0s autopkgtest [19:50:30]: starting date and time: 2025-10-20 19:50:30+0000 0s autopkgtest [19:50:30]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:50:30]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.353wj7wa/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:node-jquery --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-9.secgroup --name adt-resolute-ppc64el-apbs-20251020-195030-juju-7f2275-prod-proposed-migration-environment-15-d31c8ecc-dd40-4dc9-809a-363e41f8177d --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-20251020-195030-juju-7f2275-prod-proposed-migration-environment-15-d31c8ecc-dd40-4dc9-809a-363e41f8177d from image adt/ubuntu-resolute-ppc64el-server-20251020.img (UUID 243ad32c-1bbf-485e-924d-1d24001cd7a1)... 54s autopkgtest [19:51:24]: testbed dpkg architecture: ppc64el 55s autopkgtest [19:51:25]: testbed apt version: 3.1.8ubuntu1 55s autopkgtest [19:51:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 55s autopkgtest [19:51:25]: testbed release detected to be: None 56s autopkgtest [19:51:26]: updating testbed package index (apt update) 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 57s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 57s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 58s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 58s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 58s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 58s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [108 kB] 58s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 58s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [407 kB] 59s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [3808 B] 59s Fetched 1328 kB in 2s (536 kB/s) 60s Reading package lists... 60s Failed to check for VM: Permission denied 60s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 61s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 62s Reading package lists... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade... 62s The following packages will be upgraded: 62s libbrotli1 62s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 422 kB of archives. 62s After this operation, 0 B of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbrotli1 ppc64el 1.1.0-2build6 [422 kB] 63s dpkg-preconfigure: unable to re-open stdin: No such file or directory 63s Fetched 422 kB in 1s (502 kB/s) 63s (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 ... 76476 files and directories currently installed.) 63s Preparing to unpack .../libbrotli1_1.1.0-2build6_ppc64el.deb ... 63s Unpacking libbrotli1:ppc64el (1.1.0-2build6) over (1.1.0-2build5) ... 64s Setting up libbrotli1:ppc64el (1.1.0-2build6) ... 64s Processing triggers for libc-bin (2.42-0ubuntu3) ... 64s autopkgtest [19:51:34]: upgrading testbed (apt dist-upgrade and autopurge) 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Calculating upgrade... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Solving dependencies... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [19:51:38]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 68s autopkgtest [19:51:38]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 94s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 94s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 94s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 94s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 94s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 94s gpgv: Can't check signature: No public key 94s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 97s autopkgtest [19:52:07]: testing package apbs version 3.4.1-6build2 104s autopkgtest [19:52:14]: build not needed 111s autopkgtest [19:52:21]: test test-apbs: preparing testbed 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Solving dependencies... 112s The following NEW packages will be installed: 112s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax 112s libamd-comgr2 libamd3 libamdhip64-5 libapbs-dev libapbs3t64 libarpack2t64 112s libblas3 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdrm-amdgpu1 112s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfetk-dev 112s libfetk1.9t64 libgfortran5 libgomp1 libhsa-runtime64-1 libhsakmt1 112s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libjs-jquery libjs-mathjax 112s libjs-sphinxdoc libjs-underscore liblapack3 libllvm17t64 libmaloc-dev 112s libmaloc1 libopenmpi40 libpciaccess0 librdmacm1t64 libspqr4 112s libsuitesparseconfig7 libsuperlu7 libucx0 libumfpack6 libxnvctrl0 112s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 112s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 86.8 MB of archives. 112s After this operation, 373 MB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-lato all 2.015-1 [2781 kB] 114s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el apbs-data all 3.4.1-6build2 [1769 kB] 115s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libmaloc1 ppc64el 1.5-2 [103 kB] 115s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 115s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libsuperlu7 ppc64el 7.0.1+dfsg1-2 [237 kB] 115s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-5ubuntu1 [169 kB] 115s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsuitesparseconfig7 ppc64el 1:7.10.1+dfsg-1 [21.6 kB] 115s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libamd3 ppc64el 1:7.10.1+dfsg-1 [44.8 kB] 115s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcamd3 ppc64el 1:7.10.1+dfsg-1 [38.9 kB] 115s Get:10 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libccolamd3 ppc64el 1:7.10.1+dfsg-1 [39.6 kB] 115s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcolamd3 ppc64el 1:7.10.1+dfsg-1 [29.8 kB] 115s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-5ubuntu1 [620 kB] 115s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 116s Get:14 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libcholmod5 ppc64el 1:7.10.1+dfsg-1 [913 kB] 116s Get:15 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libumfpack6 ppc64el 1:7.10.1+dfsg-1 [343 kB] 116s Get:16 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libfetk1.9t64 ppc64el 3.4.1-6build2 [660 kB] 116s Get:17 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libapbs3t64 ppc64el 3.4.1-6build2 [310 kB] 116s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 116s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 117s Get:20 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libarpack2t64 ppc64el 3.9.1-6 [107 kB] 117s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libevent-core-2.1-7t64 ppc64el 2.1.12-stable-10build1 [109 kB] 117s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libevent-pthreads-2.1-7t64 ppc64el 2.1.12-stable-10build1 [8140 B] 117s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el librdmacm1t64 ppc64el 56.1-1ubuntu1 [80.3 kB] 117s Get:24 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libfabric1 ppc64el 2.1.0-1.1 [786 kB] 117s Get:25 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhwloc15 ppc64el 2.12.2-1 [223 kB] 117s Get:26 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libllvm17t64 ppc64el 1:17.0.6-22build1 [27.0 MB] 118s Get:27 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3build3 [15.1 MB] 119s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdrm-amdgpu1 ppc64el 2.4.125-1 [25.5 kB] 119s Get:29 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhsakmt1 ppc64el 6.2.4+ds-1 [75.9 kB] 119s Get:30 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhsa-runtime64-1 ppc64el 6.1.2-3 [350 kB] 119s Get:31 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libamdhip64-5 ppc64el 5.7.1-6 [9342 kB] 119s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libibumad3 ppc64el 56.1-1ubuntu1 [33.8 kB] 119s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libibmad5 ppc64el 56.1-1ubuntu1 [47.1 kB] 119s Get:34 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libucx0 ppc64el 1.19.0+ds-1 [1361 kB] 119s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpciaccess0 ppc64el 0.18.1-1ubuntu2 [21.9 kB] 119s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu4 [12.6 kB] 119s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el ocl-icd-libopencl1 ppc64el 2.3.3-1 [47.9 kB] 119s Get:38 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhwloc-plugins ppc64el 2.12.2-1 [17.7 kB] 119s Get:39 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libopenmpi40 ppc64el 5.0.8-8ubuntu1 [3435 kB] 119s Get:40 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libspqr4 ppc64el 1:7.10.1+dfsg-1 [198 kB] 119s Get:41 http://ftpmaster.internal/ubuntu resolute/universe ppc64el apbs ppc64el 3.4.1-6build2 [80.3 kB] 119s Get:42 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 119s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 119s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 119s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 119s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 119s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el apbs-doc all 3.4.1-6build2 [5850 kB] 120s Get:48 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libapbs-dev ppc64el 3.4.1-6build2 [99.5 kB] 120s Get:49 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libmaloc-dev ppc64el 1.5-2 [918 kB] 120s Get:50 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libfetk-dev ppc64el 3.4.1-6build2 [144 kB] 120s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-apbslib ppc64el 3.4.1-6build2 [218 kB] 120s Fetched 86.8 MB in 8s (11.4 MB/s) 120s Selecting previously unselected package fonts-lato. 120s (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 ... 76476 files and directories currently installed.) 120s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 120s Unpacking fonts-lato (2.015-1) ... 120s Selecting previously unselected package apbs-data. 120s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 120s Unpacking apbs-data (3.4.1-6build2) ... 120s Selecting previously unselected package libmaloc1:ppc64el. 120s Preparing to unpack .../02-libmaloc1_1.5-2_ppc64el.deb ... 120s Unpacking libmaloc1:ppc64el (1.5-2) ... 120s Selecting previously unselected package libblas3:ppc64el. 120s Preparing to unpack .../03-libblas3_3.12.1-6build1_ppc64el.deb ... 120s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 120s Selecting previously unselected package libsuperlu7:ppc64el. 120s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_ppc64el.deb ... 120s Unpacking libsuperlu7:ppc64el (7.0.1+dfsg1-2) ... 120s Selecting previously unselected package libgomp1:ppc64el. 120s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_ppc64el.deb ... 120s Unpacking libgomp1:ppc64el (15.2.0-5ubuntu1) ... 120s Selecting previously unselected package libsuitesparseconfig7:ppc64el. 120s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_ppc64el.deb ... 120s Unpacking libsuitesparseconfig7:ppc64el (1:7.10.1+dfsg-1) ... 121s Selecting previously unselected package libamd3:ppc64el. 121s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 121s Unpacking libamd3:ppc64el (1:7.10.1+dfsg-1) ... 121s Selecting previously unselected package libcamd3:ppc64el. 121s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 121s Unpacking libcamd3:ppc64el (1:7.10.1+dfsg-1) ... 121s Selecting previously unselected package libccolamd3:ppc64el. 121s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 121s Unpacking libccolamd3:ppc64el (1:7.10.1+dfsg-1) ... 121s Selecting previously unselected package libcolamd3:ppc64el. 121s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_ppc64el.deb ... 121s Unpacking libcolamd3:ppc64el (1:7.10.1+dfsg-1) ... 121s Selecting previously unselected package libgfortran5:ppc64el. 121s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_ppc64el.deb ... 121s Unpacking libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 121s Selecting previously unselected package liblapack3:ppc64el. 121s Preparing to unpack .../12-liblapack3_3.12.1-6build1_ppc64el.deb ... 121s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 121s Selecting previously unselected package libcholmod5:ppc64el. 121s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_ppc64el.deb ... 121s Unpacking libcholmod5:ppc64el (1:7.10.1+dfsg-1) ... 121s Selecting previously unselected package libumfpack6:ppc64el. 121s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_ppc64el.deb ... 121s Unpacking libumfpack6:ppc64el (1:7.10.1+dfsg-1) ... 121s Selecting previously unselected package libfetk1.9t64:ppc64el. 121s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_ppc64el.deb ... 121s Unpacking libfetk1.9t64:ppc64el (3.4.1-6build2) ... 121s Selecting previously unselected package libapbs3t64:ppc64el. 121s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_ppc64el.deb ... 121s Unpacking libapbs3t64:ppc64el (3.4.1-6build2) ... 121s Selecting previously unselected package fonts-mathjax. 121s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 121s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 121s Selecting previously unselected package libjs-mathjax. 121s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 121s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 123s Selecting previously unselected package libarpack2t64:ppc64el. 123s Preparing to unpack .../19-libarpack2t64_3.9.1-6_ppc64el.deb ... 123s Unpacking libarpack2t64:ppc64el (3.9.1-6) ... 123s Selecting previously unselected package libevent-core-2.1-7t64:ppc64el. 123s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_ppc64el.deb ... 123s Unpacking libevent-core-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 123s Selecting previously unselected package libevent-pthreads-2.1-7t64:ppc64el. 123s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_ppc64el.deb ... 123s Unpacking libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 123s Selecting previously unselected package librdmacm1t64:ppc64el. 123s Preparing to unpack .../22-librdmacm1t64_56.1-1ubuntu1_ppc64el.deb ... 123s Unpacking librdmacm1t64:ppc64el (56.1-1ubuntu1) ... 123s Selecting previously unselected package libfabric1:ppc64el. 123s Preparing to unpack .../23-libfabric1_2.1.0-1.1_ppc64el.deb ... 123s Unpacking libfabric1:ppc64el (2.1.0-1.1) ... 123s Selecting previously unselected package libhwloc15:ppc64el. 123s Preparing to unpack .../24-libhwloc15_2.12.2-1_ppc64el.deb ... 123s Unpacking libhwloc15:ppc64el (2.12.2-1) ... 123s Selecting previously unselected package libllvm17t64:ppc64el. 123s Preparing to unpack .../25-libllvm17t64_1%3a17.0.6-22build1_ppc64el.deb ... 123s Unpacking libllvm17t64:ppc64el (1:17.0.6-22build1) ... 123s Selecting previously unselected package libamd-comgr2:ppc64el. 123s Preparing to unpack .../26-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build3_ppc64el.deb ... 123s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build3) ... 123s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 123s Preparing to unpack .../27-libdrm-amdgpu1_2.4.125-1_ppc64el.deb ... 123s Unpacking libdrm-amdgpu1:ppc64el (2.4.125-1) ... 123s Selecting previously unselected package libhsakmt1:ppc64el. 123s Preparing to unpack .../28-libhsakmt1_6.2.4+ds-1_ppc64el.deb ... 123s Unpacking libhsakmt1:ppc64el (6.2.4+ds-1) ... 123s Selecting previously unselected package libhsa-runtime64-1:ppc64el. 123s Preparing to unpack .../29-libhsa-runtime64-1_6.1.2-3_ppc64el.deb ... 123s Unpacking libhsa-runtime64-1:ppc64el (6.1.2-3) ... 123s Selecting previously unselected package libamdhip64-5:ppc64el. 123s Preparing to unpack .../30-libamdhip64-5_5.7.1-6_ppc64el.deb ... 123s Unpacking libamdhip64-5:ppc64el (5.7.1-6) ... 123s Selecting previously unselected package libibumad3:ppc64el. 123s Preparing to unpack .../31-libibumad3_56.1-1ubuntu1_ppc64el.deb ... 123s Unpacking libibumad3:ppc64el (56.1-1ubuntu1) ... 123s Selecting previously unselected package libibmad5:ppc64el. 123s Preparing to unpack .../32-libibmad5_56.1-1ubuntu1_ppc64el.deb ... 123s Unpacking libibmad5:ppc64el (56.1-1ubuntu1) ... 123s Selecting previously unselected package libucx0:ppc64el. 123s Preparing to unpack .../33-libucx0_1.19.0+ds-1_ppc64el.deb ... 123s Unpacking libucx0:ppc64el (1.19.0+ds-1) ... 123s Selecting previously unselected package libpciaccess0:ppc64el. 123s Preparing to unpack .../34-libpciaccess0_0.18.1-1ubuntu2_ppc64el.deb ... 123s Unpacking libpciaccess0:ppc64el (0.18.1-1ubuntu2) ... 123s Selecting previously unselected package libxnvctrl0:ppc64el. 123s Preparing to unpack .../35-libxnvctrl0_510.47.03-0ubuntu4_ppc64el.deb ... 123s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ... 123s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 123s Preparing to unpack .../36-ocl-icd-libopencl1_2.3.3-1_ppc64el.deb ... 123s Unpacking ocl-icd-libopencl1:ppc64el (2.3.3-1) ... 123s Selecting previously unselected package libhwloc-plugins:ppc64el. 123s Preparing to unpack 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... 124s Setting up libgomp1:ppc64el (15.2.0-5ubuntu1) ... 124s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ... 124s Setting up libblas3:ppc64el (3.12.1-6build1) ... 124s 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 124s Setting up libllvm17t64:ppc64el (1:17.0.6-22build1) ... 124s Setting up libhwloc15:ppc64el (2.12.2-1) ... 124s Setting up libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 124s Setting up ocl-icd-libopencl1:ppc64el (2.3.3-1) ... 124s Setting up libsuitesparseconfig7:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up librdmacm1t64:ppc64el (56.1-1ubuntu1) ... 124s Setting up libevent-core-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 124s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build3) ... 124s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 124s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 124s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 124s Setting up libmaloc-dev (1.5-2) ... 124s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 124s Setting up libdrm-amdgpu1:ppc64el (2.4.125-1) ... 124s Setting up libfabric1:ppc64el (2.1.0-1.1) ... 124s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 124s 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 124s Setting up libarpack2t64:ppc64el (3.9.1-6) ... 124s Setting up libamd3:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up libcolamd3:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10build1) ... 124s Setting up libhwloc-plugins:ppc64el (2.12.2-1) ... 124s Setting up libcamd3:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up libsuperlu7:ppc64el (7.0.1+dfsg1-2) ... 124s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 124s Setting up libccolamd3:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up libhsakmt1:ppc64el (6.2.4+ds-1) ... 124s Setting up libcholmod5:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up libspqr4:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up apbs-doc (3.4.1-6build2) ... 124s Setting up libumfpack6:ppc64el (1:7.10.1+dfsg-1) ... 124s Setting up libhsa-runtime64-1:ppc64el (6.1.2-3) ... 124s Setting up libfetk1.9t64:ppc64el (3.4.1-6build2) ... 124s Setting up libapbs3t64:ppc64el (3.4.1-6build2) ... 124s Setting up libfetk-dev:ppc64el (3.4.1-6build2) ... 124s Setting up libamdhip64-5:ppc64el (5.7.1-6) ... 124s Setting up libapbs-dev:ppc64el (3.4.1-6build2) ... 124s Setting up python3-apbslib (3.4.1-6build2) ... 124s Setting up libucx0:ppc64el (1.19.0+ds-1) ... 124s Setting up libopenmpi40:ppc64el (5.0.8-8ubuntu1) ... 124s Setting up apbs (3.4.1-6build2) ... 124s Processing triggers for man-db (2.13.1-1) ... 125s Processing triggers for libc-bin (2.42-0ubuntu3) ... 