with the distribution. 312s 312s * Neither the name of the developer nor the names of its contributors may be 312s used to endorse or promote products derived from this software without 312s specific prior written permission. 312s 312s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 312s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 312s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 312s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 312s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 312s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 312s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 312s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 312s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 312s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 312s ---------------------------------------------------------------------- 312s APBS uses FETK (the Finite Element ToolKit) to solve the 312s Poisson-Boltzmann equation numerically. FETK is a portable collection 312s of finite element modeling class libraries developed by the Michael Holst 312s research group and written in an object-oriented form of C. FEtk is 312s designed to solve general coupled systems of nonlinear partial differential 312s equations using adaptive finite element methods, inexact Newton methods, 312s and algebraic multilevel methods. More information about FEtk may be found 312s at . 312s ---------------------------------------------------------------------- 312s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 312s Aqua is a modified form of the Holst group PMG library 312s which has been modified by Patrice Koehl 312s for improved efficiency and 312s memory usage when solving the Poisson-Boltzmann equation. 312s ---------------------------------------------------------------------- 312s Please cite your use of APBS as: 312s 312s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 312s nanosystems: application to microtubules and the ribosome. Proc. 312s Natl. Acad. Sci. USA 98, 10037-10041 2001. 312s 312s 312s This executable compiled on Jan 3 2025 at 11:01:42 312s 312s Parsing input file apbs-smol-vdw.in... 312s rank 0 size 1... 312s Parsed input file. 312s Got paths for 3 molecules 312s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 312s asc_getToken: Error occurred (bailing out). 312s Vio_scanf: Format problem with input. 312s 47 atoms 312s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 312s Net charge 1.11e-16 e 312s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 312s asc_getToken: Error occurred (bailing out). 312s Vio_scanf: Format problem with input. 312s 3423 atoms 312s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 312s Net charge 1.00e+00 e 312s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 312s 3470 atoms 312s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 312s Net charge 1.00e+00 e 312s Preparing to run 6 PBE calculations. 312s ---------------------------------------- 312s CALCULATION #1 (lig-coarse): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 204.292 MB total, 204.292 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.729 x 0.729 x 0.729 312s Grid lengths: 70.000 x 70.000 x 70.000 312s Grid center: (28.969, -32.507, 27.022) 312s Multigrid levels: 4 312s Molecule ID: 1 312s Linearized traditional PBE 312s Single Debye-Huckel sphere boundary conditions 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition;harmonic average smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 2.226793167046E+03 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s CALCULATION #2 (lig-fine): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 204.292 MB total, 406.001 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.250 x 0.250 x 0.250 312s Grid lengths: 24.000 x 24.000 x 24.000 312s Grid center: (24.822, -33.153, 21.545) 312s Multigrid levels: 4 312s Molecule ID: 1 312s Linearized traditional PBE 312s Boundary conditions from focusing 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition;harmonic average smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 1.050504485887E+04 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s CALCULATION #3 (pka-coarse): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 291.151 MB total, 406.001 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.729 x 0.729 x 0.729 312s Grid lengths: 70.000 x 70.000 x 70.000 312s Grid center: (28.969, -32.507, 27.022) 312s Multigrid levels: 4 312s Molecule ID: 2 312s Linearized traditional PBE 312s Single Debye-Huckel sphere boundary conditions 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition;harmonic average smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 1.827976621645E+05 kJ/mol 312s Calculating forces... 312s [focusFillBound()]: WARNING: 312s Unusually large potential values 312s detected on the focusing boundary! 312s Convergence not guaranteed for NPBE/NRPBE calculations! 312s 312s ---------------------------------------- 312s CALCULATION #4 (pka-fine): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 291.151 MB total, 533.426 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.250 x 0.250 x 0.250 312s Grid lengths: 24.000 x 24.000 x 24.000 312s Grid center: (24.822, -33.153, 21.545) 312s Multigrid levels: 4 312s Molecule ID: 2 312s Linearized traditional PBE 312s Boundary conditions from focusing 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition;harmonic average smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 3.017228546773E+05 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s CALCULATION #5 (complex-coarse): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 292.063 MB total, 533.426 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.729 x 0.729 x 0.729 312s Grid lengths: 70.000 x 70.000 x 70.000 312s Grid center: (28.969, -32.507, 27.022) 312s Multigrid levels: 4 312s Molecule ID: 3 312s Linearized traditional PBE 312s Single Debye-Huckel sphere boundary conditions 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition;harmonic average smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 1.850819075387E+05 kJ/mol 312s Calculating forces... 312s [focusFillBound()]: WARNING: 312s Unusually large potential values 312s detected on the focusing boundary! 312s Convergence not guaranteed for NPBE/NRPBE calculations! 312s 312s ---------------------------------------- 312s CALCULATION #6 (complex-fine): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 292.063 MB total, 534.806 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.250 x 0.250 x 0.250 312s Grid lengths: 24.000 x 24.000 x 24.000 312s Grid center: (24.822, -33.153, 21.545) 312s Multigrid levels: 4 312s Molecule ID: 3 312s Linearized traditional PBE 312s Boundary conditions from focusing 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition;harmonic average smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 3.122488625388E+05 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s PRINT STATEMENTS 312s 312s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 312s Local net energy (PE 0) = 2.096300255720E+01 kJ/mol 312s Global net ELEC energy = 2.096300255720E+01 kJ/mol 312s ---------------------------------------- 312s CLEANING UP AND SHUTTING DOWN... 312s Destroying force arrays. 312s No energy arrays to destroy. 312s Destroying multigrid structures. 312s Destroying finite element structures. 312s Destroying 3 molecules 312s Final memory usage: 0.001 MB total, 534.806 MB high water 312s 312s 312s Thanks for using APBS! 312s 312s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 312s *** PASSED *** 312s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 312s *** PASSED *** 312s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 312s *** PASSED *** 312s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 312s *** PASSED *** 312s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 312s *** PASSED *** 312s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 312s *** PASSED *** 312s Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) 312s *** PASSED *** 312s Elapsed time: 8.14493 seconds 312s -------------------------------------------------------------------------------- 312s -------------------------------------------------------------------------------- 312s Testing input file apbs-mol-surf.in 312s 320s Checking for intermediate energies in input file apbs-smol-vdw.out 320s EXPECTED COMPUTED: 7 320s EXPECTED EXPECTED: 7 320s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] 320s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 320s COMPUTED RESULT 2226.793167046 320s COMPUTED RESULT 10505.04485887 320s COMPUTED RESULT 182797.6621645 320s COMPUTED RESULT 301722.8546773 320s COMPUTED RESULT 185081.9075387 320s COMPUTED RESULT 312248.8625388 320s COMPUTED RESULT 20.9630025572 320s BINARY: /usr/bin/apbs 320s INPUT: apbs-mol-surf.in 320s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 320s asc_getToken: Error occurred (bailing out). 320s Vio_scanf: Format problem with input. 320s 320s 320s ---------------------------------------------------------------------- 320s APBS -- Adaptive Poisson-Boltzmann Solver 320s Version APBS 3.4.1 320s 320s Nathan A. Baker (nathan.baker@pnnl.gov) 320s Pacific Northwest National Laboratory 320s 320s Additional contributing authors listed in the code documentation. 320s 320s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 320s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 320s Northwest Division for the U.S. Department of Energy. 320s 320s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 320s Portions Copyright (c) 2002-2020, Nathan A. Baker. 320s Portions Copyright (c) 1999-2002, The Regents of the University of California. 320s Portions Copyright (c) 1995, Michael Holst. 320s All rights reserved. 320s 320s Redistribution and use in source and binary forms, with or without 320s modification, are permitted provided that the following conditions are met: 320s 320s * Redistributions of source code must retain the above copyright notice, this 320s list of conditions and the following disclaimer. 320s 320s * Redistributions in binary form must reproduce the above copyright notice, 320s this list of conditions and the following disclaimer in the documentation 320s and/or other materials provided with the distribution. 320s 320s * Neither the name of the developer nor the names of its contributors may be 320s used to endorse or promote products derived from this software without 320s specific prior written permission. 