129s autopkgtest [19:52:39]: test test-apbs: [----------------------- 129s TESTING WITH BINARY_NAME:apbs 129s START_DIR:/tmp/autopkgtest.qmJFsK/autopkgtest_tmp/build 129s -------------------------------------------------------------------------------- 129s Testing forces from apbs-forces.in 129s 129s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001172 seconds 129s -------------------------------------------------------------------------------- 129s -------------------------------------------------------------------------------- 129s Testing input file apbs-mol-auto.in 129s 131s CHECKING:/usr/local/sbin/apbs 131s CHECKING:/usr/local/bin/apbs 131s CHECKING:/usr/sbin/apbs 131s CHECKING:/usr/bin/apbs 131s NOTE: Using apbs binary:/usr/bin/apbs 131s Testing all sections 131s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 131s ================================================================================ 131s Running tests for born section 131s BINARY: /usr/bin/apbs 131s INPUT: apbs-mol-auto.in 131s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 131s asc_getToken: Error occurred (bailing out). 131s Vio_scanf: Format problem with input. 131s 131s 131s ---------------------------------------------------------------------- 131s APBS -- Adaptive Poisson-Boltzmann Solver 131s Version APBS 3.4.1 131s 131s Nathan A. Baker (nathan.baker@pnnl.gov) 131s Pacific Northwest National Laboratory 131s 131s Additional contributing authors listed in the code documentation. 131s 131s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 131s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 131s Northwest Division for the U.S. Department of Energy. 131s 131s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 131s Portions Copyright (c) 2002-2020, Nathan A. Baker. 131s Portions Copyright (c) 1999-2002, The Regents of the University of California. 131s Portions Copyright (c) 1995, Michael Holst. 131s All rights reserved. 131s 131s Redistribution and use in source and binary forms, with or without 131s modification, are permitted provided that the following conditions are met: 131s 131s * Redistributions of source code must retain the above copyright notice, this 131s list of conditions and the following disclaimer. 131s 131s * Redistributions in binary form must reproduce the above copyright notice, 131s this list of conditions and the following disclaimer in the documentation 131s and/or other materials provided with the distribution. 131s 131s * Neither the name of the developer nor the names of its contributors may be 131s used to endorse or promote products derived from this software without 131s specific prior written permission. 131s 131s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 131s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 131s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 131s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 131s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 131s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 131s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 131s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 131s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 131s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 131s ---------------------------------------------------------------------- 131s APBS uses FETK (the Finite Element ToolKit) to solve the 131s Poisson-Boltzmann equation numerically. FETK is a portable collection 131s of finite element modeling class libraries developed by the Michael Holst 131s research group and written in an object-oriented form of C. FEtk is 131s designed to solve general coupled systems of nonlinear partial differential 131s equations using adaptive finite element methods, inexact Newton methods, 131s and algebraic multilevel methods. More information about FEtk may be found 131s at . 131s ---------------------------------------------------------------------- 131s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 131s Aqua is a modified form of the Holst group PMG library 131s which has been modified by Patrice Koehl 131s for improved efficiency and 131s memory usage when solving the Poisson-Boltzmann equation. 131s ---------------------------------------------------------------------- 131s Please cite your use of APBS as: 131s 131s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 131s nanosystems: application to microtubules and the ribosome. Proc. 131s Natl. Acad. Sci. USA 98, 10037-10041 2001. 131s 131s 131s This executable compiled on Jan 3 2025 at 11:01:42 131s 131s Parsing input file apbs-mol-auto.in... 131s rank 0 size 1... 131s Parsed input file. 131s Got paths for 1 molecules 131s Reading PQR-format atom data from ion.pqr. 131s 1 atoms 131s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 131s Net charge 1.00e+00 e 131s Preparing to run 6 PBE calculations. 131s ---------------------------------------- 131s CALCULATION #1 (solvated): MULTIGRID 131s Setting up problem... 131s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 131s Debye length: 0 A 131s Current memory usage: 61.280 MB total, 61.280 MB high water 131s Using cubic spline charge discretization. 131s Grid dimensions: 65 x 65 x 65 131s Grid spacings: 0.781 x 0.781 x 0.781 131s Grid lengths: 50.000 x 50.000 x 50.000 131s Grid center: (0.000, 0.000, 0.000) 131s Multigrid levels: 5 131s Molecule ID: 1 131s Linearized traditional PBE 131s Multiple Debye-Huckel sphere boundary conditions 131s 0 ion species (0.000 M ionic strength): 131s Solute dielectric: 1.000 131s Solvent dielectric: 78.540 131s Using "molecular" surface definition; no smoothing 131s Solvent probe radius: 1.400 A 131s Temperature: 298.150 K 131s Electrostatic energies will be calculated 131s Total electrostatic energy = 9.607073836227E+02 kJ/mol 131s Calculating forces... 131s ---------------------------------------- 131s CALCULATION #2 (solvated): MULTIGRID 131s Setting up problem... 131s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 131s Debye length: 0 A 131s Current memory usage: 61.280 MB total, 122.102 MB high water 131s Using cubic spline charge discretization. 131s Grid dimensions: 65 x 65 x 65 131s Grid spacings: 0.383 x 0.383 x 0.383 131s Grid lengths: 24.495 x 24.495 x 24.495 131s Grid center: (0.000, 0.000, 0.000) 131s Multigrid levels: 5 131s Molecule ID: 1 131s Linearized traditional PBE 131s Boundary conditions from focusing 131s 0 ion species (0.000 M ionic strength): 131s Solute dielectric: 1.000 131s Solvent dielectric: 78.540 131s Using "molecular" surface definition; no smoothing 131s Solvent probe radius: 1.400 A 131s Temperature: 298.150 K 131s Electrostatic energies will be calculated 131s Total electrostatic energy = 2.200266567971E+03 kJ/mol 131s Calculating forces... 131s ---------------------------------------- 131s CALCULATION #3 (solvated): MULTIGRID 131s Setting up problem... 131s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 131s Debye length: 0 A 131s Current memory usage: 61.280 MB total, 122.102 MB high water 131s Using cubic spline charge discretization. 131s Grid dimensions: 65 x 65 x 65 131s Grid spacings: 0.188 x 0.188 x 0.188 131s Grid lengths: 12.000 x 12.000 x 12.000 131s Grid center: (0.000, 0.000, 0.000) 131s Multigrid levels: 5 131s Molecule ID: 1 131s Linearized traditional PBE 131s Boundary conditions from focusing 131s 0 ion species (0.000 M ionic strength): 131s Solute dielectric: 1.000 131s Solvent dielectric: 78.540 131s Using "molecular" surface definition; no smoothing 131s Solvent probe radius: 1.400 A 131s Temperature: 298.150 K 131s Electrostatic energies will be calculated 131s Potential to be written to potential.dx.gz 131s Total electrostatic energy = 4.732245131587E+03 kJ/mol 131s Calculating forces... 131s Writing potential to potential-PE0.dx.gz 131s ---------------------------------------- 131s CALCULATION #4 (reference): MULTIGRID 131s Setting up problem... 131s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 131s Debye length: 0 A 131s Current memory usage: 61.207 MB total, 122.102 MB high water 131s Using cubic spline charge discretization. 131s Grid dimensions: 65 x 65 x 65 131s Grid spacings: 0.781 x 0.781 x 0.781 131s Grid lengths: 50.000 x 50.000 x 50.000 131s Grid center: (0.000, 0.000, 0.000) 131s Multigrid levels: 5 131s Molecule ID: 1 131s Linearized traditional PBE 131s Multiple Debye-Huckel sphere boundary conditions 131s 0 ion species (0.000 M ionic strength): 131s Solute dielectric: 1.000 131s Solvent dielectric: 1.000 131s Using "molecular" surface definition; no smoothing 131s Solvent probe radius: 1.400 A 131s Temperature: 298.150 K 131s Electrostatic energies will be calculated 131s Total electrostatic energy = 1.190871482831E+03 kJ/mol 131s Calculating forces... 131s ---------------------------------------- 131s CALCULATION #5 (reference): MULTIGRID 131s Setting up problem... 131s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 131s Debye length: 0 A 131s Current memory usage: 61.207 MB total, 122.102 MB high water 131s Using cubic spline charge discretization. 131s Grid dimensions: 65 x 65 x 65 131s Grid spacings: 0.383 x 0.383 x 0.383 131s Grid lengths: 24.495 x 24.495 x 24.495 131s Grid center: (0.000, 0.000, 0.000) 131s Multigrid levels: 5 131s Molecule ID: 1 131s Linearized traditional PBE 131s Boundary conditions from focusing 131s 0 ion species (0.000 M ionic strength): 131s Solute dielectric: 1.000 131s Solvent dielectric: 1.000 131s Using "molecular" surface definition; no smoothing 131s Solvent probe radius: 1.400 A 131s Temperature: 298.150 K 131s Electrostatic energies will be calculated 131s Total electrostatic energy = 2.430874049735E+03 kJ/mol 131s Calculating forces... 131s [focusFillBound()]: WARNING: 131s Unusually large potential values 131s detected on the focusing boundary! 131s Convergence not guaranteed for NPBE/NRPBE calculations! 131s 131s ---------------------------------------- 131s CALCULATION #6 (reference): MULTIGRID 131s Setting up problem... 131s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 131s Debye length: 0 A 131s Current memory usage: 61.207 MB total, 122.102 MB high water 131s Using cubic spline charge discretization. 131s Grid dimensions: 65 x 65 x 65 131s Grid spacings: 0.188 x 0.188 x 0.188 131s Grid lengths: 12.000 x 12.000 x 12.000 131s Grid center: (0.000, 0.000, 0.000) 131s Multigrid levels: 5 131s Molecule ID: 1 131s Linearized traditional PBE 131s Boundary conditions from focusing 131s 0 ion species (0.000 M ionic strength): 131s Solute dielectric: 1.000 131s Solvent dielectric: 1.000 131s Using "molecular" surface definition; no smoothing 131s Solvent probe radius: 1.400 A 131s Temperature: 298.150 K 131s Electrostatic energies will be calculated 131s Total electrostatic energy = 4.962018684215E+03 kJ/mol 131s Calculating forces... 131s ---------------------------------------- 131s PRINT STATEMENTS 131s 131s print energy 1 (solvated) - 2 (reference) end 131s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 131s Global net ELEC energy = -2.297735526282E+02 kJ/mol 131s ---------------------------------------- 131s CLEANING UP AND SHUTTING DOWN... 131s Destroying force arrays. 131s No energy arrays to destroy. 131s Destroying multigrid structures. 131s Destroying finite element structures. 131s Destroying 1 molecules 131s Final memory usage: 0.001 MB total, 122.102 MB high water 131s 131s 131s Thanks for using APBS! 131s 131s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 131s *** PASSED *** 131s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 131s *** PASSED *** 131s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 131s *** PASSED *** 131s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 131s *** PASSED *** 131s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 131s *** PASSED *** 131s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 131s *** PASSED *** 131s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 131s *** PASSED *** 131s Elapsed time: 1.687602 seconds 131s -------------------------------------------------------------------------------- 131s -------------------------------------------------------------------------------- 131s Testing input file apbs-smol-auto.in 131s 133s Checking for intermediate energies in input file apbs-mol-auto.out 133s EXPECTED COMPUTED: 7 133s EXPECTED EXPECTED: 7 133s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 133s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 133s COMPUTED RESULT 960.7073836227 133s COMPUTED RESULT 2200.266567971 133s COMPUTED RESULT 4732.245131587 133s COMPUTED RESULT 1190.871482831 133s COMPUTED RESULT 2430.874049735 133s COMPUTED RESULT 4962.018684215 133s COMPUTED RESULT -229.7735526282 133s BINARY: /usr/bin/apbs 133s INPUT: apbs-smol-auto.in 133s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 133s asc_getToken: Error occurred (bailing out). 133s Vio_scanf: Format problem with input. 133s 133s 133s ---------------------------------------------------------------------- 133s APBS -- Adaptive Poisson-Boltzmann Solver 133s Version APBS 3.4.1 133s 133s Nathan A. Baker (nathan.baker@pnnl.gov) 133s Pacific Northwest National Laboratory 133s 133s Additional contributing authors listed in the code documentation. 133s 133s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 133s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 133s Northwest Division for the U.S. Department of Energy. 133s 133s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 133s Portions Copyright (c) 2002-2020, Nathan A. Baker. 133s Portions Copyright (c) 1999-2002, The Regents of the University of California. 133s Portions Copyright (c) 1995, Michael Holst. 133s All rights reserved. 133s 133s Redistribution and use in source and binary forms, with or without 133s modification, are permitted provided that the following conditions are met: 133s 133s * Redistributions of source code must retain the above copyright notice, this 133s list of conditions and the following disclaimer. 133s 133s * Redistributions in binary form must reproduce the above copyright notice, 133s this list of conditions and the following disclaimer in the documentation 133s and/or other materials provided with the distribution. 133s 133s * Neither the name of the developer nor the names of its contributors may be 133s used to endorse or promote products derived from this software without 133s specific prior written permission. 133s 133s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 133s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 133s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 133s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 133s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 133s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 133s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 133s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 133s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 133s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 133s ---------------------------------------------------------------------- 133s APBS uses FETK (the Finite Element ToolKit) to solve the 133s Poisson-Boltzmann equation numerically. FETK is a portable collection 133s of finite element modeling class libraries developed by the Michael Holst 133s research group and written in an object-oriented form of C. FEtk is 133s designed to solve general coupled systems of nonlinear partial differential 133s equations using adaptive finite element methods, inexact Newton methods, 133s and algebraic multilevel methods. More information about FEtk may be found 133s at . 133s ---------------------------------------------------------------------- 133s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 133s Aqua is a modified form of the Holst group PMG library 133s which has been modified by Patrice Koehl 133s for improved efficiency and 133s memory usage when solving the Poisson-Boltzmann equation. 133s ---------------------------------------------------------------------- 133s Please cite your use of APBS as: 133s 133s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 133s nanosystems: application to microtubules and the ribosome. Proc. 133s Natl. Acad. Sci. USA 98, 10037-10041 2001. 133s 133s 133s This executable compiled on Jan 3 2025 at 11:01:42 133s 133s Parsing input file apbs-smol-auto.in... 133s rank 0 size 1... 133s Parsed input file. 133s Got paths for 1 molecules 133s Reading PQR-format atom data from ion.pqr. 133s 1 atoms 133s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 133s Net charge 1.00e+00 e 133s Preparing to run 6 PBE calculations. 133s ---------------------------------------- 133s CALCULATION #1 (solvated): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.280 MB total, 61.280 MB high water 133s Using cubic spline charge discretization. 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.781 x 0.781 x 0.781 133s Grid lengths: 50.000 x 50.000 x 50.000 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Multiple Debye-Huckel sphere boundary conditions 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 78.540 133s Using "molecular" surface definition;harmonic average smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 9.532928767450E+02 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #2 (solvated): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.280 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.383 x 0.383 x 0.383 133s Grid lengths: 24.495 x 24.495 x 24.495 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 78.540 133s Using "molecular" surface definition;harmonic average smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 2.201243880085E+03 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #3 (solvated): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.280 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.188 x 0.188 x 0.188 133s Grid lengths: 12.000 x 12.000 x 12.000 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 78.540 133s Using "molecular" surface definition;harmonic average smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 4.733006258977E+03 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #4 (reference): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.207 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.781 x 0.781 x 0.781 133s Grid lengths: 50.000 x 50.000 x 50.000 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Multiple Debye-Huckel sphere boundary conditions 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 1.000 133s Using "molecularTesting computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 133s *** PASSED *** 133s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 133s *** PASSED *** 133s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 133s *** PASSED *** 133s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 133s *** PASSED *** 133s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 133s *** PASSED *** 133s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 133s *** PASSED *** 133s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 133s *** PASSED *** 133s Elapsed time: 1.4613610000000001 seconds 133s -------------------------------------------------------------------------------- 133s -------------------------------------------------------------------------------- 133s Testing input file apbs-mol-parallel.in 133s 133s Splitting the input file into 4 separate files using the inputgen utility 133s 133s " surface definition;harmonic average smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 1.190871482831E+03 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s CALCULATION #5 (reference): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.207 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.383 x 0.383 x 0.383 133s Grid lengths: 24.495 x 24.495 x 24.495 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 1.000 133s Using "molecular" surface definition;harmonic average smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 2.430874049735E+03 kJ/mol 133s Calculating forces... 133s [focusFillBound()]: WARNING: 133s Unusually large potential values 133s detected on the focusing boundary! 133s Convergence not guaranteed for NPBE/NRPBE calculations! 133s 133s ---------------------------------------- 133s CALCULATION #6 (reference): MULTIGRID 133s Setting up problem... 133s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 133s Debye length: 0 A 133s Current memory usage: 61.207 MB total, 122.102 MB high water 133s Using cubic spline charge discretization. 133s Grid dimensions: 65 x 65 x 65 133s Grid spacings: 0.188 x 0.188 x 0.188 133s Grid lengths: 12.000 x 12.000 x 12.000 133s Grid center: (0.000, 0.000, 0.000) 133s Multigrid levels: 5 133s Molecule ID: 1 133s Linearized traditional PBE 133s Boundary conditions from focusing 133s 0 ion species (0.000 M ionic strength): 133s Solute dielectric: 1.000 133s Solvent dielectric: 1.000 133s Using "molecular" surface definition;harmonic average smoothing 133s Solvent probe radius: 1.400 A 133s Temperature: 298.150 K 133s Electrostatic energies will be calculated 133s Total electrostatic energy = 4.962018684215E+03 kJ/mol 133s Calculating forces... 133s ---------------------------------------- 133s PRINT STATEMENTS 133s 133s print energy 1 (solvated) - 2 (reference) end 133s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 133s Global net ELEC energy = -2.290124252387E+02 kJ/mol 133s ---------------------------------------- 133s CLEANING UP AND SHUTTING DOWN... 133s Destroying force arrays. 133s No energy arrays to destroy. 133s Destroying multigrid structures. 133s Destroying finite element structures. 133s Destroying 1 molecules 133s Final memory usage: 0.001 MB total, 122.102 MB high water 133s 133s 133s Thanks for using APBS! 133s 134s Checking for intermediate energies in input file apbs-smol-auto.out 134s EXPECTED COMPUTED: 7 134s EXPECTED EXPECTED: 7 134s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 134s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 134s COMPUTED RESULT 953.292876745 134s COMPUTED RESULT 2201.243880085 134s COMPUTED RESULT 4733.006258977 134s COMPUTED RESULT 1190.871482831 134s COMPUTED RESULT 2430.874049735 134s COMPUTED RESULT 4962.018684215 134s COMPUTED RESULT -229.0124252387 134s BINARY: /usr/bin/apbs 134s INPUT: apbs-mol-parallel-PE0.in 134s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 134s asc_getToken: Error occurred (bailing out). 134s Vio_scanf: Format problem with input. 134s 134s 134s ---------------------------------------------------------------------- 134s APBS -- Adaptive Poisson-Boltzmann Solver 134s Version APBS 3.4.1 134s 134s Nathan A. Baker (nathan.baker@pnnl.gov) 134s Pacific Northwest National Laboratory 134s 134s Additional contributing authors listed in the code documentation. 134s 134s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 134s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 134s Northwest Division for the U.S. Department of Energy. 134s 134s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 134s Portions Copyright (c) 2002-2020, Nathan A. Baker. 134s Portions Copyright (c) 1999-2002, The Regents of the University of California. 134s Portions Copyright (c) 1995, Michael Holst. 134s All rights reserved. 134s 134s Redistribution and use in source and binary forms, with or without 134s modification, are permitted provided that the following conditions are met: 134s 134s * Redistributions of source code must retain the above copyright notice, this 134s list of conditions and the following disclaimer. 134s 134s * Redistributions in binary form must reproduce the above copyright notice, 134s this list of conditions and the following disclaimer in the documentation 134s and/or other materials provided with the distribution. 134s 134s * Neither the name of the developer nor the names of its contributors may be 134s used to endorse or promote products derived from this software without 134s specific prior written permission. 134s 134s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 134s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 134s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 134s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 134s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 134s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 134s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 134s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 134s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 134s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 134s ---------------------------------------------------------------------- 134s APBS uses FETK (the Finite Element ToolKit) to solve the 134s Poisson-Boltzmann equation numerically. FETK is a portable collection 134s of finite element modeling class libraries developed by the Michael Holst 134s research group and written in an object-oriented form of C. FEtk is 134s designed to solve general coupled systems of nonlinear partial differential 134s equations using adaptive finite element methods, inexact Newton methods, 134s and algebraic multilevel methods. More information about FEtk may be found 134s at . 134s ---------------------------------------------------------------------- 134s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 134s Aqua is a modified form of the Holst group PMG library 134s which has been modified by Patrice Koehl 134s for improved efficiency and 134s memory usage when solving the Poisson-Boltzmann equation. 134s ---------------------------------------------------------------------- 134s Please cite your use of APBS as: 134s 134s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 134s nanosystems: application to microtubules and the ribosome. Proc. 134s Natl. Acad. Sci. USA 98, 10037-10041 2001. 134s 134s 134s This executable compiled on Jan 3 2025 at 11:01:42 134s 134s Parsing input file apbs-mol-parallel-PE0.in... 134s rank 0 size 1... 134s Parsed input file. 134s Got paths for 1 molecules 134s Reading PQR-format atom data from ion.pqr. 134s 1 atoms 134s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 134s Net charge 1.00e+00 e 134s Preparing to run 6 PBE calculations. 134s ---------------------------------------- 134s CALCULATION #1 (solvated): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.280 MB total, 61.280 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.781 x 0.781 x 0.781 134s Grid lengths: 50.000 x 50.000 x 50.000 134s Grid center: (0.000, 0.000, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Multiple Debye-Huckel sphere boundary conditions 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 78.540 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 2.401768459022E+02 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s CALCULATION #2 (solvated): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.280 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.296 x 0.296 x 0.383 134s Grid lengths: 18.944 x 18.944 x 24.495 134s Grid center: (-2.411, -2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 78.540 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 8.142935592471E+02 kJ/mol 134s Calculating forces... 134s [focusFillBound()]: WARNING: 134s Unusually large potential values 134s detected on the focusing boundary! 134s Convergence not guaranteed for NPBE/NRPBE calculations! 134s 134s ---------------------------------------- 134s CALCULATION #3 (solvated): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.280 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.112 x 0.112 x 0.188 134s Grid lengths: 7.178 x 7.178 x 12.000 134s Grid center: (-2.411, -2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 78.540 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 1.485255308186E+03 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s CALCULATION #4 (reference): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.207 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.781 x 0.781 x 0.781 134s Grid lengths: 50.000 x 50.000 x 50.000 134s Grid center: (0.000, 0.000, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Multiple Debye-Huckel sphere boundary conditions 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 1.000 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 2.977178707009E+02 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s CALCULATION #5 (reference): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.207 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.296 x 0.296 x 0.383 134s Grid lengths: 18.944 x 18.944 x 24.495 134s Grid center: (-2.411, -2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 1.000 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 8.799304557588E+02 kJ/mol 134s Calculating forces... 134s [focusFillBound()]: WARNING: 134s Unusually large potential values 134s detected on the focusing boundary! 134s Convergence not guaranteed for NPBE/NRPBE calculations! 134s 134s ---------------------------------------- 134s CALCULATION #6 (reference): MULTIGRID 134s Setting up problem... 134s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 134s Debye length: 0 A 134s Current memory usage: 61.207 MB total, 122.102 MB high water 134s Using cubic spline charge discretization. 134s Partition overlap fraction = 0.1 134s Processor array = 2 x 2 x 1 134s Grid dimensions: 65 x 65 x 65 134s Grid spacings: 0.112 x 0.112 x 0.188 134s Grid lengths: 7.178 x 7.178 x 12.000 134s Grid center: (-2.411, -2.411, 0.000) 134s Multigrid levels: 5 134s Molecule ID: 1 134s Linearized traditional PBE 134s Boundary conditions from focusing 134s 0 ion species (0.000 M ionic strength): 134s Solute dielectric: 1.000 134s Solvent dielectric: 1.000 134s Using "molecular" surface definition; no smoothing 134s Solvent probe radius: 1.400 A 134s Temperature: 298.150 K 134s Electrostatic energies will be calculated 134s Total electrostatic energy = 1.542873949131E+03 kJ/mol 134s Calculating forces... 134s ---------------------------------------- 134s PRINT STATEMENTS 134s 134s print energy 1 (solvated) - 2 (reference) end 134s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 134s Global net ELEC energy = -5.761864094552E+01 kJ/mol 134s ---------------------------------------- 134s CLEANING UP AND SHUTTING DOWN... 134s Destroying force arrays. 134s No energy arrays to destroy. 134s Destroying multigrid structures. 134s Destroying finite element structures. 134s Destroying 1 molecules 134s Final memory usage: 0.001 MB total, 122.102 MB high water 134s 134s 134s Thanks for using APBS! 134s 134s Processor 0 results: 134s 2.401768459022e+02 134s 8.142935592471e+02 134s 1.485255308186e+03 134s 2.977178707009e+02 134s 8.799304557588e+02 134s 1.542873949131e+03 134s -5.761864094552e+01 134s 136s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 136s BINARY: /usr/bin/apbs 136s INPUT: apbs-mol-parallel-PE1.in 136s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 136s asc_getToken: Error occurred (bailing out). 136s Vio_scanf: Format problem with input. 136s 136s 136s ---------------------------------------------------------------------- 136s APBS -- Adaptive Poisson-Boltzmann Solver 136s Version APBS 3.4.1 136s 136s Nathan A. Baker (nathan.baker@pnnl.gov) 136s Pacific Northwest National Laboratory 136s 136s Additional contributing authors listed in the code documentation. 136s 136s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 136s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 136s Northwest Division for the U.S. Department of Energy. 136s 136s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 136s Portions Copyright (c) 2002-2020, Nathan A. Baker. 136s Portions Copyright (c) 1999-2002, The Regents of the University of California. 136s Portions Copyright (c) 1995, Michael Holst. 136s All rights reserved. 136s 136s Redistribution and use in source and binary forms, with or without 136s modification, are permitted provided that the following conditions are met: 136s 136s * Redistributions of source code must retain the above copyright notice, this 136s list of conditions and the following disclaimer. 136s 136s * Redistributions in binary form must reproduce the above copyright notice, 136s this list of conditions and the following disclaimer in the documentation 136s and/or other materials provided with the distribution. 136s 136s * Neither the name of the developer nor the names of its contributors may be 136s used to endorse or promote products derived from this software without 136s specific prior written permission. 136s 136s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 136s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 136s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 136s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 136s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 136s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 136s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 136s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 136s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 136s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 136s ---------------------------------------------------------------------- 136s APBS uses FETK (the Finite Element ToolKit) to solve the 136s Poisson-Boltzmann equation numerically. FETK is a portable collection 136s of finite element modeling class libraries developed by the Michael Holst 136s research group and written in an object-oriented form of C. FEtk is 136s designed to solve general coupled systems of nonlinear partial differential 136s equations using adaptive finite element methods, inexact Newton methods, 136s and algebraic multilevel methods. More information about FEtk may be found 136s at . 136s ---------------------------------------------------------------------- 136s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 136s Aqua is a modified form of the Holst group PMG library 136s which has been modified by Patrice Koehl 136s for improved efficiency and 136s memory usage when solving the Poisson-Boltzmann equation. 136s ---------------------------------------------------------------------- 136s Please cite your use of APBS as: 136s 136s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 136s nanosystems: application to microtubules and the ribosome. Proc. 136s Natl. Acad. Sci. USA 98, 10037-10041 2001. 136s 136s 136s This executable compiled on Jan 3 2025 at 11:01:42 136s 136s Parsing input file apbs-mol-parallel-PE1.in... 136s rank 0 size 1... 136s Parsed input file. 136s Got paths for 1 molecules 136s Reading PQR-format atom data from ion.pqr. 136s 1 atoms 136s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 136s Net charge 1.00e+00 e 136s Preparing to run 6 PBE calculations. 136s ---------------------------------------- 136s CALCULATION #1 (solvated): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.280 MB total, 61.280 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.781 x 0.781 x 0.781 136s Grid lengths: 50.000 x 50.000 x 50.000 136s Grid center: (0.000, 0.000, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Multiple Debye-Huckel sphere boundary conditions 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 78.540 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 2.401768459022E+02 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s CALCULATION #2 (solvated): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.280 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.296 x 0.296 x 0.383 136s Grid lengths: 18.944 x 18.944 x 24.495 136s Grid center: (2.411, -2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 78.540 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 8.142778312125E+02 kJ/mol 136s Calculating forces... 136s [focusFillBound()]: WARNING: 136s Unusually large potential values 136s detected on the focusing boundary! 136s Convergence not guaranteed for NPBE/NRPBE calculations! 136s 136s ---------------------------------------- 136s CALCULATION #3 (solvated): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.280 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.112 x 0.112 x 0.188 136s Grid lengths: 7.178 x 7.178 x 12.000 136s Grid center: (2.411, -2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 78.540 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 1.485246667424E+03 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s CALCULATION #4 (reference): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.207 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.781 x 0.781 x 0.781 136s Grid lengths: 50.000 x 50.000 x 50.000 136s Grid center: (0.000, 0.000, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Multiple Debye-Huckel sphere boundary conditions 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 1.000 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 2.977178707009E+02 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s CALCULATION #5 (reference): MULTIGRID 136s Setting up problem... 136s Processor 1 results: 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.207 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.296 x 0.296 x 0.383 136s Grid lengths: 18.944 x 18.944 x 24.495 136s Grid center: (2.411, -2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 1.000 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 8.799304557588E+02 kJ/mol 136s Calculating forces... 136s [focusFillBound()]: WARNING: 136s Unusually large potential values 136s detected on the focusing boundary! 136s Convergence not guaranteed for NPBE/NRPBE calculations! 136s 136s ---------------------------------------- 136s CALCULATION #6 (reference): MULTIGRID 136s Setting up problem... 136s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 136s Debye length: 0 A 136s Current memory usage: 61.207 MB total, 122.102 MB high water 136s Using cubic spline charge discretization. 136s Partition overlap fraction = 0.1 136s Processor array = 2 x 2 x 1 136s Grid dimensions: 65 x 65 x 65 136s Grid spacings: 0.112 x 0.112 x 0.188 136s Grid lengths: 7.178 x 7.178 x 12.000 136s Grid center: (2.411, -2.411, 0.000) 136s Multigrid levels: 5 136s Molecule ID: 1 136s Linearized traditional PBE 136s Boundary conditions from focusing 136s 0 ion species (0.000 M ionic strength): 136s Solute dielectric: 1.000 136s Solvent dielectric: 1.000 136s Using "molecular" surface definition; no smoothing 136s Solvent probe radius: 1.400 A 136s Temperature: 298.150 K 136s Electrostatic energies will be calculated 136s Total electrostatic energy = 1.542873949131E+03 kJ/mol 136s Calculating forces... 136s ---------------------------------------- 136s PRINT STATEMENTS 136s 136s print energy 1 (solvated) - 2 (reference) end 136s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 136s Global net ELEC energy = -5.762728170718E+01 kJ/mol 136s ---------------------------------------- 136s CLEANING UP AND SHUTTING DOWN... 136s Destroying force arrays. 136s No energy arrays to destroy. 136s Destroying multigrid structures. 136s Destroying finite element structures. 