320s 320s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 320s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 320s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 320s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 320s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 320s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 320s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 320s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 320s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 320s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 320s ---------------------------------------------------------------------- 320s APBS uses FETK (the Finite Element ToolKit) to solve the 320s Poisson-Boltzmann equation numerically. FETK is a portable collection 320s of finite element modeling class libraries developed by the Michael Holst 320s research group and written in an object-oriented form of C. FEtk is 320s designed to solve general coupled systems of nonlinear partial differential 320s equations using adaptive finite element methods, inexact Newton methods, 320s and algebraic multilevel methods. More information about FEtk may be found 320s at . 320s ---------------------------------------------------------------------- 320s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 320s Aqua is a modified form of the Holst group PMG library 320s which has been modified by Patrice Koehl 320s for improved efficiency and 320s memory usage when solving the Poisson-Boltzmann equation. 320s ---------------------------------------------------------------------- 320s Please cite your use of APBS as: 320s 320s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 320s nanosystems: application to microtubules and the ribosome. Proc. 320s Natl. Acad. Sci. USA 98, 10037-10041 2001. 320s 320s 320s This executable compiled on Jan 3 2025 at 11:01:42 320s 320s Parsing input file apbs-mol-surf.in... 320s rank 0 size 1... 320s Parsed input file. 320s Got paths for 3 molecules 320s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 320s asc_getToken: Error occurred (bailing out). 320s Vio_scanf: Format problem with input. 320s 47 atoms 320s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 320s Net charge 1.11e-16 e 320s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 320s asc_getToken: Error occurred (bailing out). 320s Vio_scanf: Format problem with input. 320s 3423 atoms 320s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 320s Net charge 1.00e+00 e 320s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 320s 3470 atoms 320s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 320s Net charge 1.00e+00 e 320s Preparing to run 6 PBE calculations. 320s ---------------------------------------- 320s CALCULATION #1 (lig-coarse): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 203.877 MB total, 203.877 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.729 x 0.729 x 0.729 320s Grid lengths: 70.000 x 70.000 x 70.000 320s Grid center: (28.969, -32.507, 27.022) 320s Multigrid levels: 4 320s Molecule ID: 1 320s Linearized traditional PBE 320s Single Debye-Huckel sphere boundary conditions 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition; no smoothing 320s Solvent probe radius: 1.400 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 2.244350164274E+03 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s CALCULATION #2 (lig-fine): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 203.877 MB total, 405.586 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.250 x 0.250 x 0.250 320s Grid lengths: 24.000 x 24.000 x 24.000 320s Grid center: (24.822, -33.153, 21.545) 320s Multigrid levels: 4 320s Molecule ID: 1 320s Linearized traditional PBE 320s Boundary conditions from focusing 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition; no smoothing 320s Solvent probe radius: 1.400 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 1.052149475373E+04 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s CALCULATION #3 (pka-coarse): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 251.521 MB total, 405.586 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.729 x 0.729 x 0.729 320s Grid lengths: 70.000 x 70.000 x 70.000 320s Grid center: (28.969, -32.507, 27.022) 320s Multigrid levels: 4 320s Molecule ID: 2 320s Linearized traditional PBE 320s Single Debye-Huckel sphere boundary conditions 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition; no smoothing 320s Solvent probe radius: 1.400 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 1.862615690066E+05 kJ/mol 320s Calculating forces... 320s [focusFillBound()]: WARNING: 320s Unusually large potential values 320s detected on the focusing boundary! 320s Convergence not guaranteed for NPBE/NRPBE calculations! 320s 320s ---------------------------------------- 320s CALCULATION #4 (pka-fine): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 251.521 MB total, 493.795 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.250 x 0.250 x 0.250 320s Grid lengths: 24.000 x 24.000 x 24.000 320s Grid center: (24.822, -33.153, 21.545) 320s Multigrid levels: 4 320s Molecule ID: 2 320s Linearized traditional PBE 320s Boundary conditions from focusing 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition; no smoothing 320s Solvent probe radius: 1.400 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 3.051810884053E+05 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s CALCULATION #5 (complex-coarse): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 251.858 MB total, 493.795 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.729 x 0.729 x 0.729 320s Grid lengths: 70.000 x 70.000 x 70.000 320s Grid center: (28.969, -32.507, 27.022) 320s Multigrid levels: 4 320s Molecule ID: 3 320s Linearized traditional PBE 320s Single Debye-Huckel sphere boundary conditions 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition; no smoothing 320s Solvent probe radius: 1.400 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 1.886625455219E+05 kJ/mol 320s Calculating forces... 320s [focusFillBound()]: WARNING: 320s Unusually large potential values 320s detected on the focusing boundary! 320s Convergence not guaranteed for NPBE/NRPBE calculations! 320s 320s ---------------------------------------- 320s CALCULATION #6 (complex-fine): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 251.858 MB total, 494.601 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.250 x 0.250 x 0.250 320s Grid lengths: 24.000 x 24.000 x 24.000 320s Grid center: (24.822, -33.153, 21.545) 320s Multigrid levels: 4 320s Molecule ID: 3 320s Linearized traditional PBE 320s Boundary conditions from focusing 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition; no smoothing 320s Solvent probe radius: 1.400 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 3.158218439277E+05 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s PRINT STATEMENTS 320s 320s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 320s Local net energy (PE 0) = 1.192607686582E+02 kJ/mol 320s Global net ELEC energy = 1.192607686582E+02 kJ/mol 320s ---------------------------------------- 320s CLEANING UP AND SHUTTING DOWN... 320s Destroying force arrays. 320s No energy arrays to destroy. 320s Destroying multigrid structures. 320s Destroying finite element structures. 320s Destroying 3 molecules 320s Final memory usage: 0.001 MB total, 494.601 MB high water 320s 320s 320s Thanks for using APBS! 320s 320s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 320s *** PASSED *** 320s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 320s *** PASSED *** 320s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 320s *** PASSED *** 320s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 320s *** PASSED *** 320s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 320s *** PASSED *** 320s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 320s *** PASSED *** 320s Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) 320s *** PASSED *** 320s Elapsed time: 8.193196 seconds 320s -------------------------------------------------------------------------------- 320s -------------------------------------------------------------------------------- 320s Testing input file apbs-smol-surf.in 320s 328s Checking for intermediate energies in input file apbs-mol-surf.out 328s EXPECTED COMPUTED: 7 328s EXPECTED EXPECTED: 7 328s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] 328s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 328s COMPUTED RESULT 2244.350164274 328s COMPUTED RESULT 10521.49475373 328s COMPUTED RESULT 186261.5690066 328s COMPUTED RESULT 305181.0884053 328s COMPUTED RESULT 188662.5455219 328s COMPUTED RESULT 315821.8439277 328s COMPUTED RESULT 119.2607686582 328s BINARY: /usr/bin/apbs 328s INPUT: apbs-smol-surf.in 328s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 328s 328s ---------------------------------------------------------------------- 328s APBS -- Adaptive Poisson-Boltzmann Solver 328s Version APBS 3.4.1 328s 328s Nathan A. Baker (nathan.baker@pnnl.gov) 328s Pacific Northwest National Laboratory 328s 328s Additional contributing authors listed in the code documentation. 328s 328s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 328s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 328s Northwest Division for the U.S. Department of Energy. 328s 328s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 328s Portions Copyright (c) 2002-2020, Nathan A. Baker. 328s Portions Copyright (c) 1999-2002, The Regents of the University of California. 328s Portions Copyright (c) 1995, Michael Holst. 328s All rights reserved. 328s 328s Redistribution and use in source and binary forms, with or without 328s modification, are permitted provided that the following conditions are met: 328s 328s * Redistributions of source code must retain the above copyright notice, this 328s list of conditions and the following disclaimer. 328s 328s * Redistributions in binary form must reproduce the above copyright notice, 328s this list of conditions and the following disclaimer in the documentation 328s and/or other materials provided with the distribution. 328s 328s * Neither the name of the developer nor the names of its contributors may be 328s used to endorse or promote products derived from this software without 328s specific prior written permission. 