136s Destroying 1 molecules 136s Final memory usage: 0.001 MB total, 122.102 MB high water 136s 136s 136s Thanks for using APBS! 136s 136s 2.401768459022e+02 136s 8.142778312125e+02 136s 1.485246667424e+03 136s 2.977178707009e+02 136s 8.799304557588e+02 136s 1.542873949131e+03 136s -5.762728170718e+01 136s 138s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 138s BINARY: /usr/bin/apbs 138s INPUT: apbs-mol-parallel-PE2.in 138s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 138s Processor 2 results: 138s 2.401768459091e+02 138s 8.142935605695e+02 138s 1.485255306569e+03 138s 2.977178707146e+02 138s 8.799304557596e+02 138s 1.542873949141e+03 138s -5.761864257239e+01 138s 138s asc_getToken: Error occurred (bailing out). 138s Vio_scanf: Format problem with input. 138s 138s 138s ---------------------------------------------------------------------- 138s APBS -- Adaptive Poisson-Boltzmann Solver 138s Version APBS 3.4.1 138s 138s Nathan A. Baker (nathan.baker@pnnl.gov) 138s Pacific Northwest National Laboratory 138s 138s Additional contributing authors listed in the code documentation. 138s 138s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 138s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 138s Northwest Division for the U.S. Department of Energy. 138s 138s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 138s Portions Copyright (c) 2002-2020, Nathan A. Baker. 138s Portions Copyright (c) 1999-2002, The Regents of the University of California. 138s Portions Copyright (c) 1995, Michael Holst. 138s All rights reserved. 138s 138s Redistribution and use in source and binary forms, with or without 138s modification, are permitted provided that the following conditions are met: 138s 138s * Redistributions of source code must retain the above copyright notice, this 138s list of conditions and the following disclaimer. 138s 138s * Redistributions in binary form must reproduce the above copyright notice, 138s this list of conditions and the following disclaimer in the documentation 138s and/or other materials provided with the distribution. 138s 138s * Neither the name of the developer nor the names of its contributors may be 138s used to endorse or promote products derived from this software without 138s specific prior written permission. 138s 138s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 138s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 138s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 138s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 138s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 138s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 138s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 138s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 138s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 138s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 138s ---------------------------------------------------------------------- 138s APBS uses FETK (the Finite Element ToolKit) to solve the 138s Poisson-Boltzmann equation numerically. FETK is a portable collection 138s of finite element modeling class libraries developed by the Michael Holst 138s research group and written in an object-oriented form of C. FEtk is 138s designed to solve general coupled systems of nonlinear partial differential 138s equations using adaptive finite element methods, inexact Newton methods, 138s and algebraic multilevel methods. More information about FEtk may be found 138s at . 138s ---------------------------------------------------------------------- 138s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 138s Aqua is a modified form of the Holst group PMG library 138s which has been modified by Patrice Koehl 138s for improved efficiency and 138s memory usage when solving the Poisson-Boltzmann equation. 138s ---------------------------------------------------------------------- 138s Please cite your use of APBS as: 138s 138s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 138s nanosystems: application to microtubules and the ribosome. Proc. 138s Natl. Acad. Sci. USA 98, 10037-10041 2001. 138s 138s 138s This executable compiled on Jan 3 2025 at 11:01:42 138s 138s Parsing input file apbs-mol-parallel-PE2.in... 138s rank 0 size 1... 138s Parsed input file. 138s Got paths for 1 molecules 138s Reading PQR-format atom data from ion.pqr. 138s 1 atoms 138s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 138s Net charge 1.00e+00 e 138s Preparing to run 6 PBE calculations. 138s ---------------------------------------- 138s CALCULATION #1 (solvated): MULTIGRID 138s Setting up problem... 138s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 138s Debye length: 0 A 138s Current memory usage: 61.280 MB total, 61.280 MB high water 138s Using cubic spline charge discretization. 138s Partition overlap fraction = 0.1 138s Processor array = 2 x 2 x 1 138s Grid dimensions: 65 x 65 x 65 138s Grid spacings: 0.781 x 0.781 x 0.781 138s Grid lengths: 50.000 x 50.000 x 50.000 138s Grid center: (0.000, 0.000, 0.000) 138s Multigrid levels: 5 138s Molecule ID: 1 138s Linearized traditional PBE 138s Multiple Debye-Huckel sphere boundary conditions 138s 0 ion species (0.000 M ionic strength): 138s Solute dielectric: 1.000 138s Solvent dielectric: 78.540 138s Using "molecular" surface definition; no smoothing 138s Solvent probe radius: 1.400 A 138s Temperature: 298.150 K 138s Electrostatic energies will be calculated 138s Total electrostatic energy = 2.401768459091E+02 kJ/mol 138s Calculating forces... 138s ---------------------------------------- 138s CALCULATION #2 (solvated): MULTIGRID 138s Setting up problem... 138s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 138s Debye length: 0 A 138s Current memory usage: 61.280 MB total, 122.102 MB high water 138s Using cubic spline charge discretization. 138s Partition overlap fraction = 0.1 138s Processor array = 2 x 2 x 1 138s Grid dimensions: 65 x 65 x 65 138s Grid spacings: 0.296 x 0.296 x 0.383 138s Grid lengths: 18.944 x 18.944 x 24.495 138s Grid center: (-2.411, 2.411, 0.000) 138s Multigrid levels: 5 138s Molecule ID: 1 138s Linearized traditional PBE 138s Boundary conditions from focusing 138s 0 ion species (0.000 M ionic strength): 138s Solute dielectric: 1.000 138s Solvent dielectric: 78.540 138s Using "molecular" surface definition; no smoothing 138s Solvent probe radius: 1.400 A 138s Temperature: 298.150 K 138s Electrostatic energies will be calculated 138s Total electrostatic energy = 8.142935605695E+02 kJ/mol 138s Calculating forces... 138s [focusFillBound()]: WARNING: 138s Unusually large potential values 138s detected on the focusing boundary! 138s Convergence not guaranteed for NPBE/NRPBE calculations! 138s 138s ---------------------------------------- 138s CALCULATION #3 (solvated): MULTIGRID 138s Setting up problem... 138s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 138s Debye length: 0 A 138s Current memory usage: 61.280 MB total, 122.102 MB high water 138s Using cubic spline charge discretization. 138s Partition overlap fraction = 0.1 138s Processor array = 2 x 2 x 1 138s Grid dimensions: 65 x 65 x 65 138s Grid spacings: 0.112 x 0.112 x 0.188 138s Grid lengths: 7.178 x 7.178 x 12.000 138s Grid center: (-2.411, 2.411, 0.000) 138s Multigrid levels: 5 138s Molecule ID: 1 138s Linearized traditional PBE 138s Boundary conditions from focusing 138s 0 ion species (0.000 M ionic strength): 138s Solute dielectric: 1.000 138s Solvent dielectric: 78.540 138s Using "molecular" surface definition; no smoothing 138s Solvent probe radius: 1.400 A 138s Temperature: 298.150 K 138s Electrostatic energies will be calculated 138s Total electrostatic energy = 1.485255306569E+03 kJ/mol 138s Calculating forces... 138s ---------------------------------------- 138s CALCULATION #4 (reference): MULTIGRID 138s Setting up problem... 138s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 138s Debye length: 0 A 138s Current memory usage: 61.207 MB total, 122.102 MB high water 138s Using cubic spline charge discretization. 138s Partition overlap fraction = 0.1 138s Processor array = 2 x 2 x 1 138s Grid dimensions: 65 x 65 x 65 138s Grid spacings: 0.781 x 0.781 x 0.781 138s Grid lengths: 50.000 x 50.000 x 50.000 138s Grid center: (0.000, 0.000, 0.000) 138s Multigrid levels: 5 138s Molecule ID: 1 138s Linearized traditional PBE 138s Multiple Debye-Huckel sphere boundary conditions 138s 0 ion species (0.000 M ionic strength): 138s Solute dielectric: 1.000 138s Solvent dielectric: 1.000 138s Using "molecular" surface definition; no smoothing 138s Solvent probe radius: 1.400 A 138s Temperature: 298.150 K 138s Electrostatic energies will be calculated 138s Total electrostatic energy = 2.977178707146E+02 kJ/mol 138s Calculating forces... 138s ---------------------------------------- 138s CALCULATION #5 (reference): MULTIGRID 138s Setting up problem... 138s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 138s Debye length: 0 A 138s Current memory usage: 61.207 MB total, 122.102 MB high water 138s Using cubic spline charge discretization. 138s Partition overlap fraction = 0.1 138s Processor array = 2 x 2 x 1 138s Grid dimensions: 65 x 65 x 65 138s Grid spacings: 0.296 x 0.296 x 0.383 138s Grid lengths: 18.944 x 18.944 x 24.495 138s Grid center: (-2.411, 2.411, 0.000) 138s Multigrid levels: 5 138s Molecule ID: 1 138s Linearized traditional PBE 138s Boundary conditions from focusing 138s 0 ion species (0.000 M ionic strength): 138s Solute dielectric: 1.000 138s Solvent dielectric: 1.000 138s Using "molecular" surface definition; no smoothing 138s Solvent probe radius: 1.400 A 138s Temperature: 298.150 K 138s Electrostatic energies will be calculated 138s Total electrostatic energy = 8.799304557596E+02 kJ/mol 138s Calculating forces... 138s [focusFillBound()]: WARNING: 138s Unusually large potential values 138s detected on the focusing boundary! 138s Convergence not guaranteed for NPBE/NRPBE calculations! 138s 138s ---------------------------------------- 138s CALCULATION #6 (reference): MULTIGRID 138s Setting up problem... 138s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 138s Debye length: 0 A 138s Current memory usage: 61.207 MB total, 122.102 MB high water 138s Using cubic spline charge discretization. 138s Partition overlap fraction = 0.1 138s Processor array = 2 x 2 x 1 138s Grid dimensions: 65 x 65 x 65 138s Grid spacings: 0.112 x 0.112 x 0.188 138s Grid lengths: 7.178 x 7.178 x 12.000 138s Grid center: (-2.411, 2.411, 0.000) 138s Multigrid levels: 5 138s Molecule ID: 1 138s Linearized traditional PBE 138s Boundary conditions from focusing 138s 0 ion species (0.000 M ionic strength): 138s Solute dielectric: 1.000 138s Solvent dielectric: 1.000 138s Using "molecular" surface definition; no smoothing 138s Solvent probe radius: 1.400 A 138s Temperature: 298.150 K 138s Electrostatic energies will be calculated 138s Total electrostatic energy = 1.542873949141E+03 kJ/mol 138s Calculating forces... 138s ---------------------------------------- 138s PRINT STATEMENTS 138s 138s print energy 1 (solvated) - 2 (reference) end 138s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 138s Global net ELEC energy = -5.761864257239E+01 kJ/mol 138s ---------------------------------------- 138s CLEANING UP AND SHUTTING DOWN... 138s Destroying force arrays. 138s No energy arrays to destroy. 138s Destroying multigrid structures. 138s Destroying finite element structures. 138s Destroying 1 molecules 138s Final memory usage: 0.001 MB total, 122.102 MB high water 138s 138s 138s Thanks for using APBS! 138s 140s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 140s BINARY: /usr/bin/apbs 140s INPUT: apbs-mol-parallel-PE3.in 140s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 140s asc_getToken: Error occurred (bailing out). 140s Vio_scanf: Format problem with input. 140s 140s 140s ---------------------------------------------------------------------- 140s APBS -- Adaptive Poisson-Boltzmann Solver 140s Version APBS 3.4.1 140s 140s Nathan A. Baker (nathan.baker@pnnl.gov) 140s Pacific Northwest National Laboratory 140s 140s Additional contributing authors listed in the code documentation. 140s 140s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 140s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 140s Northwest Division for the U.S. Department of Energy. 140s 140s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 140s Portions Copyright (c) 2002-2020, Nathan A. Baker. 140s Portions Copyright (c) 1999-2002, The Regents of the University of California. 140s Portions Copyright (c) 1995, Michael Holst. 140s All rights reserved. 140s 140s Redistribution and use in source and binary forms, with or without 140s modification, are permitted provided that the following conditions are met: 140s 140s * Redistributions of source code must retain the above copyright notice, this 140s list of conditions and the following disclaimer. 140s 140s * Redistributions in binary form must reproduce the above copyright notice, 140s this list of conditions and the following disclaimer in the documentation 140s and/or other materials provided with the distribution. 140s 140s * Neither the name of the developer nor the names of its contributors may be 140s used to endorse or promote products derived from this software without 140s specific prior written permission. 140s 140s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 140s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 140s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 140s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 140s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 140s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 140s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 140s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 140s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 140s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 140s ---------------------------------------------------------------------- 140s APBS uses FETK (the Finite Element ToolKit) to solve the 140s Poisson-Boltzmann equation numerically. FETK is a portable collection 140s of finite element modeling class libraries developed by the Michael Holst 140s research group and written in an object-oriented form of C. FEtk is 140s designed to solve general coupled systems of nonlinear partial differential 140s equations using adaptive finite element methods, inexact Newton methods, 140s and algebraic multilevel methods. More information about FEtk may be found 140s at . 140s ---------------------------------------------------------------------- 140s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 140s Aqua is a modified form of the Holst group PMG library 140s which has been modified by Patrice Koehl 140s for improved efficiency and 140s memory usage when solving the Poisson-Boltzmann equation. 140s ---------------------------------------------------------------------- 140s Please cite your use of APBS as: 140s 140s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 140s nanosystems: application to microtubules and the ribosome. Proc. 140s Natl. Acad. Sci. USA 98, 10037-10041 2001. 140s 140s 140s This executable compiled on Jan 3 2025 at 11:01:42 140s 140s Parsing input file apbs-mol-parallel-PE3.in... 140s rank 0 size 1... 140s Parsed input file. 140s Got paths for 1 molecules 140s Reading PQR-format atom data from ion.pqr. 140s 1 atoms 140s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 140s Net charge 1.00e+00 e 140s Preparing to run 6 PBE calculations. 140s ---------------------------------------- 140s CALCULATION #1 (solvated): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.280 MB total, 61.280 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.781 x 0.781 x 0.781 140s Grid lengths: 50.000 x 50.000 x 50.000 140s Grid center: (0.000, 0.000, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Multiple Debye-Huckel sphere boundary conditions 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 78.540 140s Using "molecular" surface definition; no smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 2.401768459091E+02 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s CALCULATION #2 (solvated): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.280 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.296 x 0.296 x 0.383 140s Grid lengths: 18.944 x 18.944 x 24.495 140s Grid center: (2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 78.540 140s Using "molecular" surface definition; no smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 8.142778325440E+02 kJ/mol 140s Calculating forces... 140s [focusFillBound()]: WARNING: 140s Unusually large potential values 140s detected on the focusing boundary! 140s Convergence not guaranteed for NPBE/NRPBE calculations! 140s 140s ---------------------------------------- 140s CALCULATION #3 (solvated): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.280 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.112 x 0.112 x 0.188 140s Grid lengths: 7.178 x 7.178 x 12.000 140s Grid center: (2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 78.540 140s Using "molecular" surface definition; no smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 1.485246665692E+03 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s CALCULATION #4 (reference): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.207 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.781 x 0.781 x 0.781 140s Grid lengths: 50.000 x 50.000 x 50.000 140s Grid center: (0.000, 0.000, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Multiple Debye-Huckel sphere boundary conditions 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 1.000 140s Using "molecular" surface definition; no smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 2.977178707146E+02 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s CALCULATION #5 (reference): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.207 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.296 x 0.296 x 0.383 140s Grid lengths: 18.944 x 18.944 x 24.495 140s Grid center: (2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 1.000 140s Using "molecular" surface definition; no smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 8.799304557596E+02 kJ/mol 140s Calculating forces... 140s [focusFillBound()]: WARNING: 140s Unusually large potential values 140s detected on the focusing boundary! 140s Convergence not guaranteed for NPBE/NRPBE calculations! 140s 140s ---------------------------------------- 140s CALCULATION #6 (reference): MULTIGRID 140s Setting up problem... 140s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 140s Debye length: 0 A 140s Current memory usage: 61.207 MB total, 122.102 MB high water 140s Using cubic spline charge discretization. 140s Partition overlap fraction = 0.1 140s Processor array = 2 x 2 x 1 140s Grid dimensions: 65 x 65 x 65 140s Grid spacings: 0.112 x 0.112 x 0.188 140s Grid lengths: 7.178 x 7.178 x 12.000 140s Grid center: (2.411, 2.411, 0.000) 140s Multigrid levels: 5 140s Molecule ID: 1 140s Linearized traditional PBE 140s Boundary conditions from focusing 140s 0 ion species (0.000 M ionic strength): 140s Solute dielectric: 1.000 140s Solvent dielectric: 1.000 140s Using "molecular" surface definition; no smoothing 140s Solvent probe radius: 1.400 A 140s Temperature: 298.150 K 140s Electrostatic energies will be calculated 140s Total electrostatic energy = 1.542873949141E+03 kJ/mol 140s Calculating forces... 