328s 328s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 328s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 328s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 328s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 328s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 328s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 328s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 328s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 328s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 328s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 328s ---------------------------------------------------------------------- 328s APBS uses FETK (the Finite Element ToolKit) to solve the 328s Poisson-Boltzmann equation numerically. FETK is a portable collection 328s of finite element modeling class libraries developed by the Michael Holst 328s research group and written in an object-oriented form of C. FEtk is 328s designed to solve general coupled systems of nonlinear partial differential 328s equations using adaptive finite element methods, inexact Newton methods, 328s and algebraic multilevel methods. More information about FEtk may be found 328s at . 328s ---------------------------------------------------------------------- 328s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 328s Aqua is a modified form of the Holst group PMG library 328s which has been modified by Patrice Koehl 328s for improved efficiency and 328s memory usage when solving the Poisson-Boltzmann equation. 328s ---------------------------------------------------------------------- 328s Please cite your use of APBS as: 328s 328s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 328s nanosystems: application to microtubules and the ribosome. Proc. 328s Natl. Acad. Sci. USA 98, 10037-10041 2001. 328s 328s 328s This executable compiled on Jan 3 2025 at 11:01:42 328s 328s Parsing input file apbs-smol-surf.in... 328s rank 0 size 1... 328s Parsed input file. 328s Got paths for 3 molecules 328s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 47 atoms 328s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 328s Net charge 1.11e-16 e 328s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 3423 atoms 328s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 328s Net charge 1.00e+00 e 328s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 328s 3470 atoms 328s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 328s Net charge 1.00e+00 e 328s Preparing to run 6 PBE calculations. 328s ---------------------------------------- 328s CALCULATION #1 (lig-coarse): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 203.877 MB total, 203.877 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.729 x 0.729 x 0.729 328s Grid lengths: 70.000 x 70.000 x 70.000 328s Grid center: (28.969, -32.507, 27.022) 328s Multigrid levels: 4 328s Molecule ID: 1 328s Linearized traditional PBE 328s Single Debye-Huckel sphere boundary conditions 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition;harmonic average smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 2.251466789420E+03 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #2 (lig-fine): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 203.877 MB total, 405.586 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.250 x 0.250 x 0.250 328s Grid lengths: 24.000 x 24.000 x 24.000 328s Grid center: (24.822, -33.153, 21.545) 328s Multigrid levels: 4 328s Molecule ID: 1 328s Linearized traditional PBE 328s Boundary conditions from focusing 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition;harmonic average smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 1.052814502873E+04 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #3 (pka-coarse): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.521 MB total, 405.586 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.729 x 0.729 x 0.729 328s Grid lengths: 70.000 x 70.000 x 70.000 328s Grid center: (28.969, -32.507, 27.022) 328s Multigrid levels: 4 328s Molecule ID: 2 328s Linearized traditional PBE 328s Single Debye-Huckel sphere boundary conditions 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition;harmonic average smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 1.864071689626E+05 kJ/mol 328s Calculating forces... 328s [focusFillBound()]: WARNING: 328s Unusually large potential values 328s detected on the focusing boundary! 328s Convergence not guaranteed for NPBE/NRPBE calculations! 328s 328s ---------------------------------------- 328s CALCULATION #4 (pka-fine): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.521 MB total, 493.795 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.250 x 0.250 x 0.250 328s Grid lengths: 24.000 x 24.000 x 24.000 328s Grid center: (24.822, -33.153, 21.545) 328s Multigrid levels: 4 328s Molecule ID: 2 328s Linearized traditional PBE 328s Boundary conditions from focusing 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition;harmonic average smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 3.053319953673E+05 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #5 (complex-coarse): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.858 MB total, 493.795 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.729 x 0.729 x 0.729 328s Grid lengths: 70.000 x 70.000 x 70.000 328s Grid center: (28.969, -32.507, 27.022) 328s Multigrid levels: 4 328s Molecule ID: 3 328s Linearized traditional PBE 328s Single Debye-Huckel sphere boundary conditions 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition;harmonic average smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 1.888027142979E+05 kJ/mol 328s Calculating forces... 328s [focusFillBound()]: WARNING: 328s Unusually large potential values 328s detected on the focusing boundary! 328s Convergence not guaranteed for NPBE/NRPBE calculations! 328s 328s ---------------------------------------- 328s CALCULATION #6 (complex-fine): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.858 MB total, 494.601 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.250 x 0.250 x 0.250 328s Grid lengths: 24.000 x 24.000 x 24.000 328s Grid center: (24.822, -33.153, 21.545) 328s Multigrid levels: 4 328s Molecule ID: 3 328s Linearized traditional PBE 328s Boundary conditions from focusing 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition;harmonic average smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 3.159690177241E+05 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s PRINT STATEMENTS 328s 328s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 328s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 328s Global net ELEC energy = 1.088773280806E+02 kJ/mol 328s ---------------------------------------- 328s CLEANING UP AND SHUTTING DOWN... 328s Destroying force arrays. 328s No energy arrays to destroy. 328s Destroying multigrid structures. 328s Destroying finite element structures. 328s Destroying 3 molecules 328s Final memory usage: 0.001 MB total, 494.601 MB high water 328s 328s 328s Thanks for using APBS! 328s 328s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 328s *** PASSED *** 328s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 328s *** PASSED *** 328s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 328s *** PASSED *** 328s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 328s *** PASSED *** 328s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 328s *** PASSED *** 328s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 328s *** PASSED *** 328s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 328s *** PASSED *** 328s Elapsed time: 7.582169 seconds 328s -------------------------------------------------------------------------------- 328s Total elapsed time: 33.743218 seconds 328s Test results have been logged 328s -------------------------------------------------------------------------------- 328s -------------------------------------------------------------------------------- 328s Testing input file complex-0_1.in 328s 328s Checking for intermediate energies in input file apbs-smol-surf.out 328s EXPECTED COMPUTED: 7 328s EXPECTED EXPECTED: 7 328s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 328s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 328s COMPUTED RESULT 2251.46678942 328s COMPUTED RESULT 10528.14502873 328s COMPUTED RESULT 186407.1689626 328s COMPUTED RESULT 305331.9953673 328s COMPUTED RESULT 188802.7142979 328s COMPUTED RESULT 315969.0177241 328s COMPUTED RESULT 108.8773280806 328s Running tests for point-pmf section 328s BINARY: /usr/bin/apbs 328s INPUT: complex-0_1.in 328s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 328s 328s ---------------------------------------------------------------------- 328s APBS -- Adaptive Poisson-Boltzmann Solver 328s Version APBS 3.4.1 328s 328s Nathan A. Baker (nathan.baker@pnnl.gov) 328s Pacific Northwest National Laboratory 328s 328s Additional contributing authors listed in the code documentation. 328s 328s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 328s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 328s Northwest Division for the U.S. Department of Energy. 328s 328s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 328s Portions Copyright (c) 2002-2020, Nathan A. Baker. 328s Portions Copyright (c) 1999-2002, The Regents of the University of California. 328s Portions Copyright (c) 1995, Michael Holst. 328s All rights reserved. 328s 328s Redistribution and use in source and binary forms, with or without 328s modification, are permitted provided that the following conditions are met: 328s 328s * Redistributions of source code must retain the above copyright notice, this 328s list of conditions and the following disclaimer. 328s 328s * Redistributions in binary form must reproduce the above copyright notice, 328s this list of conditions and the following disclaimer in the documentation 328s and/or other materials provided with the distribution. 328s 328s * Neither the name of the developer nor the names of its contributors may be 328s used to endorse or promote products derived from this software without 328s specific prior written permission. 328s 328s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 328s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 328s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 328s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 328s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 328s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 328s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 328s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 328s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 328s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 328s ---------------------------------------------------------------------- 328s APBS uses FETK (the Finite Element ToolKit) to solve the 328s Poisson-Boltzmann equation numerically. FETK is a portable collection 328s of finite element modeling class libraries developed by the Michael Holst 328s research group and written in an object-oriented form of C. FEtk is 328s designed to solve general coupled systems of nonlinear partial differential 328s equations using adaptive finite element methods, inexact Newton methods, 328s and algebraic multilevel methods. More information about FEtk may be found 328s at . 328s ---------------------------------------------------------------------- 328s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 328s Aqua is a modified form of the Holst group PMG library 328s which has been modified by Patrice Koehl 328s for improved efficiency and 328s memory usage when solving the Poisson-Boltzmann equation. 328s ---------------------------------------------------------------------- 328s Please cite your use of APBS as: 328s 328s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 328s nanosystems: application to microtubules and the ribosome. Proc. 328s Natl. Acad. Sci. USA 98, 10037-10041 2001. 328s 328s 328s This executable compiled on Jan 3 2025 at 11:01:42 328s 328s Parsing input file complex-0_1.in... 328s rank 0 size 1... 328s Parsed input file. 328s Got paths for 3 molecules 328s Reading PQR-format atom data from mol0.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 1 atoms 328s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 328s Net charge 1.00e+00 e 328s Reading PQR-format atom data from mol1.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 1 atoms 328s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 328s Net charge 1.00e+00 e 328s Reading PQR-format atom data from complex-0_1.pqr. 328s 2 atoms 328s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 328s Net charge 2.00e+00 e 328s Preparing to run 3 PBE calculations. 328s ---------------------------------------- 328s CALCULATION #1 (point1): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 61.060 MB total, 61.060 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 65 x 65 x 65 328s Grid spacings: 0.210 x 0.210 x 0.210 328s Grid lengths: 13.440 x 13.440 x 13.440 328s Grid center: (0.000, 0.000, 0.000) 328s Multigrid levels: 5 328s Molecule ID: 1 328s Linearized traditional PBE 328s Multiple Debye-Huckel sphere boundary conditions 328s 0 ion species (0.000 M ionic strength): 328s Solute dielectric: 78.540 328s Solvent dielectric: 78.540 328s Using spline-based surface definition;window = 0.300 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 9.776035707281E+01 kJ/mol 328s Fixed charge energy = 97.7604 kJ/mol 328s Mobile charge energy = 0 kJ/mol 328s Dielectric energy = 96.5336 kJ/mol 328s Per-atom energies: 328s Atom 0: 9.776035707281E+01 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #2 (point2): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 61.060 MB total, 61.067 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 65 x 65 x 65 328s Grid spacings: 0.210 x 0.210 x 0.210 328s Grid lengths: 13.440 x 13.440 x 13.440 328s Grid center: (0.000, 0.000, 0.000) 328s Multigrid levels: 5 328s Molecule ID: 2 328s Linearized traditional PBE 328s Multiple Debye-Huckel sphere boundary conditions 328s 0 ion species (0.000 M ionic strength): 328s Solute dielectric: 78.540 328s Solvent dielectric: 78.540 328s Using spline-based surface definition;window = 0.300 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 8.975920687031E+01 kJ/mol 328s Fixed charge energy = 89.7592 kJ/mol 328s Mobile charge energy = 0 kJ/mol 328s Dielectric energy = 88.6151 kJ/mol 328s Per-atom energies: 328s Atom 0: 8.975920687031E+01 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #3 (complex): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 61.060 MB total, 61.067 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 65 x 65 x 65 328s Grid spacings: 0.210 x 0.210 x 0.210 328s Grid lengths: 13.440 x 13.440 x 13.440 328s Grid center: (0.000, 0.000, 0.000) 328s Multigrid levels: 5 328s Molecule ID: 3 328s Linearized traditional PBE 328s Multiple Debye-Huckel sphere boundary conditions 328s 0 ion species (0.000 M ionic strength): 328s Solute dielectric: 78.540 328s Solvent dielectric: 78.540 328s Using spline-based surface definition;window = 0.300 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 2.058277719334E+02 kJ/mol 328s Fixed charge energy = 205.828 kJ/mol 328s Mobile charge energy = 0 kJ/mol 328s Dielectric energy = 201.106 kJ/mol 328s Per-atom energies: 328s Atom 0: 1.069144350786E+02 kJ/mol 328s Atom 1: 9.891333685475E+01 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s PRINT STATEMENTS 328s 328s print energy 3 (complex) - 1 (point1) - 2 (point2) end 328s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 328s Global net ELEC energy = 1.830820799027E+01 kJ/mol 328s ---------------------------------------- 328s CLEANING UP AND SHUTTING DOWN... 328s Destroying force arrays. 328s No energy arrays to destroy. 328s Destroying multigrid structures. 328s Destroying finite element structures. 328s Destroying 3 molecules 328s Final memory usage: 0.001 MB total, 61.067 MB high water 328s 328s 328s Thanks for using APBS! 328s 328s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 328s *** PASSED *** 328s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 328s *** PASSED *** 328s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 328s *** PASSED *** 328s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 328s *** PASSED *** 328s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 328s *** PASSED *** 328s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 328s *** PASSED *** 328s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 328s *** PASSED *** 328s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 328s *** PASSED *** 328s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 328s *** PASSED *** 328s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 328s *** PASSED *** 328s Elapsed time: 0.381724 seconds 328s -------------------------------------------------------------------------------- 328s -------------------------------------------------------------------------------- 328s Testing input file complex-0_2.in 328s 328s Checking for intermediate energies in input file complex-0_1.out 328s EXPECTED COMPUTED: 13 328s EXPECTED EXPECTED: 13 328s 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] 328s 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'] 328s COMPUTED RESULT 97.76035707281 328s COMPUTED RESULT 89.75920687031 328s COMPUTED RESULT 205.8277719334 328s COMPUTED RESULT 0.0 328s COMPUTED RESULT 0.0 328s COMPUTED RESULT 0.0 328s COMPUTED RESULT 97.7604 328s COMPUTED RESULT 89.7592 328s COMPUTED RESULT 205.828 328s COMPUTED RESULT 96.5336 328s COMPUTED RESULT 88.6151 328s COMPUTED RESULT 201.106 328s COMPUTED RESULT 18.30820799027 328s BINARY: /usr/bin/apbs 328s INPUT: complex-0_2.in 328s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 328s 328s ---------------------------------------------------------------------- 328s APBS -- Adaptive Poisson-Boltzmann Solver 328s Version APBS 3.4.1 328s 328s Nathan A. Baker (nathan.baker@pnnl.gov) 328s Pacific Northwest National Laboratory 328s 328s Additional contributing authors listed in the code documentation. 328s 328s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 328s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 328s Northwest Division for the U.S. Department of Energy. 328s 328s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 328s Portions Copyright (c) 2002-2020, Nathan A. Baker. 328s Portions Copyright (c) 1999-2002, The Regents of the University of California. 328s Portions Copyright (c) 1995, Michael Holst. 328s All rights reserved. 328s 328s Redistribution and use in source and binary forms, with or without 328s modification, are permitted provided that the following conditions are met: 328s 328s * Redistributions of source code must retain the above copyright notice, this 328s list of conditions and the following disclaimer. 328s 328s * Redistributions in binary form must reproduce the above copyright notice, 328s this list of conditions and the following disclaimer in the documentation 328s and/or other materials provided with the distribution. 328s 328s * Neither the name of the developer nor the names of its contributors may be 328s used to endorse or promote products derived from this software without 328s specific prior written permission. 328s 328s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 328s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 328s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 328s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 328s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 328s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 328s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 328s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 328s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 328s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 328s ---------------------------------------------------------------------- 328s APBS uses FETK (the Finite Element ToolKit) to solve the 328s Poisson-Boltzmann equation numerically. FETK is a portable collection 328s of finite element modeling class libraries developed by the Michael Holst 328s research group and written in an object-oriented form of C. FEtk is 328s designed to solve general coupled systems of nonlinear partial differential 328s equations using adaptive finite element methods, inexact Newton methods, 328s and algebraic multilevel methods. More information about FEtk may be found 328s at . 328s ---------------------------------------------------------------------- 328s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 328s Aqua is a modified form of the Holst group PMG library 328s which has been modified by Patrice Koehl 328s for improved efficiency and 328s memory usage when solving the Poisson-Boltzmann equation. 328s ---------------------------------------------------------------------- 328s Please cite your use of APBS as: 328s 328s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 328s nanosystems: application to microtubules and the ribosome. Proc. 328s Natl. Acad. Sci. USA 98, 10037-10041 2001. 328s 328s 328s This executable compiled on Jan 3 2025 at 11:01:42 328s 328s Parsing input file complex-0_2.in... 328s rank 0 size 1... 328s Parsed input file. 328s Got paths for 3 molecules 328s Reading PQR-format atom data from mol0.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 1 atoms 328s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 328s Net charge 1.00e+00 e 328s Reading PQR-format atom data from mol2.