140s ---------------------------------------- 140s PRINT STATEMENTS 140s 140s print energy 1 (solvated) - 2 (reference) end 140s Local net energy (PE 0) = -5.762728344953E+01 kJ/mol 140s Global net ELEC energy = -5.762728344953E+01 kJ/mol 140s ---------------------------------------- 140s CLEANING UP AND SHUTTING DOWN... 140s Destroying force arrays. 140s No energy arrays to destroy. 140s Destroying multigrid structures. 140s Destroying finite element structures. 140s Destroying 1 molecules 140s Final memory usage: 0.001 MB total, 122.102 MB high water 140s 140s 140s Thanks for using APBS! 140s 140s Processor 3 results: 140s 2.401768459091e+02 140s 8.142778325440e+02 140s 1.485246665692e+03 140s 2.977178707146e+02 140s 8.799304557596e+02 140s 1.542873949141e+03 140s -5.762728344953e+01 140s 140s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 140s *** PASSED *** 140s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 140s *** PASSED *** 140s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 140s *** PASSED *** 140s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 140s *** PASSED *** 140s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 140s *** PASSED *** 140s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 140s *** PASSED *** 140s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 140s *** PASSED *** 140s Elapsed time: 8.011113 seconds 140s -------------------------------------------------------------------------------- 140s -------------------------------------------------------------------------------- 140s Testing input file apbs-smol-parallel.in 140s 140s Splitting the input file into 4 separate files using the inputgen utility 140s 142s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 142s EXPECTED COMPUTED: 7 142s EXPECTED EXPECTED: 7 142s COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 142s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 142s COMPUTED RESULT 960.7073836226 142s COMPUTED RESULT 3257.1427835730997 142s COMPUTED RESULT 5941.0039478710005 142s COMPUTED RESULT 1190.8714828309999 142s COMPUTED RESULT 3519.7218230368003 142s COMPUTED RESULT 6171.495796544 142s COMPUTED RESULT -230.49184867462003 142s BINARY: /usr/bin/apbs 142s INPUT: apbs-smol-parallel-PE0.in 142s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 142s asc_getToken: Error occurred (bailing out). 142s Vio_scanf: Format problem with input. 142s 142s 142s ---------------------------------------------------------------------- 142s APBS -- Adaptive Poisson-Boltzmann Solver 142s Version APBS 3.4.1 142s 142s Nathan A. Baker (nathan.baker@pnnl.gov) 142s Pacific Northwest National Laboratory 142s 142s Additional contributing authors listed in the code documentation. 142s 142s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 142s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 142s Northwest Division for the U.S. Department of Energy. 142s 142s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 142s Portions Copyright (c) 2002-2020, Nathan A. Baker. 142s Portions Copyright (c) 1999-2002, The Regents of the University of California. 142s Portions Copyright (c) 1995, Michael Holst. 142s All rights reserved. 142s 142s Redistribution and use in source and binary forms, with or without 142s modification, are permitted provided that the following conditions are met: 142s 142s * Redistributions of source code must retain the above copyright notice, this 142s list of conditions and the following disclaimer. 142s 142s * Redistributions in binary form must reproduce the above copyright notice, 142s this list of conditions and the following disclaimer in the documentation 142s and/or other materials provided with the distribution. 142s 142s * Neither the name of the developer nor the names of its contributors may be 142s used to endorse or promote products derived from this software without 142s specific prior written permission. 142s 142s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 142s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 142s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 142s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 142s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 142s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 142s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 142s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 142s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 142s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 142s ---------------------------------------------------------------------- 142s APBS uses FETK (the Finite Element ToolKit) to solve the 142s Poisson-Boltzmann equation numerically. FETK is a portable collection 142s of finite element modeling class libraries developed by the Michael Holst 142s research group and written in an object-oriented form of C. FEtk is 142s designed to solve general coupled systems of nonlinear partial differential 142s equations using adaptive finite element methods, inexact Newton methods, 142s and algebraic multilevel methods. More information about FEtk may be found 142s at . 142s ---------------------------------------------------------------------- 142s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 142s Aqua is a modified form of the Holst group PMG library 142s which has been modified by Patrice Koehl 142s for improved efficiency and 142s memory usage when solving the Poisson-Boltzmann equation. 142s ---------------------------------------------------------------------- 142s Please cite your use of APBS as: 142s 142s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 142s nanosystems: application to microtubules and the ribosome. Proc. 142s Natl. Acad. Sci. USA 98, 10037-10041 2001. 142s 142s 142s This executable compiled on Jan 3 2025 at 11:01:42 142s 142s Parsing input file apbs-smol-parallel-PE0.in... 142s rank 0 size 1... 142s Parsed input file. 142s Got paths for 1 molecules 142s Reading PQR-format atom data from ion.pqr. 142s 1 atoms 142s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 142s Net charge 1.00e+00 e 142s Preparing to run 6 PBE calculations. 142s ---------------------------------------- 142s CALCULATION #1 (solvated): MULTIGRID 142s Setting up problem... 142s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 142s Debye length: 0 A 142s Current memory usage: 61.280 MB total, 61.280 MB high water 142s Using cubic spline charge discretization. 142s Partition overlap fraction = 0.1 142s Processor array = 2 x 2 x 1 142s Grid dimensions: 65 x 65 x 65 142s Grid spacings: 0.781 x 0.781 x 0.781 142s Grid lengths: 50.000 x 50.000 x 50.000 142s Grid center: (0.000, 0.000, 0.000) 142s Multigrid levels: 5 142s Molecule ID: 1 142s Linearized traditional PBE 142s Multiple Debye-Huckel sphere boundary conditions 142s 0 ion species (0.000 M ionic strength): 142s Solute dielectric: 1.000 142s Solvent dielectric: 78.540 142s Using "molecular" surface definition;harmonic average smoothing 142s Solvent probe radius: 1.400 A 142s Temperature: 298.150 K 142s Electrostatic energies will be calculated 142s Total electrostatic energy = 2.383232191816E+02 kJ/mol 142s Calculating forces... 142s ---------------------------------------- 142s CALCULATION #2 (solvated): MULTIGRID 142s Setting up problem... 142s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 142s Debye length: 0 A 142s Current memory usage: 61.280 MB total, 122.102 MB high water 142s Using cubic spline charge discretization. 142s Partition overlap fraction = 0.1 142s Processor array = 2 x 2 x 1 142s Grid dimensions: 65 x 65 x 65 142s Grid spacings: 0.296 x 0.296 x 0.383 142s Grid lengths: 18.944 x 18.944 x 24.495 142s Grid center: (-2.411, -2.411, 0.000) 142s Multigrid levels: 5 142s Molecule ID: 1 142s Linearized traditional PBE 142s Boundary conditions from focusing 142s 0 ion species (0.000 M ionic strength): 142s Solute dielectric: 1.000 142s Solvent dielectric: 78.540 142s Using "molecular" surface definition;harmonic average smoothing 142s Solvent probe radius: 1.400 A 142s Temperature: 298.150 K 142s Electrostatic energies will be calculated 142s Total electrostatic energy = 8.145369591602E+02 kJ/mol 142s Calculating forces... 142s [focusFillBound()]: WARNING: 142s Unusually large potential values 142s detected on the focusing boundary! 142s Convergence not guaranteed for NPBE/NRPBE calculations! 142s 142s ---------------------------------------- 142s CALCULATION #3 (solvated): MULTIGRID 142s Setting up problem... 142s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 142s Debye length: 0 A 142s Current memory usage: 61.280 MB total, 122.102 MB high water 142s Using cubic spline charge discretization. 142s Partition overlap fraction = 0.1 142s Processor array = 2 x 2 x 1 142s Grid dimensions: 65 x 65 x 65 142s Grid spacings: 0.112 x 0.112 x 0.188 142s Grid lengths: 7.178 x 7.178 x 12.000 142s Grid center: (-2.411, -2.411, 0.000) 142s Multigrid levels: 5 142s Molecule ID: 1 142s Linearized traditional PBE 142s Boundary conditions from focusing 142s 0 ion species (0.000 M ionic strength): 142s Solute dielectric: 1.000 142s Solvent dielectric: 78.540 142s Using "molecular" surface definition;harmonic average smoothing 142s Solvent probe radius: 1.400 A 142s Temperature: 298.150 K 142s Electrostatic energies will be calculated 142s Total electrostatic energy = 1.485524998001E+03 kJ/mol 142s Calculating forces... 142s ---------------------------------------- 142s CALCULATION #4 (reference): MULTIGRID 142s Setting up problem... 142s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 142s Debye length: 0 A 142s Current memory usage: 61.207 MB total, 122.102 MB high water 142s Using cubic spline charge discretization. 142s Partition overlap fraction = 0.1 142s Processor array = 2 x 2 x 1 142s Grid dimensions: 65 x 65 x 65 142s Grid spacings: 0.781 x 0.781 x 0.781 142s Grid lengths: 50.000 x 50.000 x 50.000 142s Grid center: (0.000, 0.000, 0.000) 142s Multigrid levels: 5 142s Molecule ID: 1 142s Linearized traditional PBE 142s Multiple Debye-Huckel sphere boundary conditions 142s 0 ion species (0.000 M ionic strength): 142s Solute dielectric: 1.000 142s Solvent dielectric: 1.000 142s Using "molecular" surface definition;harmonic average smoothing 142s Solvent probe radius: 1.400 A 142s Temperature: 298.150 K 142s Electrostatic energies will be calculated 142s Total electrostatic energy = 2.977178707009E+02 kJ/mol 142s Calculating forces... 142s ---------------------------------------- 142s CALCULATION #5 (reference): MULTIGRID 142s Setting up problem... 142s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 142s Debye length: 0 A 142s Current memory usage: 61.207 MB total, 122.102 MB high water 142s Using cubic spline charge discretization. 142s Partition overlap fraction = 0.1 142s Processor array = 2 x 2 x 1 142s Grid dimensions: 65 x 65 x 65 142s Grid spacings: 0.296 x 0.296 x 0.383 142s Grid lengths: 18.944 x 18.944 x 24.495 142s Grid center: (-2.411, -2.411, 0.000) 142s Multigrid levels: 5 142s Molecule ID: 1 142s Linearized traditional PBE 142s Boundary conditions from focusing 142s 0 ion species (0.000 M ionic strength): 142s Solute dielectric: 1.000 142s Solvent dielectric: 1.000 142s Using "molecular" surface definition;harmonic average smoothing 142s Solvent probe radius: 1.400 A 142s Temperature: 298.150 K 142s Electrostatic energies will be calculated 142s Total electrostatic energy = 8.799304557588E+02 kJ/mol 142s Calculating forces... 142s [focusFillBound()]: WARNING: 142s Unusually large potential values 142s detected on the focusing boundary! 142s Convergence not guaranteed for NPBE/NRPBE calculations! 142s 142s ---------------------------------------- 142s CALCULATION #6 (reference): MULTIGRID 142s Setting up problem... 142s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 142s Debye length: 0 A 142s Current memory usage: 61.207 MB total, 122.102 MB high water 142s Using cubic spline charge discretization. 142s Partition overlap fraction = 0.1 142s Processor array = 2 x 2 x 1 142s Grid dimensions: 65 x 65 x 65 142s Grid spacings: 0.112 x 0.112 x 0.188 142s Grid lengths: 7.178 x 7.178 x 12.000 142s Grid center: (-2.411, -2.411, 0.000) 142s Multigrid levels: 5 142s Molecule ID: 1 142s Linearized traditional PBE 142s Boundary conditions from focusing 142s 0 ion species (0.000 M ionic strength): 142s Solute dielectric: 1.000 142s Solvent dielectric: 1.000 142s Using "molecular" surface definition;harmonic average smoothing 142s Solvent probe radius: 1.400 A 142s Temperature: 298.150 K 142s Electrostatic energies will be calculated 142s Total electrostatic energy = 1.542873949131E+03 kJ/mol 142s Calculating forces... 142s ---------------------------------------- 142s PRINT STATEMENTS 142s 142s print energy 1 (solvated) - 2 (reference) end 142s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 142s Global net ELEC energy = -5.734895113069E+01 kJ/mol 142s ---------------------------------------- 142s CLEANING UP AND SHUTTING DOWN... 142s Destroying force arrays. 142s No energy arrays to destroy. 142s Destroying multigrid structures. 142s Destroying finite element structures. 142s Destroying 1 molecules 142s Final memory usage: 0.001 MB total, 122.102 MB high water 142s 142s 142s Thanks for using APBS! 142s 142s Processor 0 results: 142s 2.383232191816e+02 142s 8.145369591602e+02 142s 1.485524998001e+03 142s 2.977178707009e+02 142s 8.799304557588e+02 142s 1.542873949131e+03 142s -5.734895113069e+01 142s 143s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 143s BINARY: /usr/bin/apbs 143s INPUT: apbs-smol-parallel-PE1.in 143s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 143s asc_getToken: Error occurred (bailing out). 143s Vio_scanf: Format problem with input. 143s 143s 143s ---------------------------------------------------------------------- 143s APBS -- Adaptive Poisson-Boltzmann Solver 143s Version APBS 3.4.1 143s 143s Nathan A. Baker (nathan.baker@pnnl.gov) 143s Pacific Northwest National Laboratory 143s 143s Additional contributing authors listed in the code documentation. 143s 143s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 143s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 143s Northwest Division for the U.S. Department of Energy. 143s 143s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 143s Portions Copyright (c) 2002-2020, Nathan A. Baker. 143s Portions Copyright (c) 1999-2002, The Regents of the University of California. 143s Portions Copyright (c) 1995, Michael Holst. 143s All rights reserved. 143s 143s Redistribution and use in source and binary forms, with or without 143s modification, are permitted provided that the following conditions are met: 143s 143s * Redistributions of source code must retain the above copyright notice, this 143s list of conditions and the following disclaimer. 143s 143s * Redistributions in binary form must reproduce the above copyright notice, 143s this list of conditions and the following disclaimer in the documentation 143s and/or other materials provided with the distribution. 143s 143s * Neither the name of the developer nor the names of its contributors may be 143s used to endorse or promote products derived from this software without 143s specific prior written permission. 143s 143s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 143s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 143s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 143s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 143s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 143s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 143s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 143s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 143s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 143s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 143s ---------------------------------------------------------------------- 143s APBS uses FETK (the Finite Element ToolKit) to solve the 143s Poisson-Boltzmann equation numerically. FETK is a portable collection 143s of finite element modeling class libraries developed by the Michael Holst 143s research group and written in an object-oriented form of C. FEtk is 143s designed to solve general coupled systems of nonlinear partial differential 143s equations using adaptive finite element methods, inexact Newton methods, 143s and algebraic multilevel methods. More information about FEtk may be found 143s at . 143s ---------------------------------------------------------------------- 143s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 143s Aqua is a modified form of the Holst group PMG library 143s which has been modified by Patrice Koehl 143s for improved efficiency and 143s memory usage when solving the Poisson-Boltzmann equation. 143s ---------------------------------------------------------------------- 143s Please cite your use of APBS as: 143s 143s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 143s nanosystems: application to microtubules and the ribosome. Proc. 143s Natl. Acad. Sci. USA 98, 10037-10041 2001. 143s 143s 143s This executable compiled on Jan 3 2025 at 11:01:42 143s 143s Parsing input file apbs-smol-parallel-PE1.in... 143s rank 0 size 1... 143s Parsed input file. 143s Got paths for 1 molecules 143s Reading PQR-format atom data from ion.pqr. 143s 1 atoms 143s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 143s Net charge 1.00e+00 e 143s Preparing to run 6 PBE calculations. 143s ---------------------------------------- 143s CALCULATION #1 (solvated): MULTIGRID 143s Setting up problem... 143s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 143s Debye length: 0 A 143s Current memory usage: 61.280 MB total, 61.280 MB high water 143s Using cubic spline charge discretization. 143s Partition overlap fraction = 0.1 143s Processor array = 2 x 2 x 1 143s Grid dimensions: 65 x 65 x 65 143s Grid spacings: 0.781 x 0.781 x 0.781 143s Grid lengths: 50.000 x 50.000 x 50.000 143s Grid center: (0.000, 0.000, 0.000) 143s Multigrid levels: 5 143s Molecule ID: 1 143s Linearized traditional PBE 143s Multiple Debye-Huckel sphere boundary conditions 143s 0 ion species (0.000 M ionic strength): 143s Solute dielectric: 1.000 143s Solvent dielectric: 78.540 143s Using "molecular" surface definition;harmonic average smoothing 143s Solvent probe radius: 1.400 A 143s Temperature: 298.150 K 143s Electrostatic energies will be calculated 143s Total electrostatic energy = 2.383232191816E+02 kJ/mol 143s Calculating forces... 143s ---------------------------------------- 143s CALCULATION #2 (solvated): MULTIGRID 143s Setting up problem... 143s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 143s Debye length: 0 A 143s Current memory usage: 61.280 MB total, 122.102 MB high water 143s Using cubic spline charge discretization. 143s Partition overlap fraction = 0.1 143s Processor array = 2 x 2 x 1 143s Grid dimensions: 65 x 65 x 65 143s Grid spacings: 0.296 x 0.296 x 0.383 143s Grid lengths: 18.944 x 18.944 x 24.495 143s Grid center: (2.411, -2.411, 0.000) 143s Multigrid levels: 5 143s Molecule ID: 1 143s Linearized traditional PBE 143s Boundary conditions from focusing 143s 0 ion species (0.000 M ionic strength): 143s Solute dielectric: 1.000 143s Solvent dielectric: 78.540 143s Using "molecular" surface definition;harmonic average smoothing 143s Solvent probe radius: 1.400 A 143s Temperature: 298.150 K 143s Electrostatic energies will be calculated 143s Total electrostatic energy = 8.145419898332E+02 kJ/mol 143s Calculating forces... 143s [focusFillBound()]: WARNING: 143s Unusually large potential values 143s detected on the focusing boundary! 