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 1 atoms 328s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 328s Net charge 1.00e+00 e 328s Reading PQR-format atom data from complex-0_2.pqr. 328s 2 atoms 328s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 328s Net charge 2.00e+00 e 328s Preparing to run 3 PBE calculations. 328s ---------------------------------------- 328s CALCULATION #1 (point1): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 61.060 MB total, 61.060 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 65 x 65 x 65 328s Grid spacings: 0.210 x 0.210 x 0.210 328s Grid lengths: 13.440 x 13.440 x 13.440 328s Grid center: (0.000, 0.000, 0.000) 328s Multigrid levels: 5 328s Molecule ID: 1 328s Linearized traditional PBE 328s Multiple Debye-Huckel sphere boundary conditions 328s 0 ion species (0.000 M ionic strength): 328s Solute dielectric: 78.540 328s Solvent dielectric: 78.540 328s Using spline-based surface definition;window = 0.300 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 9.776035707281E+01 kJ/mol 328s Fixed charge energy = 97.7604 kJ/mol 328s Mobile charge energy = 0 kJ/mol 328s Dielectric energy = 96.5336 kJ/mol 328s Per-atom energies: 328s Atom 0: 9.776035707281E+01 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #2 (point2): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 61.060 MB total, 61.067 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 65 x 65 x 65 328s Grid spacings: 0.210 x 0.210 x 0.210 328s Grid lengths: 13.440 x 13.440 x 13.440 328s Grid center: (0.000, 0.000, 0.000) 328s Multigrid levels: 5 328s Molecule ID: 2 328s Linearized traditional PBE 328s Multiple Debye-Huckel sphere boundary conditions 328s 0 ion species (0.000 M ionic strength): 328s Solute dielectric: 78.540 328s Solvent dielectric: 78.540 328s Using spline-based surface definition;window = 0.300 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 1.017611498797E+02 kJ/mol 328s Fixed charge energy = 101.761 kJ/mol 328s Mobile charge energy = 0 kJ/mol 328s Dielectric energy = 100.656 kJ/mol 328s Per-atom energies: 328s Atom 0: 1.017611498797E+02 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #3 (complex): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 61.060 MB total, 61.068 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 65 x 65 x 65 328s Grid spacings: 0.210 x 0.210 x 0.210 328s Grid lengths: 13.440 x 13.440 x 13.440 328s Grid center: (0.000, 0.000, 0.000) 328s Multigrid levels: 5 328s Molecule ID: 3 328s Linearized traditional PBE 328s Multiple Debye-Huckel sphere boundary conditions 328s 0 ion species (0.000 M ionic strength): 328s Solute dielectric: 78.540 328s Solvent dielectric: 78.540 328s Using spline-based surface definition;window = 0.300 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 2.084282010393E+02 kJ/mol 328s Fixed charge energy = 208.428 kJ/mol 328s Mobile charge energy = 0 kJ/mol 328s Dielectric energy = 203.83 kJ/mol 328s Per-atom energies: 328s Atom 0: 1.022136878480E+02 kJ/mol 328s Atom 1: 1.062145131913E+02 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s PRINT STATEMENTS 328s 328s print energy 3 (complex) - 1 (point1) - 2 (point2) end 328s Local net energy (PE 0) = 8.906694086751E+00 kJ/mol 328s Global net ELEC energy = 8.906694086751E+00 kJ/mol 328s ---------------------------------------- 328s CLEANING UP AND SHUTTING DOWN... 328s Destroying force arrays. 328s No energy arrays to destroy. 328s Destroying multigrid structures. 328s Destroying finite element structures. 328s Destroying 3 molecules 328s Final memory usage: 0.001 MB total, 61.068 MB high water 328s 328s 328s Thanks for using APBS! 328s 328s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 328s *** PASSED *** 328s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 328s *** PASSED *** 328s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 328s *** PASSED *** 328s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 328s *** PASSED *** 328s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 328s *** PASSED *** 328s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 328s *** PASSED *** 328s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 328s *** PASSED *** 328s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 328s *** PASSED *** 328s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 328s *** PASSED *** 328s Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) 328s *** PASSED *** 328s Elapsed time: 0.359819 seconds 328s -------------------------------------------------------------------------------- 328s -------------------------------------------------------------------------------- 328s Testing input file complex-0_3.in 328s 329s Checking for intermediate energies in input file complex-0_2.out 329s EXPECTED COMPUTED: 13 329s EXPECTED EXPECTED: 13 329s COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.906694086751] 329s 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'] 329s COMPUTED RESULT 97.76035707281 329s COMPUTED RESULT 101.7611498797 329s COMPUTED RESULT 208.4282010393 329s COMPUTED RESULT 0.0 329s COMPUTED RESULT 0.0 329s COMPUTED RESULT 0.0 329s COMPUTED RESULT 97.7604 329s COMPUTED RESULT 101.761 329s COMPUTED RESULT 208.428 329s COMPUTED RESULT 96.5336 329s COMPUTED RESULT 100.656 329s COMPUTED RESULT 203.83 329s COMPUTED RESULT 8.906694086751 329s BINARY: /usr/bin/apbs 329s INPUT: complex-0_3.in 329s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 329s asc_getToken: Error occurred (bailing out). 329s Vio_scanf: Format problem with input. 329s 329s 329s ---------------------------------------------------------------------- 329s APBS -- Adaptive Poisson-Boltzmann Solver 329s Version APBS 3.4.1 329s 329s Nathan A. Baker (nathan.baker@pnnl.gov) 329s Pacific Northwest National Laboratory 329s 329s Additional contributing authors listed in the code documentation. 329s 329s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 329s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 329s Northwest Division for the U.S. Department of Energy. 329s 329s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 329s Portions Copyright (c) 2002-2020, Nathan A. Baker. 329s Portions Copyright (c) 1999-2002, The Regents of the University of California. 329s Portions Copyright (c) 1995, Michael Holst. 329s All rights reserved. 329s 329s Redistribution and use in source and binary forms, with or without 329s modification, are permitted provided that the following conditions are met: 329s 329s * Redistributions of source code must retain the above copyright notice, this 329s list of conditions and the following disclaimer. 329s 329s * Redistributions in binary form must reproduce the above copyright notice, 329s this list of conditions and the following disclaimer in the documentation 329s and/or other materials provided with the distribution. 329s 329s * Neither the name of the developer nor the names of its contributors may be 329s used to endorse or promote products derived from this software without 329s specific prior written permission. 329s 329s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 329s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 329s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 329s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 329s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 329s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 329s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 329s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 329s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 329s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 329s ---------------------------------------------------------------------- 329s APBS uses FETK (the Finite Element ToolKit) to solve the 329s Poisson-Boltzmann equation numerically. FETK is a portable collection 329s of finite element modeling class libraries developed by the Michael Holst 329s research group and written in an object-oriented form of C. FEtk is 329s designed to solve general coupled systems of nonlinear partial differential 329s equations using adaptive finite element methods, inexact Newton methods, 329s and algebraic multilevel methods. More information about FEtk may be found 329s at . 329s ---------------------------------------------------------------------- 329s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 329s Aqua is a modified form of the Holst group PMG library 329s which has been modified by Patrice Koehl 329s for improved efficiency and 329s memory usage when solving the Poisson-Boltzmann equation. 329s ---------------------------------------------------------------------- 329s Please cite your use of APBS as: 329s 329s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 329s nanosystems: application to microtubules and the ribosome. Proc. 329s Natl. Acad. Sci. USA 98, 10037-10041 2001. 329s 329s 329s This executable compiled on Jan 3 2025 at 11:01:42 329s 329s Parsing input file complex-0_3.in... 329s rank 0 size 1... 329s Parsed input file. 329s Got paths for 3 molecules 329s Reading PQR-format atom data from mol0.pqr. 329s asc_getToken: Error occurred (bailing out). 329s Vio_scanf: Format problem with input. 329s 1 atoms 329s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 329s Net charge 1.00e+00 e 329s Reading PQR-format atom data from mol3.pqr. 329s asc_getToken: Error occurred (bailing out). 329s Vio_scanf: Format problem with input. 329s 1 atoms 329s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 329s Net charge 1.00e+00 e 329s Reading PQR-format atom data from complex-0_3.pqr. 329s 2 atoms 329s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 329s Net charge 2.00e+00 e 329s Preparing to run 3 PBE calculations. 329s ---------------------------------------- 329s CALCULATION #1 (point1): MULTIGRID 329s Setting up problem... 329s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 329s Debye length: 0 A 329s Current memory usage: 61.060 MB total, 61.060 MB high water 329s Using linear spline charge discretization. 329s Grid dimensions: 65 x 65 x 65 329s Grid spacings: 0.210 x 0.210 x 0.210 329s Grid lengths: 13.440 x 13.440 x 13.440 329s Grid center: (0.000, 0.000, 0.000) 329s Multigrid levels: 5 329s Molecule ID: 1 329s Linearized traditional PBE 329s Multiple Debye-Huckel sphere boundary conditions 329s 0 ion species (0.000 M ionic strength): 329s Solute dielectric: 78.540 329s Solvent dielectric: 78.540 329s Using spline-based surface definition;window = 0.300 329s Temperature: 298.150 K 329s Electrostatic energies will be calculated 329s Total electrostatic energy = 9.776035707281E+01 kJ/mol 329s Fixed charge energy = 97.7604 kJ/mol 329s Mobile charge energy = 0 kJ/mol 329s Dielectric energy = 96.5336 kJ/mol 329s Per-atom energies: 329s Atom 0: 9.776035707281E+01 kJ/mol 329s Calculating forces... 329s ---------------------------------------- 329s CALCULATION #2 (point2): MULTIGRID 329s Setting up problem... 329s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 329s Debye length: 0 A 329s Current memory usage: 61.060 MB total, 61.067 MB high water 329s Using linear spline charge discretization. 329s Grid dimensions: 65 x 65 x 65 329s Grid spacings: 0.210 x 0.210 x 0.210 329s Grid lengths: 13.440 x 13.440 x 13.440 329s Grid center: (0.000, 0.000, 0.000) 329s Multigrid levels: 5 329s Molecule ID: 2 329s Linearized traditional PBE 329s Multiple Debye-Huckel sphere boundary conditions 329s 0 ion species (0.000 M ionic strength): 329s Solute dielectric: 78.540 329s Solvent dielectric: 78.540 329s Using spline-based surface definition;window = 0.300 329s Temperature: 298.150 K 329s Electrostatic energies will be calculated 329s Total electrostatic energy = 1.337661883222E+02 kJ/mol 329s Fixed charge energy = 133.766 kJ/mol 329s Mobile charge energy = 0 kJ/mol 329s Dielectric energy = 132.672 kJ/mol 329s Per-atom energies: 329s Atom 0: 1.337661883222E+02 kJ/mol 329s Calculating forces... 329s ---------------------------------------- 329s CALCULATION #3 (complex): MULTIGRID 329s Setting up problem... 329s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 329s Debye length: 0 A 329s Current memory usage: 61.060 MB total, 61.068 MB high water 329s Using linear spline charge discretization. 329s Grid dimensions: 65 x 65 x 65 329s Grid spacings: 0.210 x 0.210 x 0.210 329s Grid lengths: 13.440 x 13.440 x 13.440 329s Grid center: (0.000, 0.000, 0.000) 329s Multigrid levels: 5 329s Molecule ID: 3 329s Linearized traditional PBE 329s Multiple Debye-Huckel sphere boundary conditions 329s 0 ion species (0.000 M ionic strength): 329s Solute dielectric: 78.540 329s Solvent dielectric: 78.540 329s Using spline-based surface definition;window = 0.300 329s Temperature: 298.150 K 329s Electrostatic energies will be calculated 329s Total electrostatic energy = 2.374361452120E+02 kJ/mol 329s Fixed charge energy = 237.436 kJ/mol 329s Mobile charge energy = 0 kJ/mol 329s Dielectric energy = 232.924 kJ/mol 329s Per-atom energies: 329s Atom 0: 1.007151570480E+02 kJ/mol 329s Atom 1: 1.367209881640E+02 kJ/mol 329s Calculating forces... 329s ---------------------------------------- 329s PRINT STATEMENTS 329s 329s print energy 3 (complex) - 1 (point1) - 2 (point2) end 329s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 329s Global net ELEC energy = 5.909599816984E+00 kJ/mol 329s ---------------------------------------- 329s CLEANING UP AND SHUTTING DOWN... 329s Destroying force arrays. 329s No energy arrays to destroy. 329s Destroying multigrid structures. 329s Destroying finite element structures. 329s Destroying 3 molecules 329s Final memory usage: 0.001 MB total, 61.068 MB high water 329s 329s 329s Thanks for using APBS! 329s 329s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 329s *** PASSED *** 329s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 329s *** PASSED *** 329s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 329s *** PASSED *** 329s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 329s *** PASSED *** 329s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 329s *** PASSED *** 329s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 329s *** PASSED *** 329s Elapsed time: 0.346043 seconds 329s -------------------------------------------------------------------------------- 329s -------------------------------------------------------------------------------- 329s Testing input file complex-0_4.in 329s 329s Checking for intermediate energies in input file complex-0_3.out 329s EXPECTED COMPUTED: 13 329s EXPECTED EXPECTED: 13 329s 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] 329s 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'] 329s COMPUTED RESULT 97.76035707281 329s COMPUTED RESULT 133.7661883222 329s COMPUTED RESULT 237.436145212 329s COMPUTED RESULT 0.0 329s COMPUTED RESULT 0.0 329s COMPUTED RESULT 0.0 329s COMPUTED RESULT 97.7604 329s COMPUTED RESULT 133.766 329s COMPUTED RESULT 237.436 329s COMPUTED RESULT 96.5336 329s COMPUTED RESULT 132.672 329s COMPUTED RESULT 232.924 329s COMPUTED RESULT 5.909599816984 329s BINARY: /usr/bin/apbs 329s INPUT: complex-0_4.in 329s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 329s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 329s *** PASSED *** 329s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 329s asc_getToken: Error occurred (bailing out). 329s Vio_scanf: Format problem with input. 329s 329s 329s ---------------------------------------------------------------------- 329s APBS -- Adaptive Poisson-Boltzmann Solver 329s Version APBS 3.4.1 329s 329s Nathan A. Baker (nathan.baker@pnnl.gov) 329s Pacific Northwest National Laboratory 329s 329s Additional contributing authors listed in the code documentation. 329s 329s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 329s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 329s Northwest Division for the U.S. Department of Energy. 329s 329s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 329s Portions Copyright (c) 2002-2020, Nathan A. Baker. 329s Portions Copyright (c) 1999-2002, The Regents of the University of California. 329s Portions Copyright (c) 1995, Michael Holst. 329s All rights reserved. 329s 329s Redistribution and use in source and binary forms, with or without 329s modification, are permitted provided that the following conditions are met: 329s 329s * Redistributions of source code must retain the above copyright notice, this 329s list of conditions and the following disclaimer. 329s 329s * Redistributions in binary form must reproduce the above copyright notice, 329s this list of conditions and the following disclaimer in the documentation 329s and/or other materials provided with the distribution. 329s 329s * Neither the name of the developer nor the names of its contributors may be 329s used to endorse or promote products derived from this software without 329s specific prior written permission. 329s 329s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 329s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 329s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 329s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 329s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 329s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 329s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 329s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 329s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 329s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 329s ---------------------------------------------------------------------- 329s APBS uses FETK (the Finite Element ToolKit) to solve the 329s Poisson-Boltzmann equation numerically. FETK is a portable collection 329s of finite element modeling class libraries developed by the Michael Holst 329s research group and written in an object-oriented form of C. FEtk is 329s designed to solve general coupled systems of nonlinear partial differential 329s equations using adaptive finite element methods, inexact Newton methods, 329s and algebraic multilevel methods. More information about FEtk may be found 329s at . 329s ---------------------------------------------------------------------- 329s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 329s Aqua is a modified form of the Holst group PMG library 329s which has been modified by Patrice Koehl 329s for improved efficiency and 329s memory usage when solving the Poisson-Boltzmann equation. 329s ---------------------------------------------------------------------- 329s Please cite your use of APBS as: 329s 329s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 329s nanosystems: application to microtubules and the ribosome. Proc. 329s Natl. Acad. Sci. USA 98, 10037-10041 2001. 329s 329s 329s This executable compiled on Jan 3 2025 at 11:01:42 329s 329s Parsing input file complex-0_4.in... 329s rank 0 size 1... 329s Parsed input file. 329s Got paths for 3 molecules 329s Reading PQR-format atom data from mol0.pqr. 329s asc_getToken: Error occurred (bailing out). 329s Vio_scanf: Format problem with input. 329s 1 atoms 329s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 329s Net charge 1.00e+00 e 329s Reading PQR-format atom data from mol4.pqr. 329s asc_getToken: Error occurred (bailing out). 329s Vio_scanf: Format problem with input. 329s 1 atoms 329s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 329s Net charge 1.00e+00 e 329s Reading PQR-format atom data from complex-0_4.pqr. 329s 2 atoms 329s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 329s Net charge 2.00e+00 e 329s Preparing to run 3 PBE calculations. 329s ---------------------------------------- 329s CALCULATION #1 (point1): MULTIGRID 329s Setting up problem... 329s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 329s Debye length: 0 A 329s Current memory usage: 61.060 MB total, 61.060 MB high water 329s Using linear spline charge discretization. 329s Grid dimensions: 65 x 65 x 65 329s Grid spacings: 0.210 x 0.210 x 0.210 329s Grid lengths: 13.440 x 13.440 x 13.440 329s Grid center: (0.000, 0.000, 0.000) 329s Multigrid levels: 5 329s Molecule ID: 1 329s Linearized traditional PBE 329s Multiple Debye-Huckel sphere boundary conditions 329s 0 ion species (0.000 M ionic strength): 329s Solute dielectric: 78.540 329s Solvent dielectric: 78.540 329s Using spline-based surface definition;window = 0.300 329s Temperature: 298.150 K 329s Electrostatic energies will be calculated 329s Total electrostatic energy = 9.776035707281E+01 kJ/mol 329s Fixed charge energy = 97.7604 kJ/mol 329s Mobile charge energy = 0 kJ/mol 329s Dielectric energy = 96.5336 kJ/mol 329s Per-atom energies: 329s Atom 0: 9.776035707281E+01 kJ/mol 329s Calculating forces... 329s ---------------------------------------- 329s CALCULATION #2 (point2): MULTIGRID 329s Setting up problem... 329s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 329s Debye length: 0 A 329s Current memory usage: 61.060 MB total, 61.067 MB high water 329s Using linear spline charge discretization. 