143s Convergence not guaranteed for NPBE/NRPBE calculations! 143s 143s ---------------------------------------- 143s CALCULATION #3 (solvated): MULTIGRID 143s Setting up problem... 143s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 143s Debye length: 0 A 143s Current memory usage: 61.280 MB total, 122.102 MB high water 143s Using cubic spline charge discretization. 143s Partition overlap fraction = 0.1 143s Processor array = 2 x 2 x 1 143s Grid dimensions: 65 x 65 x 65 143s Grid spacings: 0.112 x 0.112 x 0.188 143s Grid lengths: 7.178 x 7.178 x 12.000 143s Grid center: (2.411, -2.411, 0.000) 143s Multigrid levels: 5 143s Molecule ID: 1 143s Linearized traditional PBE 143s Boundary conditions from focusing 143s 0 ion species (0.000 M ionic strength): 143s Solute dielectric: 1.000 143s Solvent dielectric: 78.540 143s Using "molecular" surface definition;harmonic average smoothing 143s Solvent probe radius: 1.400 A 143s Temperature: 298.150 K 143s Electrostatic energies will be calculated 143s Total electrostatic energy = 1.485529328612E+03 kJ/mol 143s Calculating forces... 143s ---------------------------------------- 143s CALCULATION #4 (reference): MULTIGRID 143s Setting up problem... 143s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 143s Debye length: 0 A 143s Current memory usage: 61.207 MB total, 122.102 MB high water 143s Using cubic spline charge discretization. 143s Partition overlap fraction = 0.1 143s Processor array = 2 x 2 x 1 143s Grid dimensions: 65 x 65 x 65 143s Grid spacings: 0.781 x 0.781 x 0.781 143s Grid lengths: 50.000 x 50.000 x 50.000 143s Grid center: (0.000, 0.000, 0.000) 143s Multigrid levels: 5 143s Molecule ID: 1 143s Linearized traditional PBE 143s Multiple Debye-Huckel sphere boundary conditions 143s 0 ion species (0.000 M ionic strength): 143s Solute dielectric: 1.000 143s Solvent dielectric: 1.000 143s Using "molecular" surface definition;harmonic average smoothing 143s Solvent probe radius: 1.400 A 143s TemperatureProcessor 1 results: 143s 2.383232191816e+02 143s 8.145419898332e+02 143s 1.485529328612e+03 143s 2.977178707009e+02 143s 8.799304557588e+02 143s 1.542873949131e+03 143s -5.734462051928e+01 143s 143s : 298.150 K 143s Electrostatic energies will be calculated 143s Total electrostatic energy = 2.977178707009E+02 kJ/mol 143s Calculating forces... 143s ---------------------------------------- 143s CALCULATION #5 (reference): MULTIGRID 143s Setting up problem... 143s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 143s Debye length: 0 A 143s Current memory usage: 61.207 MB total, 122.102 MB high water 143s Using cubic spline charge discretization. 143s Partition overlap fraction = 0.1 143s Processor array = 2 x 2 x 1 143s Grid dimensions: 65 x 65 x 65 143s Grid spacings: 0.296 x 0.296 x 0.383 143s Grid lengths: 18.944 x 18.944 x 24.495 143s Grid center: (2.411, -2.411, 0.000) 143s Multigrid levels: 5 143s Molecule ID: 1 143s Linearized traditional PBE 143s Boundary conditions from focusing 143s 0 ion species (0.000 M ionic strength): 143s Solute dielectric: 1.000 143s Solvent dielectric: 1.000 143s Using "molecular" surface definition;harmonic average smoothing 143s Solvent probe radius: 1.400 A 143s Temperature: 298.150 K 143s Electrostatic energies will be calculated 143s Total electrostatic energy = 8.799304557588E+02 kJ/mol 143s Calculating forces... 143s [focusFillBound()]: WARNING: 143s Unusually large potential values 143s detected on the focusing boundary! 143s Convergence not guaranteed for NPBE/NRPBE calculations! 143s 143s ---------------------------------------- 143s CALCULATION #6 (reference): MULTIGRID 143s Setting up problem... 143s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 143s Debye length: 0 A 143s Current memory usage: 61.207 MB total, 122.102 MB high water 143s Using cubic spline charge discretization. 143s Partition overlap fraction = 0.1 143s Processor array = 2 x 2 x 1 143s Grid dimensions: 65 x 65 x 65 143s Grid spacings: 0.112 x 0.112 x 0.188 143s Grid lengths: 7.178 x 7.178 x 12.000 143s Grid center: (2.411, -2.411, 0.000) 143s Multigrid levels: 5 143s Molecule ID: 1 143s Linearized traditional PBE 143s Boundary conditions from focusing 143s 0 ion species (0.000 M ionic strength): 143s Solute dielectric: 1.000 143s Solvent dielectric: 1.000 143s Using "molecular" surface definition;harmonic average smoothing 143s Solvent probe radius: 1.400 A 143s Temperature: 298.150 K 143s Electrostatic energies will be calculated 143s Total electrostatic energy = 1.542873949131E+03 kJ/mol 143s Calculating forces... 143s ---------------------------------------- 143s PRINT STATEMENTS 143s 143s print energy 1 (solvated) - 2 (reference) end 143s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 143s Global net ELEC energy = -5.734462051928E+01 kJ/mol 143s ---------------------------------------- 143s CLEANING UP AND SHUTTING DOWN... 143s Destroying force arrays. 143s No energy arrays to destroy. 143s Destroying multigrid structures. 143s Destroying finite element structures. 143s Destroying 1 molecules 143s Final memory usage: 0.001 MB total, 122.102 MB high water 143s 143s 143s Thanks for using APBS! 143s 144s Processor 2 results: 144s 2.383232191909e+02 144s 8.145369593489e+02 144s 1.485524997676e+03 144s 2.977178707146e+02 144s 8.799304557596e+02 144s 1.542873949141e+03 144s -5.734895146550e+01 144s 144s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 144s BINARY: /usr/bin/apbs 144s INPUT: apbs-smol-parallel-PE2.in 144s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 144s asc_getToken: Error occurred (bailing out). 144s Vio_scanf: Format problem with input. 144s 144s 144s ---------------------------------------------------------------------- 144s APBS -- Adaptive Poisson-Boltzmann Solver 144s Version APBS 3.4.1 144s 144s Nathan A. Baker (nathan.baker@pnnl.gov) 144s Pacific Northwest National Laboratory 144s 144s Additional contributing authors listed in the code documentation. 144s 144s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 144s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 144s Northwest Division for the U.S. Department of Energy. 144s 144s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 144s Portions Copyright (c) 2002-2020, Nathan A. Baker. 144s Portions Copyright (c) 1999-2002, The Regents of the University of California. 144s Portions Copyright (c) 1995, Michael Holst. 144s All rights reserved. 144s 144s Redistribution and use in source and binary forms, with or without 144s modification, are permitted provided that the following conditions are met: 144s 144s * Redistributions of source code must retain the above copyright notice, this 144s list of conditions and the following disclaimer. 144s 144s * Redistributions in binary form must reproduce the above copyright notice, 144s this list of conditions and the following disclaimer in the documentation 144s and/or other materials provided with the distribution. 144s 144s * Neither the name of the developer nor the names of its contributors may be 144s used to endorse or promote products derived from this software without 144s specific prior written permission. 144s 144s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 144s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 144s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 144s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 144s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 144s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 144s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 144s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 144s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 144s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 144s ---------------------------------------------------------------------- 144s APBS uses FETK (the Finite Element ToolKit) to solve the 144s Poisson-Boltzmann equation numerically. FETK is a portable collection 144s of finite element modeling class libraries developed by the Michael Holst 144s research group and written in an object-oriented form of C. FEtk is 144s designed to solve general coupled systems of nonlinear partial differential 144s equations using adaptive finite element methods, inexact Newton methods, 144s and algebraic multilevel methods. More information about FEtk may be found 144s at . 144s ---------------------------------------------------------------------- 144s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 144s Aqua is a modified form of the Holst group PMG library 144s which has been modified by Patrice Koehl 144s for improved efficiency and 144s memory usage when solving the Poisson-Boltzmann equation. 144s ---------------------------------------------------------------------- 144s Please cite your use of APBS as: 144s 144s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 144s nanosystems: application to microtubules and the ribosome. Proc. 144s Natl. Acad. Sci. USA 98, 10037-10041 2001. 144s 144s 144s This executable compiled on Jan 3 2025 at 11:01:42 144s 144s Parsing input file apbs-smol-parallel-PE2.in... 144s rank 0 size 1... 144s Parsed input file. 144s Got paths for 1 molecules 144s Reading PQR-format atom data from ion.pqr. 144s 1 atoms 144s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 144s Net charge 1.00e+00 e 144s Preparing to run 6 PBE calculations. 144s ---------------------------------------- 144s CALCULATION #1 (solvated): MULTIGRID 144s Setting up problem... 144s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 144s Debye length: 0 A 144s Current memory usage: 61.280 MB total, 61.280 MB high water 144s Using cubic spline charge discretization. 144s Partition overlap fraction = 0.1 144s Processor array = 2 x 2 x 1 144s Grid dimensions: 65 x 65 x 65 144s Grid spacings: 0.781 x 0.781 x 0.781 144s Grid lengths: 50.000 x 50.000 x 50.000 144s Grid center: (0.000, 0.000, 0.000) 144s Multigrid levels: 5 144s Molecule ID: 1 144s Linearized traditional PBE 144s Multiple Debye-Huckel sphere boundary conditions 144s 0 ion species (0.000 M ionic strength): 144s Solute dielectric: 1.000 144s Solvent dielectric: 78.540 144s Using "molecular" surface definition;harmonic average smoothing 144s Solvent probe radius: 1.400 A 144s Temperature: 298.150 K 144s Electrostatic energies will be calculated 144s Total electrostatic energy = 2.383232191909E+02 kJ/mol 144s Calculating forces... 144s ---------------------------------------- 144s CALCULATION #2 (solvated): MULTIGRID 144s Setting up problem... 144s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 144s Debye length: 0 A 144s Current memory usage: 61.280 MB total, 122.102 MB high water 144s Using cubic spline charge discretization. 144s Partition overlap fraction = 0.1 144s Processor array = 2 x 2 x 1 144s Grid dimensions: 65 x 65 x 65 144s Grid spacings: 0.296 x 0.296 x 0.383 144s Grid lengths: 18.944 x 18.944 x 24.495 144s Grid center: (-2.411, 2.411, 0.000) 144s Multigrid levels: 5 144s Molecule ID: 1 144s Linearized traditional PBE 144s Boundary conditions from focusing 144s 0 ion species (0.000 M ionic strength): 144s Solute dielectric: 1.000 144s Solvent dielectric: 78.540 144s Using "molecular" surface definition;harmonic average smoothing 144s Solvent probe radius: 1.400 A 144s Temperature: 298.150 K 144s Electrostatic energies will be calculated 144s Total electrostatic energy = 8.145369593489E+02 kJ/mol 144s Calculating forces... 144s [focusFillBound()]: WARNING: 144s Unusually large potential values 144s detected on the focusing boundary! 144s Convergence not guaranteed for NPBE/NRPBE calculations! 144s 144s ---------------------------------------- 144s CALCULATION #3 (solvated): MULTIGRID 144s Setting up problem... 144s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 144s Debye length: 0 A 144s Current memory usage: 61.280 MB total, 122.102 MB high water 144s Using cubic spline charge discretization. 144s Partition overlap fraction = 0.1 144s Processor array = 2 x 2 x 1 144s Grid dimensions: 65 x 65 x 65 144s Grid spacings: 0.112 x 0.112 x 0.188 144s Grid lengths: 7.178 x 7.178 x 12.000 144s Grid center: (-2.411, 2.411, 0.000) 144s Multigrid levels: 5 144s Molecule ID: 1 144s Linearized traditional PBE 144s Boundary conditions from focusing 144s 0 ion species (0.000 M ionic strength): 144s Solute dielectric: 1.000 144s Solvent dielectric: 78.540 144s Using "molecular" surface definition;harmonic average smoothing 144s Solvent probe radius: 1.400 A 144s Temperature: 298.150 K 144s Electrostatic energies will be calculated 144s Total electrostatic energy = 1.485524997676E+03 kJ/mol 144s Calculating forces... 144s ---------------------------------------- 144s CALCULATION #4 (reference): MULTIGRID 144s Setting up problem... 144s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 144s Debye length: 0 A 144s Current memory usage: 61.207 MB total, 122.102 MB high water 144s Using cubic spline charge discretization. 144s Partition overlap fraction = 0.1 144s Processor array = 2 x 2 x 1 144s Grid dimensions: 65 x 65 x 65 144s Grid spacings: 0.781 x 0.781 x 0.781 144s Grid lengths: 50.000 x 50.000 x 50.000 144s Grid center: (0.000, 0.000, 0.000) 144s Multigrid levels: 5 144s Molecule ID: 1 144s Linearized traditional PBE 144s Multiple Debye-Huckel sphere boundary conditions 144s 0 ion species (0.000 M ionic strength): 144s Solute dielectric: 1.000 144s Solvent dielectric: 1.000 144s Using "molecular" surface definition;harmonic average smoothing 144s Solvent probe radius: 1.400 A 144s Temperature: 298.150 K 144s Electrostatic energies will be calculated 144s Total electrostatic energy = 2.977178707146E+02 kJ/mol 144s Calculating forces... 144s ---------------------------------------- 144s CALCULATION #5 (reference): MULTIGRID 144s Setting up problem... 144s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 144s Debye length: 0 A 144s Current memory usage: 61.207 MB total, 122.102 MB high water 144s Using cubic spline charge discretization. 144s Partition overlap fraction = 0.1 144s Processor array = 2 x 2 x 1 144s Grid dimensions: 65 x 65 x 65 144s Grid spacings: 0.296 x 0.296 x 0.383 144s Grid lengths: 18.944 x 18.944 x 24.495 144s Grid center: (-2.411, 2.411, 0.000) 144s Multigrid levels: 5 144s Molecule ID: 1 144s Linearized traditional PBE 144s Boundary conditions from focusing 144s 0 ion species (0.000 M ionic strength): 144s Solute dielectric: 1.000 144s Solvent dielectric: 1.000 144s Using "molecular" surface definition;harmonic average smoothing 144s Solvent probe radius: 1.400 A 144s Temperature: 298.150 K 144s Electrostatic energies will be calculated 144s Total electrostatic energy = 8.799304557596E+02 kJ/mol 144s Calculating forces... 144s [focusFillBound()]: WARNING: 144s Unusually large potential values 144s detected on the focusing boundary! 144s Convergence not guaranteed for NPBE/NRPBE calculations! 144s 144s ---------------------------------------- 144s CALCULATION #6 (reference): MULTIGRID 144s Setting up problem... 144s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 144s Debye length: 0 A 144s Current memory usage: 61.207 MB total, 122.102 MB high water 144s Using cubic spline charge discretization. 144s Partition overlap fraction = 0.1 144s Processor array = 2 x 2 x 1 144s Grid dimensions: 65 x 65 x 65 144s Grid spacings: 0.112 x 0.112 x 0.188 144s Grid lengths: 7.178 x 7.178 x 12.000 144s Grid center: (-2.411, 2.411, 0.000) 144s Multigrid levels: 5 144s Molecule ID: 1 144s Linearized traditional PBE 144s Boundary conditions from focusing 144s 0 ion species (0.000 M ionic strength): 144s Solute dielectric: 1.000 144s Solvent dielectric: 1.000 144s Using "molecular" surface definition;harmonic average smoothing 144s Solvent probe radius: 1.400 A 144s Temperature: 298.150 K 144s Electrostatic energies will be calculated 144s Total electrostatic energy = 1.542873949141E+03 kJ/mol 144s Calculating forces... 144s ---------------------------------------- 144s PRINT STATEMENTS 144s 144s print energy 1 (solvated) - 2 (reference) end 144s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 144s Global net ELEC energy = -5.734895146550E+01 kJ/mol 144s ---------------------------------------- 144s CLEANING UP AND SHUTTING DOWN... 144s Destroying force arrays. 144s No energy arrays to destroy. 144s Destroying multigrid structures. 144s Destroying finite element structures. 144s Destroying 1 molecules 144s Final memory usage: 0.001 MB total, 122.102 MB high water 144s 144s 144s Thanks for using APBS! 144s 146s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 146s BINARY: /usr/bin/apbs 146s INPUT: apbs-smol-parallel-PE3.in 146s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 146s asc_getToken: Error occurred (bailing out). 146s Vio_scanf: Format problem with input. 146s 146s 146s ---------------------------------------------------------------------- 146s APBS -- Adaptive Poisson-Boltzmann Solver 146s Version APBS 3.4.1 146s 146s Nathan A. Baker (nathan.baker@pnnl.gov) 146s Pacific Northwest National Laboratory 146s 146s Additional contributing authors listed in the code documentation. 146s 146s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 146s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 146s Northwest Division for the U.S. Department of Energy. 146s 146s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 146s Portions Copyright (c) 2002-2020, Nathan A. Baker. 146s Portions Copyright (c) 1999-2002, The Regents of the University of California. 146s Portions Copyright (c) 1995, Michael Holst. 146s All rights reserved. 146s 146s Redistribution and use in source and binary forms, with or without 146s modification, are permitted provided that the following conditions are met: 146s 146s * Redistributions of source code must retain the above copyright notice, this 146s list of conditions and the following disclaimer. 146s 146s * Redistributions in binary form must reproduce the above copyright notice, 146s this list of conditions and the following disclaimer in the documentation 146s and/or other materials provided with the distribution. 146s 146s * Neither the name of the developer nor the names of its contributors may be 146s used to endorse or promote products derived from this software without 146s specific prior written permission. 146s 146s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 146s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 146s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 146s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 146s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 146s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 146s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 146s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 146s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 146s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 146s ---------------------------------------------------------------------- 146s APBS uses FETK (the Finite Element ToolKit) to solve the 146s Poisson-Boltzmann equation numerically. FETK is a portable collection 146s of finite element modeling class libraries developed by the Michael Holst 146s research group and written in an object-oriented form of C. FEtk is 146s designed to solve general coupled systems of nonlinear partial differential 146s equations using adaptive finite element methods, inexact Newton methods, 146s and algebraic multilevel methods. More information about FEtk may be found 146s at . 