329s Grid dimensions: 65 x 65 x 65 329s Grid spacings: 0.210 x 0.210 x 0.210 329s Grid lengths: 13.440 x 13.440 x 13.440 329s Grid center: (0.000, 0.000, 0.000) 329s Multigrid levels: 5 329s Molecule ID: 2 329s Linearized traditional PBE 329s Multiple Debye-Huckel sphere boundary conditions 329s 0 ion species (0.000 M ionic strength): 329s Solute dielectric: 78.540 329s Solvent dielectric: 78.540 329s Using spline-based surface definition;window = 0.300 329s Temperature: 298.150 K 329s Electrostatic energies will be calculated 329s Total electrostatic energy = 1.017611498797E+02 kJ/mol 329s Fixed charge energy = 101.761 kJ/mol 329s Mobile charge energy = 0 kJ/mol 329s Dielectric energy = 100.654 kJ/mol 329s Per-atom energies: 329s Atom 0: 1.017611498797E+02 kJ/mol 329s Calculating forces... 329s ---------------------------------------- 329s CALCULATION #3 (complex): MULTIGRID 329s Setting up problem... 329s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 329s Debye length: 0 A 329s Current memory usage: 61.061 MB total, 61.068 MB high water 329s Using linear spline charge discretization. 329s Grid dimensions: 65 x 65 x 65 329s Grid spacings: 0.210 x 0.210 x 0.210 329s Grid lengths: 13.440 x 13.440 x 13.440 329s Grid center: (0.000, 0.000, 0.000) 329s Multigrid levels: 5 329s Molecule ID: 3 329s Linearized traditional PBE 329s Multiple Debye-Huckel sphere boundary conditions 329s 0 ion species (0.000 M ionic strength): 329s Solute dielectric: 78.540 329s Solvent dielectric: 78.540 329s Using spline-based surface definition;window = 0.300 329s Temperature: 298.150 K 329s Electrostatic energies will be calculated 329s Total electrostatic energy = 2.039516519000E+02 kJ/mol 329s Fixed charge energy = 203.952 kJ/mol 329s Mobile charge energy = 0 kJ/mol 329s Dielectric energy = 199.493 kJ/mol 329s Per-atom energies: 329s Atom 0: 9.997541697022E+01 kJ/mol 329s Atom 1: 1.039762349297E+02 kJ/mol 329s Calculating forces... 329s ---------------------------------------- 329s PRINT STATEMENTS 329s 329s print energy 3 (complex) - 1 (point1) - 2 (point2) end 329s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 329s Global net ELEC energy = 4.430144947418E+00 kJ/mol 329s ---------------------------------------- 329s CLEANING UP AND SHUTTING DOWN... 329s Destroying force arrays. 329s No energy arrays to destroy. 329s Destroying multigrid structures. 329s Destroying finite element structures. 329s Destroying 3 molecules 329s Final memory usage: 0.001 MB total, 61.068 MB high water 329s 329s 329s Thanks for using APBS! 329s 329s *** PASSED *** 329s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 329s *** PASSED *** 329s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 329s *** PASSED *** 329s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 329s *** PASSED *** 329s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 329s *** PASSED *** 329s Elapsed time: 0.357747 seconds 329s -------------------------------------------------------------------------------- 329s Total elapsed time: 1.445333 seconds 329s Test results have been logged 329s -------------------------------------------------------------------------------- 329s -------------------------------------------------------------------------------- 329s Testing input file apbs-mol.in 329s 330s Checking for intermediate energies in input file complex-0_4.out 330s EXPECTED COMPUTED: 13 330s EXPECTED EXPECTED: 13 330s 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] 330s 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'] 330s COMPUTED RESULT 97.76035707281 330s COMPUTED RESULT 101.7611498797 330s COMPUTED RESULT 203.9516519 330s COMPUTED RESULT 0.0 330s COMPUTED RESULT 0.0 330s COMPUTED RESULT 0.0 330s COMPUTED RESULT 97.7604 330s COMPUTED RESULT 101.761 330s COMPUTED RESULT 203.952 330s COMPUTED RESULT 96.5336 330s COMPUTED RESULT 100.654 330s COMPUTED RESULT 199.493 330s COMPUTED RESULT 4.430144947418 330s Running tests for solv section 330s BINARY: /usr/bin/apbs 330s INPUT: apbs-mol.in 330s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 330s asc_getToken: Error occurred (bailing out). 330s Vio_scanf: Format problem with input. 330s 330s 330s ---------------------------------------------------------------------- 330s APBS -- Adaptive Poisson-Boltzmann Solver 330s Version APBS 3.4.1 330s 330s Nathan A. Baker (nathan.baker@pnnl.gov) 330s Pacific Northwest National Laboratory 330s 330s Additional contributing authors listed in the code documentation. 330s 330s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 330s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 330s Northwest Division for the U.S. Department of Energy. 330s 330s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 330s Portions Copyright (c) 2002-2020, Nathan A. Baker. 330s Portions Copyright (c) 1999-2002, The Regents of the University of California. 330s Portions Copyright (c) 1995, Michael Holst. 330s All rights reserved. 330s 330s Redistribution and use in source and binary forms, with or without 330s modification, are permitted provided that the following conditions are met: 330s 330s * Redistributions of source code must retain the above copyright notice, this 330s list of conditions and the following disclaimer. 330s 330s * Redistributions in binary form must reproduce the above copyright notice, 330s this list of conditions and the following disclaimer in the documentation 330s and/or other materials provided with the distribution. 330s 330s * Neither the name of the developer nor the names of its contributors may be 330s used to endorse or promote products derived from this software without 330s specific prior written permission. 330s 330s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 330s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 330s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 330s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 330s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 330s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 330s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 330s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 330s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 330s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 330s ---------------------------------------------------------------------- 330s APBS uses FETK (the Finite Element ToolKit) to solve the 330s Poisson-Boltzmann equation numerically. FETK is a portable collection 330s of finite element modeling class libraries developed by the Michael Holst 330s research group and written in an object-oriented form of C. FEtk is 330s designed to solve general coupled systems of nonlinear partial differential 330s equations using adaptive finite element methods, inexact Newton methods, 330s and algebraic multilevel methods. More information about FEtk may be found 330s at . 330s ---------------------------------------------------------------------- 330s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 330s Aqua is a modified form of the Holst group PMG library 330s which has been modified by Patrice Koehl 330s for improved efficiency and 330s memory usage when solving the Poisson-Boltzmann equation. 330s ---------------------------------------------------------------------- 330s Please cite your use of APBS as: 330s 330s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 330s nanosystems: application to microtubules and the ribosome. Proc. 330s Natl. Acad. Sci. USA 98, 10037-10041 2001. 330s 330s 330s This executable compiled on Jan 3 2025 at 11:01:42 330s 330s Parsing input file apbs-mol.in... 330s rank 0 size 1... 330s Parsed input file. 330s Got paths for 2 molecules 330s Reading PQR-format atom data from methanol.pqr. 330s asc_getToken: Error occurred (bailing out). 330s Vio_scanf: Format problem with input. 330s 3 atoms 330s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 330s Net charge 5.55e-17 e 330s Reading PQR-format atom data from methoxide.pqr. 330s 2 atoms 330s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 330s Net charge -1.00e+00 e 330s Preparing to run 4 PBE calculations. 330s ---------------------------------------- 330s CALCULATION #1 (methanol-solv): MULTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.253 MB total, 61.253 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.309, 0.000, -0.242) 330s Multigrid levels: 5 330s Molecule ID: 1 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 78.000 330s Using "molecular" surface definition; no smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 1.847663548071E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s CALCULATION #2 (methanol-ref): MULTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.253 MB total, 61.328 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.309, 0.000, -0.242) 330s Multigrid levels: 5 330s Molecule ID: 1 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 1.000 330s Using "molecular" surface definition; no smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 1.883912182952E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s CALCULATION #3 (methoxide-solv): MULTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.250 MB total, 61.328 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.000, 0.000, -0.128) 330s Multigrid levels: 5 330s Molecule ID: 2 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 78.000 330s Using "molecular" surface definition; no smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 2.732623683321E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s CALCULATION #4 (methoxide-ref): MULTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.250 MB total, 61.328 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.000, 0.000, -0.128) 330s Multigrid levels: 5 330s Molecule ID: 2 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 1.000 330s Using "molecular" surface definition; no smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 3.123035854133E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s PRINT STATEMENTS 330s 330s print energy 1 (methanol-solv) - 2 (methanol-ref) end 330s Local net energy (PE 0) = -3.624863488075E+01 kJ/mol 330s Global net ELEC energy = -3.624863488075E+01 kJ/mol 330s 330s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 330s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 330s Global net ELEC energy = -3.904121708125E+02 kJ/mol 330s 330s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 330s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 330s Global net ELEC energy = -3.541635359318E+02 kJ/mol 330s ---------------------------------------- 330s CLEANING UP AND SHUTTING DOWN... 330s Destroying force arrays. 330s No energy arrays to destroy. 330s Destroying multigrid structures. 330s Destroying finite element structures. 330s Destroying 2 molecules 330s Final memory usage: 0.001 MB total, 61.328 MB high water 330s 330s 330s Thanks for using APBS! 330s 330s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 330s *** PASSED *** 330s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 330s *** PASSED *** 330s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 330s *** PASSED *** 330s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 330s *** PASSED *** 330s Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) 330s *** PASSED *** 330s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 330s *** PASSED *** 330s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 330s *** PASSED *** 330s Elapsed time: 0.534202 seconds 330s -------------------------------------------------------------------------------- 330s -------------------------------------------------------------------------------- 330s Testing input file apbs-smol.in 330s 330s Checking for intermediate energies in input file apbs-mol.out 330s EXPECTED COMPUTED: 7 330s EXPECTED EXPECTED: 7 330s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] 330s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 330s COMPUTED RESULT 1847.663548071 330s COMPUTED RESULT 1883.912182952 330s COMPUTED RESULT 2732.623683321 330s COMPUTED RESULT 3123.035854133 330s COMPUTED RESULT -36.24863488075 330s COMPUTED RESULT -390.4121708125 330s COMPUTED RESULT -354.1635359318 330s BINARY: /usr/bin/apbs 330s INPUT: apbs-smol.in 330s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 330s asc_getToken: Error occurred (bailing out). 330s Vio_scanf: Format problem with input. 330s 330s 330s ---------------------------------------------------------------------- 330s APBS -- Adaptive Poisson-Boltzmann Solver 330s Version APBS 3.4.1 330s 330s Nathan A. Baker (nathan.baker@pnnl.gov) 330s Pacific Northwest National Laboratory 330s 330s Additional contributing authors listed in the code documentation. 330s 330s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 330s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 330s Northwest Division for the U.S. Department of Energy. 330s 330s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 330s Portions Copyright (c) 2002-2020, Nathan A. Baker. 330s Portions Copyright (c) 1999-2002, The Regents of the University of California. 330s Portions Copyright (c) 1995, Michael Holst. 330s All rights reserved. 330s 330s Redistribution and use in source and binary forms, with or without 330s modification, are permitted provided that the following conditions are met: 330s 330s * Redistributions of source code must retain the above copyright notice, this 330s list of conditions and the following disclaimer. 330s 330s * Redistributions in binary form must reproduce the above copyright notice, 330s this list of conditions and the following disclaimer in the documentation 330s and/or other materials provided with the distribution. 330s 330s * Neither the name of the developer nor the names of its contributors may be 330s used to endorse or promote products derived from this software without 330s specific prior written permission. 330s 330s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 330s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 330s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 330s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 330s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 330s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 330s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 330s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 330s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 330s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 330s ---------------------------------------------------------------------- 330s APBS uses FETK (the Finite Element ToolKit) to solve the 330s Poisson-Boltzmann equation numerically. FETK is a portable collection 330s of finite element modeling class libraries developed by the Michael Holst 330s research group and written in an object-oriented form of C. FEtk is 330s designed to solve general coupled systems of nonlinear partial differential 330s equations using adaptive finite element methods, inexact Newton methods, 330s and algebraic multilevel methods. More information about FEtk may be found 330s at . 330s ---------------------------------------------------------------------- 330s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 330s Aqua is a modified form of the Holst group PMG library 330s which has been modified by Patrice Koehl 330s for improved efficiency and 330s memory usage when solving the Poisson-Boltzmann equation. 330s ---------------------------------------------------------------------- 330s Please cite your use of APBS as: 330s 330s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 330s nanosystems: application to microtubules and the ribosome. Proc. 330s Natl. Acad. Sci. USA 98, 10037-10041 2001. 330s 330s 330s This executable compiled on Jan 3 2025 at 11:01:42 330s 330s Parsing input file apbs-smol.in... 330s rank 0 size 1... 330s Parsed input file. 330s Got paths for 2 molecules 330s Reading PQR-format atom data from methanol.pqr. 330s asc_getToken: Error occurred (bailing out). 330s Vio_scanf: Format problem with input. 330s 3 atoms 330s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 330s Net charge 5.55e-17 e 330s Reading PQR-format atom data from methoxide.pqr. 330s 2 atoms 330s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 330s Net charge -1.00e+00 e 330s Preparing to run 4 PBE calculations. 330s ---------------------------------------- 330s CALCULATION #1 (methanol-solv): MULTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.253 MB total, 61.253 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.309, 0.000, -0.242) 330s Multigrid levels: 5 330s Molecule ID: 1 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 78.000 330s Using "molecular" surface definition;harmonic average smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 1.847860440020E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s CALCULATION #2 (methanol-ref): MULTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.253 MB total, 61.328 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.309, 0.000, -0.242) 330s Multigrid levels: 5 330s Molecule ID: 1 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 1.000 330s Using "molecular" surface definition;harmonic average smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 1.885436377745E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s CALCULATION #3 (methoxide-solv): MULTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.250 MB total, 61.328 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.000, 0.000, -0.128) 330s Multigrid levels: 5 330s Molecule ID: 2 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 78.000 330s Using "molecular" surface definition;harmonic average smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 2.734040568569E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s CALCULATION #4 (methoxide-ref): MUTesting computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 330s *** PASSED *** 330s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 330s *** PASSED *** 330s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 330s *** PASSED *** 330s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 330s *** PASSED *** 330s Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) 330s *** PASSED *** 330s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 330s *** PASSED *** 330s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 330s *** PASSED *** 330s Elapsed time: 0.559898 seconds 330s -------------------------------------------------------------------------------- 330s Total elapsed time: 1.0941 seconds 330s Test results have been logged 330s -------------------------------------------------------------------------------- 330s LTIGRID 330s Setting up problem... 330s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 330s Debye length: 0 A 330s Current memory usage: 61.250 MB total, 61.328 MB high water 330s Using linear spline charge discretization. 330s Grid dimensions: 65 x 65 x 65 330s Grid spacings: 0.250 x 0.250 x 0.250 330s Grid lengths: 16.000 x 16.000 x 16.000 330s Grid center: (0.000, 0.000, -0.128) 330s Multigrid levels: 5 330s Molecule ID: 2 330s Linearized traditional PBE 330s Multiple Debye-Huckel sphere boundary conditions 330s 2 ion species (0.000 M ionic strength): 330s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 330s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 330s Solute dielectric: 2.000 330s Solvent dielectric: 1.000 330s Using "molecular" surface definition;harmonic average smoothing 330s Solvent probe radius: 0.000 A 330s Temperature: 300.000 K 330s Electrostatic energies will be calculated 330s Total electrostatic energy = 3.125279428954E+03 kJ/mol 330s Calculating forces... 330s ---------------------------------------- 330s PRINT STATEMENTS 330s 330s print energy 1 (methanol-solv) - 2 (methanol-ref) end 330s Local net energy (PE 0) = -3.757593772492E+01 kJ/mol 330s Global net ELEC energy = -3.757593772492E+01 kJ/mol 330s 330s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 330s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 330s Global net ELEC energy = -3.912388603848E+02 kJ/mol 330s 330s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 330s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 330s Global net ELEC energy = -3.536629226599E+02 kJ/mol 330s ---------------------------------------- 330s CLEANING UP AND SHUTTING DOWN... 330s Destroying force arrays. 330s No energy arrays to destroy. 330s Destroying multigrid structures. 330s Destroying finite element structures. 330s Destroying 2 molecules 330s Final memory usage: 0.001 MB total, 61.328 MB high water 330s 330s 330s Thanks for using APBS! 330s 330s Checking for intermediate energies in input file apbs-smol.out 330s EXPECTED COMPUTED: 7 330s EXPECTED EXPECTED: 7 330s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] 330s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 330s COMPUTED RESULT 1847.86044002 330s COMPUTED RESULT 1885.436377745 330s COMPUTED RESULT 2734.040568569 330s COMPUTED RESULT 3125.279428954 330s COMPUTED RESULT -37.57593772492 330s COMPUTED RESULT -391.2388603848 330s COMPUTED RESULT -353.6629226599 330s autopkgtest [15:40:46]: test test-apbs: -----------------------] 331s autopkgtest [15:40:47]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 331s test-apbs PASS 332s autopkgtest [15:40:48]: @@@@@@@@@@@@@@@@@@@@ summary 332s test-apbs PASS