146s ---------------------------------------------------------------------- 146s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 146s Aqua is a modified form of the Holst group PMG library 146s which has been modified by Patrice Koehl 146s for improved efficiency and 146s memory usage when solving the Poisson-Boltzmann equation. 146s ---------------------------------------------------------------------- 146s Please cite your use of APBS as: 146s 146s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 146s nanosystems: application to microtubules and the ribosome. Proc. 146s Natl. Acad. Sci. USA 98, 10037-10041 2001. 146s 146s 146s This executable compiled on Jan 3 2025 at 11:01:42 146s 146s Parsing input file apbs-smol-parallel-PE3.in... 146s rank 0 size 1... 146s Parsed input file. 146s Got paths for 1 molecules 146s Reading PQR-format atom data from ion.pqr. 146s 1 atoms 146s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 146s Net charge 1.00e+00 e 146s Preparing to run 6 PBE calculations. 146s ---------------------------------------- 146s CALCULATION #1 (solvated): MULTIGRID 146s Setting up problem... 146s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 146s Debye length: 0 A 146s Current memory usage: 61.280 MB total, 61.280 MB high water 146s Using cubic spline charge discretization. 146s Partition overlap fraction = 0.1 146s Processor array = 2 x 2 x 1 146s Grid dimensions: 65 x 65 x 65 146s Grid spacings: 0.781 x 0.781 x 0.781 146s Grid lengths: 50.000 x 50.000 x 50.000 146s Grid center: (0.000, 0.000, 0.000) 146s Multigrid levels: 5 146s Molecule ID: 1 146s Linearized traditional PBE 146s Multiple Debye-Huckel sphere boundary conditions 146s 0 ion species (0.000 M ionic strength): 146s Solute dielectric: 1.000 146s Solvent dielectric: 78.540 146s Using "molecular" surface definition;harmonic average smoothing 146s Solvent probe radius: 1.400 A 146s Temperature: 298.150 K 146s Electrostatic energies will be calculated 146s Total electrostatic energy = 2.383232191909E+02 kJ/mol 146s Calculating forces... 146s ---------------------------------------- 146s CALCULATION #2 (solvated): MULTIGRID 146s Setting up problem... 146s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 146s Debye length: 0 A 146s Current memory usage: 61.280 MB total, 122.102 MB high water 146s Using cubic spline charge discretization. 146s Partition overlap fraction = 0.1 146s Processor array = 2 x 2 x 1 146s Grid dimensions: 65 x 65 x 65 146s Grid spacings: 0.296 x 0.296 x 0.383 146s Grid lengths: 18.944 x 18.944 x 24.495 146s Grid center: (2.411, 2.411, 0.000) 146s Multigrid levels: 5 146s Molecule ID: 1 146s Linearized traditional PBE 146s Boundary conditions from focusing 146s 0 ion species (0.000 M ionic strength): 146s Solute dielectric: 1.000 146s Solvent dielectric: 78.540 146s Using "molecular" surface definition;harmonic average smoothing 146s Solvent probe radius: 1.400 A 146s Temperature: 298.150 K 146s Electrostatic energies will be calculated 146s Total electrostatic energy = 8.145419900310E+02 kJ/mol 146s Calculating forces... 146s [focusFillBound()]: WARNING: 146s Unusually large potential values 146s detected on the focusing boundary! 146s Convergence not guaranteed for NPBE/NRPBE calculations! 146s 146s ---------------------------------------- 146s CALCULATION #3 (solvated): MULTIGRID 146s Setting up problem... 146s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 146s Debye length: 0 A 146s Current memory usage: 61.280 MB total, 122.102 MB high water 146s Using cubic spline charge discretization. 146s Partition overlap fraction = 0.1 146s Processor array = 2 x 2 x 1 146s Grid dimensions: 65 x 65 x 65 146s Grid spacings: 0.112 x 0.112 x 0.188 146s Grid lengths: 7.178 x 7.178 x 12.000 146s Grid center: (2.411, 2.411, 0.000) 146s Multigrid levels: 5 146s Molecule ID: 1 146s Linearized traditional PBE 146s Boundary conditions from focusing 146s 0 ion species (0.000 M ionic strength): 146s Solute dielectric: 1.000 146s Solvent dielectric: 78.540 146s Using "molecular" surface definition;harmonic average smoothing 146s Solvent probe radius: 1.400 A 146s Temperature: 298.150 K 146s Electrostatic energies will be calculated 146s Total electrostatic energy = 1.485529328301E+03 kJ/mol 146s Calculating forces... 146s ---------------------------------------- 146s CALCULATION #4 (reference): MULTIGRID 146s Setting up problem... 146s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 146s Debye length: 0 A 146s Current memory usage: 61.207 MB total, 122.102 MB high water 146s Using cubic spline charge discretization. 146s Partition overlap fraction = 0.1 146s Processor array = 2 x 2 x 1 146s Grid dimensions: 65 x 65 x 65 146s Grid spacings: 0.781 x 0.781 x 0.781 146s Grid lengths: 50.000 x 50.000 x 50.000 146s Grid center: (0.000, 0.000, 0.000) 146s Multigrid levels: 5 146s Molecule ID: 1 146s Linearized traditional PBE 146s Multiple Debye-Huckel sphere boundary conditions 146s 0 ion species (0.000 M ionic strength): 146s Solute dielectric: 1.000 146s Solvent dielectric: 1.000 146s Using "molecular" surface definition;harmonic average smoothing 146s Solvent probe radius: 1.400 A 146s Temperature: 298.150 K 146s Electrostatic energies will be calculated 146s Total electrostatic energy = 2.977178707146E+02 kJ/mol 146s Calculating forces... 146s ---------------------------------------- 146s CALCULATION #5 (reference): MULTIGRID 146s Setting up problem... 146s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 146s Debye length: 0 A 146s Current memory usage: 61.207 MB total, 122.102 MB high water 146s Using cubic spline charge discretization. 146s Partition overlap fraction = 0.1 146s Processor array = 2 x 2 x 1 146s Grid dimensions: 65 x 65 x 65 146s Grid spacings: 0.296 x 0.296 x 0.383 146s Grid lengths: 18.944 x 18.944 x 24.495 146s Grid center: (2.411, 2.411, 0.000) 146s Multigrid levels: 5 146s Molecule ID: 1 146s Linearized traditional PBE 146s Boundary conditions from focusing 146s 0 ion species (0.000 M ionic strength): 146s Solute dielectric: 1.000 146s Solvent dielectric: 1.000 146s Using "molecular" surface definition;harmonic average smoothing 146s Solvent probe radius: 1.400 A 146s Temperature: 298.150 K 146s Electrostatic energies will be calculated 146s Total electrostatic energy = 8.799304557596E+02 kJ/mol 146s Calculating forces... 146s [focusFillBound()]: WARNING: 146s Unusually large potential values 146s detected on the focusing boundary! 146s Convergence not guaranteed for NPBE/NRPBE calculations! 146s 146s ---------------------------------------- 146s CALCULATION #6 (reference): MULTIGRID 146s Setting up problem... 146s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 146s Debye length: 0 A 146s Current memory usage: 61.207 MB total, 122.102 MB high water 146s Using cubic spline charge discretization. 146s Partition overlap fraction = 0.1 146s Processor array = 2 x 2 x 1 146s Grid dimensions: 65 x 65 x 65 146s Grid spacings: 0.112 x 0.112 x 0.188 146s Grid lengths: 7.178 x 7.178 x 12.000 146s Grid center: (2.411, 2.411, 0.000) 146s Multigrid levels: 5 146s Molecule ID: 1 146s Linearized traditional PBE 146s Boundary conditions from focusing 146s 0 ion species (0.000 M ionic strength): 146s Solute dielectric: 1.000 146s Solvent dielectric: 1.000 146s Using "molecular" surface definition;harmonic average smoothing 146s Solvent probe radius: 1.400 A 146s Temperature: 298.150 K 146s Electrostatic energies will be calculated 146s Total electrostatic energy = 1.542873949141E+03 kJ/mol 146s Calculating forces... 146s ---------------------------------------- 146s PRINT STATEMENTS 146s 146s print energy 1 (solvated) - 2 (reference) end 146s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 146s Global net ELEC energy = -5.734462084052E+01 kJ/mol 146s ---------------------------------------- 146s CLEANING UP AND SHUTTING DOWN... 146s Destroying force arrays. 146s No energy arrays to destroy. 146s Destroying multigrid structures. 146s Destroying finite element structures. 146s Destroying 1 molecules 146s Final memory usage: 0.001 MB total, 122.102 MB high water 146s 146s 146s Thanks for using APBS! 146s 146s Processor 3 results: 146s 2.383232191909e+02 146s 8.145419900310e+02 146s 1.485529328301e+03 146s 2.977178707146e+02 146s 8.799304557596e+02 146s 1.542873949141e+03 146s -5.734462084052e+01 146s 146s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 146s *** PASSED *** 146s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 146s *** PASSED *** 146s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 146s *** PASSED *** 146s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 146s *** PASSED *** 146s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 146s *** PASSED *** 146s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 146s *** PASSED *** 146s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 146s *** PASSED *** 146s Elapsed time: 6.099061 seconds 146s -------------------------------------------------------------------------------- 146s Total elapsed time: 17.260309 seconds 146s Test results have been logged 146s -------------------------------------------------------------------------------- 146s -------------------------------------------------------------------------------- 146s Testing input file apbs-mol-auto.in 146s 215s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 215s EXPECTED COMPUTED: 7 215s EXPECTED EXPECTED: 7 215s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 215s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 215s COMPUTED RESULT 953.292876745 215s COMPUTED RESULT 3258.1578983732998 215s COMPUTED RESULT 5942.108652589999 215s COMPUTED RESULT 1190.8714828309999 215s COMPUTED RESULT 3519.7218230368003 215s COMPUTED RESULT 6171.495796544 215s COMPUTED RESULT -229.38714395599 215s Running tests for actin-dimer-auto section 215s BINARY: /usr/bin/apbs 215s INPUT: apbs-mol-auto.in 215s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 215s asc_getToken: Error occurred (bailing out). 215s Vio_scanf: Format problem with input. 215s 215s 215s ---------------------------------------------------------------------- 215s APBS -- Adaptive Poisson-Boltzmann Solver 215s Version APBS 3.4.1 215s 215s Nathan A. Baker (nathan.baker@pnnl.gov) 215s Pacific Northwest National Laboratory 215s 215s Additional contributing authors listed in the code documentation. 215s 215s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 215s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 215s Northwest Division for the U.S. Department of Energy. 215s 215s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 215s Portions Copyright (c) 2002-2020, Nathan A. Baker. 215s Portions Copyright (c) 1999-2002, The Regents of the University of California. 215s Portions Copyright (c) 1995, Michael Holst. 215s All rights reserved. 215s 215s Redistribution and use in source and binary forms, with or without 215s modification, are permitted provided that the following conditions are met: 215s 215s * Redistributions of source code must retain the above copyright notice, this 215s list of conditions and the following disclaimer. 215s 215s * Redistributions in binary form must reproduce the above copyright notice, 215s this list of conditions and the following disclaimer in the documentation 215s and/or other materials provided with the distribution. 215s 215s * Neither the name of the developer nor the names of its contributors may be 215s used to endorse or promote products derived from this software without 215s specific prior written permission. 215s 215s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 215s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 215s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 215s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 215s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 215s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 215s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 215s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 215s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 215s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 215s ---------------------------------------------------------------------- 215s APBS uses FETK (the Finite Element ToolKit) to solve the 215s Poisson-Boltzmann equation numerically. FETK is a portable collection 215s of finite element modeling class libraries developed by the Michael Holst 215s research group and written in an object-oriented form of C. FEtk is 215s designed to solve general coupled systems of nonlinear partial differential 215s equations using adaptive finite element methods, inexact Newton methods, 215s and algebraic multilevel methods. More information about FEtk may be found 215s at . 215s ---------------------------------------------------------------------- 215s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 215s Aqua is a modified form of the Holst group PMG library 215s which has been modified by Patrice Koehl 215s for improved efficiency and 215s memory usage when solving the Poisson-Boltzmann equation. 215s ---------------------------------------------------------------------- 215s Please cite your use of APBS as: 215s 215s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 215s nanosystems: application to microtubules and the ribosome. Proc. 215s Natl. Acad. Sci. USA 98, 10037-10041 2001. 215s 215s 215s This executable compiled on Jan 3 2025 at 11:01:42 215s 215s Parsing input file apbs-mol-auto.in... 215s rank 0 size 1... 215s Parsed input file. 215s Got paths for 3 molecules 215s Reading PQR-format atom data from mol1.pqr. 215s asc_getToken: Error occurred (bailing out). 215s Vio_scanf: Format problem with input. 215s 5877 atoms 215s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 215s Net charge -1.20e+01 e 215s Reading PQR-format atom data from mol2.pqr. 215s asc_getToken: Error occurred (bailing out). 215s Vio_scanf: Format problem with input. 215s 5877 atoms 215s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 215s Net charge -1.20e+01 e 215s Reading PQR-format atom data from complex.pqr. 215s 11754 atoms 215s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 215s Net charge -2.40e+01 e 215s Preparing to run 6 PBE calculations. 215s ---------------------------------------- 215s CALCULATION #1 (mol1): MULTIGRID 215s Setting up problem... 215s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 215s Debye length: 13.5959 A 215s Current memory usage: 1028.322 MB total, 1028.322 MB high water 215s Using linear spline charge discretization. 215s Grid dimensions: 161 x 161 x 161 215s Grid spacings: 0.975 x 0.756 x 1.012 215s Grid lengths: 156.000 x 121.000 x 162.000 215s Grid center: (2.518, -2.465, 16.742) 215s Multigrid levels: 4 215s Molecule ID: 1 215s Nonlinear traditional PBE 215s Single Debye-Huckel sphere boundary conditions 215s 2 ion species (0.050 M ionic strength): 215s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 215s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 215s Solute dielectric: 2.000 215s Solvent dielectric: 78.400 215s Using "molecular" surface definition; no smoothing 215s Solvent probe radius: 1.400 A 215s Temperature: 298.150 K 215s Electrostatic energies will be calculated 215s Total electrostatic energy = 1.527617850342E+05 kJ/mol 215s Calculating forces... 215s ---------------------------------------- 215s CALCULATION #2 (mol1): MULTIGRID 215s Setting up problem... 215s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 215s Debye length: 13.5959 A 215s Current memory usage: 1028.322 MB total, 2042.113 MB high water 215s Using linear spline charge discretization. 215s Grid dimensions: 161 x 161 x 161 215s Grid spacings: 0.700 x 0.569 x 0.725 215s Grid lengths: 112.000 x 91.000 x 116.000 215s Grid center: (2.518, -2.465, 16.742) 215s Multigrid levels: 4 215s Molecule ID: 1 215s Nonlinear traditional PBE 215s Boundary conditions from focusing 215s 2 ion species (0.050 M ionic strength): 215s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 215s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 215s Solute dielectric: 2.000 215s Solvent dielectric: 78.400 215s Using "molecular" surface definition; no smoothing 215s Solvent probe radius: 1.400 A 215s Temperature: 298.150 K 215s Electrostatic energies will be calculated 215s Total electrostatic energy = 2.919510754196E+05 kJ/mol 215s Calculating forces... 215s ---------------------------------------- 215s CALCULATION #3 (mol2): MULTIGRID 215s Setting up problem... 215s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 215s Debye length: 13.5959 A 215s Current memory usage: 1030.291 MB total, 2042.113 MB high water 215s Using linear spline charge discretization. 215s Grid dimensions: 161 x 161 x 161 215s Grid spacings: 0.975 x 0.756 x 1.012 215s Grid lengths: 156.000 x 121.000 x 162.000 215s Grid center: (2.518, -2.465, 16.742) 215s Multigrid levels: 4 215s Molecule ID: 2 215s Nonlinear traditional PBE 215s Single Debye-Huckel sphere boundary conditions 215s 2 ion species (0.050 M ionic strength): 215s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 215s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 215s Solute dielectric: 2.000 215s Solvent dielectric: 78.400 215s Using "molecular" surface definition; no smoothing 215s Solvent probe radius: 1.400 A 215s Temperature: 298.150 K 215s Electrostatic energies will be calculated 215s Total electrostatic energy = 1.527671844880E+05 kJ/mol 215s Calculating forces... 215s ---------------------------------------- 215s CALCULATION #4 (mol2): MULTIGRID 215s Setting up problem... 215s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 215s Debye length: 13.5959 A 215s Current memory usage: 1030.291 MB total, 2046.048 MB high water 215s Using linear spline charge discretization. 215s Grid dimensions: 161 x 161 x 161 215s Grid spacings: 0.700 x 0.569 x 0.725 215s Grid lengths: 112.000 x 91.000 x 116.000 215s Grid center: (2.518, -2.465, 16.742) 215s Multigrid levels: 4 215s Molecule ID: 2 215s Nonlinear traditional PBE 215s Boundary conditions from focusing 215s 2 ion species (0.050 M ionic strength): 215s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 215s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 215s Solute dielectric: 2.000 215s Solvent dielectric: 78.400 215s Using "molecular" surface definition; no smoothing 215s Solvent probe radius: 1.400 A 215s Temperature: 298.150 K 215s Electrostatic energies will be calculated 215s Total electrostatic energy = 2.915468859278E+05 kJ/mol 215s Calculating forces... 215s ---------------------------------------- 215s CALCULATION #5 (complex): MULTIGRID 215s Setting up problem... 215s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 215s Debye length: 13.5959 A 215s Current memory usage: 1046.446 MB total, 2046.048 MB high water 215s Using linear spline charge discretization. 215s Grid dimensions: 161 x 161 x 161 215s Grid spacings: 0.975 x 0.756 x 1.012 215s Grid lengths: 156.000 x 121.000 x 162.000 215s Grid center: (2.518, -2.465, 16.742) 215s Multigrid levels: 4 215s Molecule ID: 3 215s Nonlinear traditional PBE 215s Single Debye-Huckel sphere boundary conditions 215s 2 ion species (0.050 M ionic strength): 215s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 215s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 215s Solute dielectric: 2.000 215s Solvent dielectric: 78.400 215s Using "molecular" surface definition; no smoothing 215s Solvent probe radius: 1.400 A 215s Temperature: 298.150 K 215s Electrostatic energies will be calculated 215s Total electrostatic energy = 3.056317807611E+05 kJ/mol 215s Calculating forces... 215s ---------------------------------------- 215s CALCULATION #6 (complex): MULTIGRID 215s Setting up problem... 215s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 215s Debye length: 13.5959 A 215s Current memory usage: 1046.446 MB total, 2069.492 MB high water 215s Using linear spline charge discretization. 215s Grid dimensions: 161 x 161 x 161 215s Grid spacings: 0.700 x 0.569 x 0.725 215s Grid lengths: 112.000 x 91.000 x 116.000 215s Grid center: (2.518, -2.465, 16.742) 215s Multigrid levels: 4 215s Molecule ID: 3 215s Nonlinear traditional PBE 215s Boundary conditions from focusing 215s 2 ion species (0.050 M ionic strength): 215s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 215s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 215s Solute dielectric: 2.000 215s Solvent dielectric: 78.400 215s Using "molecular" surface definition; no smoothing 215s Solvent probe radius: 1.400 A 215s Temperature: 298.150 K 215s Electrostatic energies will be calculated 215s Total electrostatic energy = 5.836028296532E+05 kJ/mol 215s Calculating forces... 215s ---------------------------------------- 215s PRINT STATEMENTS 215s 215s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 215s Local net energy (PE 0) = 1.048683058621E+02 kJ/mol 215s Global net ELEC energy = 1.048683058621E+02 kJ/mol 215s ---------------------------------------- 215s CLEANING UP AND SHUTTING DOWN... 215s Destroying force arrays. 215s No energy arrays to destroy. 215s Destroying multigrid structures. 215s Destroying finite element structures. 215s Destroying 3 molecules 215s Final memory usage: 0.001 MB total, 2069.492 MB high water 215s 215s 215s Thanks for using APBS! 215s 215s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 215s *** PASSED *** 215s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 215s *** PASSED *** 215s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 215s *** PASSED *** 215s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 215s *** PASSED *** 215s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 215s *** PASSED *** 215s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 215s *** PASSED *** 215s Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) 215s *** PASSED *** 215s Elapsed time: 68.468256 seconds 215s -------------------------------------------------------------------------------- 215s -------------------------------------------------------------------------------- 215s Testing input file apbs-smol-auto.in 215s 268s Checking for intermediate energies in input file apbs-mol-auto.out 268s EXPECTED COMPUTED: 7 268s EXPECTED EXPECTED: 7 268s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] 268s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 268s COMPUTED RESULT 152761.7850342 268s COMPUTED RESULT 291951.0754196 268s COMPUTED RESULT 152767.184488 268s COMPUTED RESULT 291546.8859278 268s COMPUTED RESULT 305631.7807611 268s COMPUTED RESULT 583602.8296532 268s COMPUTED RESULT 104.8683058621 268s BINARY: /usr/bin/apbs 268s INPUT: apbs-smol-auto.in 268s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.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 apbs-smol-auto.in... 268s rank 0 size 1... 268s Parsed input file. 268s Got paths for 3 molecules 268s Reading PQR-format atom data from mol1.pqr. 268s asc_getToken: Error occurred (bailing out). 268s Vio_scanf: Format problem with input. 268s 5877 atoms 268s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 268s Net charge -1.20e+01 e 268s Reading PQR-format atom data from mol2.pqr. 268s asc_getToken: Error occurred (bailing out). 268s Vio_scanf: Format problem with input. 268s 5877 atoms 268s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 268s Net charge -1.20e+01 e 268s Reading PQR-format atom data from complex.pqr. 268s 11754 atoms 268s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 268s Net charge -2.40e+01 e 268s Preparing to run 6 PBE calculations. 268s ---------------------------------------- 268s CALCULATION #1 (mol1): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 13.5959 A 268s Current memory usage: 1028.322 MB total, 1028.322 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 161 x 161 x 161 268s Grid spacings: 0.975 x 0.756 x 1.012 268s Grid lengths: 156.000 x 121.000 x 162.000 268s Grid center: (2.518, -2.465, 16.742) 268s Multigrid levels: 4 268s Molecule ID: 1 268s Nonlinear traditional PBE 268s Single Debye-Huckel sphere boundary conditions 268s 2 ion species (0.050 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.400 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.528632421825E+05 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #2 (mol1): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 13.5959 A 268s Current memory usage: 1028.322 MB total, 2042.113 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 161 x 161 x 161 268s Grid spacings: 0.700 x 0.569 x 0.725 268s Grid lengths: 112.000 x 91.000 x 116.000 268s Grid center: (2.518, -2.465, 16.742) 268s Multigrid levels: 4 268s Molecule ID: 1 268s Nonlinear traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.050 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.400 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 2.920618662320E+05 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #3 (mol2): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 13.5959 A 268s Current memory usage: 1030.291 MB total, 2042.113 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 161 x 161 x 161 268s Grid spacings: 0.975 x 0.756 x 1.012 268s Grid lengths: 156.000 x 121.000 x 162.000 268s Grid center: (2.518, -2.465, 16.742) 268s Multigrid levels: 4 268s Molecule ID: 2 268s Nonlinear traditional PBE 268s Single Debye-Huckel sphere boundary conditions 268s 2 ion species (0.050 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.400 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 1.529297900572E+05 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #4 (mol2): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 13.5959 A 268s Current memory usage: 1030.291 MB total, 2046.048 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 161 x 161 x 161 268s Grid spacings: 0.700 x 0.569 x 0.725 268s Grid lengths: 112.000 x 91.000 x 116.000 268s Grid center: (2.518, -2.465, 16.742) 268s Multigrid levels: 4 268s Molecule ID: 2 268s Nonlinear traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.050 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.400 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 2.916592202835E+05 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #5 (complex): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 13.5959 A 268s Current memory usage: 1046.446 MB total, 2046.048 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 161 x 161 x 161 268s Grid spacings: 0.975 x 0.756 x 1.012 268s Grid lengths: 156.000 x 121.000 x 162.000 268s Grid center: (2.518, -2.465, 16.742) 268s Multigrid levels: 4 268s Molecule ID: 3 268s Nonlinear traditional PBE 268s Single Debye-Huckel sphere boundary conditions 268s 2 ion species (0.050 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.400 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 3.059244262535E+05 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s CALCULATION #6 (complex): MULTIGRID 268s Setting up problem... 268s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 268s Debye length: 13.5959 A 268s Current memory usage: 1046.446 MB total, 2069.492 MB high water 268s Using linear spline charge discretization. 268s Grid dimensions: 161 x 161 x 161 268s Grid spacings: 0.700 x 0.569 x 0.725 268s Grid lengths: 112.000 x 91.000 x 116.000 268s Grid center: (2.518, -2.465, 16.742) 268s Multigrid levels: 4 268s Molecule ID: 3 268s Nonlinear traditional PBE 268s Boundary conditions from focusing 268s 2 ion species (0.050 M ionic strength): 268s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 268s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 268s Solute dielectric: 2.000 268s Solvent dielectric: 78.400 268s Using "molecular" surface definition;harmonic average smoothing 268s Solvent probe radius: 1.400 A 268s Temperature: 298.150 K 268s Electrostatic energies will be calculated 268s Total electrostatic energy = 5.838306706232E+05 kJ/mol 268s Calculating forces... 268s ---------------------------------------- 268s PRINT STATEMENTS 268s 268s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 268s Local net energy (PE 0) = 1.095841077688E+02 kJ/mol 268s Global net ELEC energy = 1.095841077688E+02 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, 2069.492 MB high water 268s 268s 268s Thanks for using APBS! 268s 268s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 268s *** PASSED *** 268s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 268s *** PASSED *** 268s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 268s *** PASSED *** 268s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 268s *** PASSED *** 268s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 268s *** PASSED *** 268s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 268s *** PASSED *** 268s Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) 268s *** PASSED *** 268s Elapsed time: 52.932201 seconds 268s -------------------------------------------------------------------------------- 268s Total elapsed time: 121.400457 seconds 268s Test results have been logged 268s -------------------------------------------------------------------------------- 268s -------------------------------------------------------------------------------- 268s Testing input file alkanes.in 268s 283s Checking for intermediate energies in input file apbs-smol-auto.out 283s EXPECTED COMPUTED: 7 283s EXPECTED EXPECTED: 7 283s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] 283s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 283s COMPUTED RESULT 152863.2421825 283s COMPUTED RESULT 292061.866232 283s COMPUTED RESULT 152929.7900572 283s COMPUTED RESULT 291659.2202835 283s COMPUTED RESULT 305924.4262535 283s COMPUTED RESULT 583830.6706232 283s COMPUTED RESULT 109.5841077688 283s Running tests for alkanes section 283s BINARY: /usr/bin/apbs 283s INPUT: alkanes.in 283s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 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 alkanes.in... 283s rank 0 size 1... 283s Parsed input file. 283s Reading parameter data from parm.dat. 283s Got paths for 11 molecules 283s Reading PDB-format atom data from 2-methylbutane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 17 atoms 283s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 283s Net charge 4.33e+00 e 283s Reading PDB-format atom data from butane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 14 atoms 283s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 283s Net charge 3.51e+00 e 283s Reading PDB-format atom data from cyclohexane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 18 atoms 283s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 283s Net charge 4.93e+00 e 283s Reading PDB-format atom data from cyclopentane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 13 atoms 283s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 283s Net charge 3.88e+00 e 283s Reading PDB-format atom data from ethane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 8 atoms 283s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 283s Net charge 1.87e+00 e 283s Reading PDB-format atom data from hexane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 20 atoms 283s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 283s Net charge 5.16e+00 e 283s Reading PDB-format atom data from isobutane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 14 atoms 283s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 283s Net charge 3.51e+00 e 283s Reading PDB-format atom data from methane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 5 atoms 283s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 283s Net charge 1.05e+00 e 283s Reading PDB-format atom data from neopentane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 17 atoms 283s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 283s Net charge 4.33e+00 e 283s Reading PDB-format atom data from pentane.pdb. 283s asc_getToken: Error occurred (bailing out). 283s Vio_scanf: Format problem with input. 283s 17 atoms 283s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 283s Net charge 4.33e+00 e 283s Reading PDB-format atom data from propane.pdb. 283s 11 atoms 283s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 283s Net charge 2.69e+00 e 283s Preparing to run 11 PBE calculations. 283s ---------------------------------------- 283s CALCULATION #1 (solvated-2-methylbutane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 3.815624614267E+00 283s SASA for atom 1: 0.000000000000E+00 283s SASA for atom 2: 6.122920124655E-01 283s SASA for atom 3: 3.957497153740E+00 283s SASA for atom 4: 4.308445014544E+00 283s SASA for atom 5: 1.843264951960E+01 283s SASA for atom 6: 1.837011296483E+01 283s SASA for atom 7: 1.666599184724E+01 283s SASA for atom 8: 1.480031796315E+01 283s SASA for atom 9: 1.603020354037E+01 283s SASA for atom 10: 1.473778140838E+01 283s SASA for atom 11: 1.611879699297E+01 283s SASA for atom 12: 1.810954398660E+01 283s SASA for atom 13: 1.420100931324E+01 283s SASA for atom 14: 1.437298483886E+01 283s SASA for atom 15: 1.814081226399E+01 283s SASA for atom 16: 2.152820898091E+01 283s 283s Total solvent accessible surface area: 214.202 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 3.243280922127E-02 283s Surface tension*area energy for atom 1: 0.000000000000E+00 283s Surface tension*area energy for atom 2: 5.204482105957E-03 283s Surface tension*area energy for atom 3: 3.363872580679E-02 283s Surface tension*area energy for atom 4: 3.662178262362E-02 283s Surface tension*area energy for atom 5: 1.566775209166E-01 283s Surface tension*area energy for atom 6: 1.561459602010E-01 283s Surface tension*area energy for atom 7: 1.416609307015E-01 283s Surface tension*area energy for atom 8: 1.258027026868E-01 283s Surface tension*area energy for atom 9: 1.362567300932E-01 283s Surface tension*area energy for atom 10: 1.252711419712E-01 283s Surface tension*area energy for atom 11: 1.370097744402E-01 283s Surface tension*area energy for atom 12: 1.539311238861E-01 283s Surface tension*area energy for atom 13: 1.207085791625E-01 283s Surface tension*area energy for atom 14: 1.221703711303E-01 283s Surface tension*area energy for atom 15: 1.541969042439E-01 283s Surface tension*area energy for atom 16: 1.829897763377E-01 283s 283s Total surface tension energy: 1.82072 kJ/mol 283s 283s Total solvent accessible volume: 253.665 A^3 283s 283s Total pressure*volume energy: 60.7274 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.271287875274E+00 283s WCA energy for atom 1: -5.600872869478E+00 283s WCA energy for atom 2: -5.773775123943E+00 283s WCA energy for atom 3: -6.072801488986E+00 283s WCA energy for atom 4: -6.378470721845E+00 283s WCA energy for atom 5: -1.573474558351E+00 283s WCA energy for atom 6: -1.582338715648E+00 283s WCA energy for atom 7: -1.504044838266E+00 283s WCA energy for atom 8: -1.351002262819E+00 283s WCA energy for atom 9: -1.437367175239E+00 283s WCA energy for atom 10: -1.384626257493E+00 283s WCA energy for atom 11: -1.468867560891E+00 283s WCA energy for atom 12: -1.557005662832E+00 283s WCA energy for atom 13: -1.473759654043E+00 283s WCA energy for atom 14: -1.502261431335E+00 283s WCA energy for atom 15: -1.550940901474E+00 283s WCA energy for atom 16: -1.667828659696E+00 283s 283s Total WCA energy: -48.1507 kJ/mol 283s 283s Total non-polar energy = 1.439739455792E+01 kJ/mol 283s ---------------------------------------- 283s CALCULATION #2 (solvated-butane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 4.405515699447E+00 283s SASA for atom 1: 8.213673337951E-01 283s SASA for atom 2: 8.064333822716E-01 283s SASA for atom 3: 4.375647796400E+00 283s SASA for atom 4: 1.855251124959E+01 283s SASA for atom 5: 2.147609518526E+01 283s SASA for atom 6: 1.852645435176E+01 283s SASA for atom 7: 1.660345529247E+01 283s SASA for atom 8: 1.658782115377E+01 283s SASA for atom 9: 1.658260977421E+01 283s SASA for atom 10: 1.658260977421E+01 283s SASA for atom 11: 2.145003828744E+01 283s SASA for atom 12: 1.852124297220E+01 283s SASA for atom 13: 1.856293400871E+01 283s 283s Total solvent accessible surface area: 193.855 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 3.744688344530E-02 283s Surface tension*area energy for atom 1: 6.981622337259E-03 283s Surface tension*area energy for atom 2: 6.854683749309E-03 283s Surface tension*area energy for atom 3: 3.719300626940E-02 283s Surface tension*area energy for atom 4: 1.576963456215E-01 283s Surface tension*area energy for atom 5: 1.825468090747E-01 283s Surface tension*area energy for atom 6: 1.574748619900E-01 283s Surface tension*area energy for atom 7: 1.411293699860E-01 283s Surface tension*area energy for atom 8: 1.409964798071E-01 283s Surface tension*area energy for atom 9: 1.409521830808E-01 283s Surface tension*area energy for atom 10: 1.409521830808E-01 283s Surface tension*area energy for atom 11: 1.823253254433E-01 283s Surface tension*area energy for atom 12: 1.574305652637E-01 283s Surface tension*area energy for atom 13: 1.577849390741E-01 283s 283s Total surface tension energy: 1.64777 kJ/mol 283s 283s Total solvent accessible volume: 217.863 A^3 283s 283s Total pressure*volume energy: 52.1564 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.728858147814E+00 283s WCA energy for atom 1: -6.204037472587E+00 283s WCA energy for atom 2: -6.202937735018E+00 283s WCA energy for atom 3: -6.728762249931E+00 283s WCA energy for atom 4: -1.623549989062E+00 283s WCA energy for atom 5: -1.709092300778E+00 283s WCA energy for atom 6: -1.625196457114E+00 283s WCA energy for atom 7: -1.484289341167E+00 283s WCA energy for atom 8: -1.485410538626E+00 283s WCA energy for atom 9: -1.485593139015E+00 283s WCA energy for atom 10: -1.484878734279E+00 283s WCA energy for atom 11: -1.708585062695E+00 283s WCA energy for atom 12: -1.625094916482E+00 283s WCA energy for atom 13: -1.624416805392E+00 283s 283s Total WCA energy: -41.7207 kJ/mol 283s 283s Total non-polar energy = 1.208346456826E+01 kJ/mol 283s ---------------------------------------- 283s CALCULATION #3 (solvated-cyclohexane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 7.840324549863E-01 283s SASA for atom 1: 8.064333822716E-01 283s SASA for atom 2: 8.288343095569E-01 283s SASA for atom 3: 7.840324549863E-01 283s SASA for atom 4: 7.989664065098E-01 283s SASA for atom 5: 8.363012853187E-01 283s SASA for atom 6: 2.001169752764E+01 283s SASA for atom 7: 1.616048802948E+01 283s SASA for atom 8: 2.001169752764E+01 283s SASA for atom 9: 1.619175630687E+01 283s SASA for atom 10: 1.616048802948E+01 283s SASA for atom 11: 1.993352683418E+01 283s SASA for atom 12: 2.001169752764E+01 283s SASA for atom 13: 1.618133354774E+01 283s SASA for atom 14: 1.617091078861E+01 283s SASA for atom 15: 2.001690890721E+01 283s SASA for atom 16: 1.993873821374E+01 283s SASA for atom 17: 1.617091078861E+01 283s 283s Total solvent accessible surface area: 221.799 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 6.664275867383E-03 283s Surface tension*area energy for atom 1: 6.854683749309E-03 283s Surface tension*area energy for atom 2: 7.045091631234E-03 283s Surface tension*area energy for atom 3: 6.664275867383E-03 283s Surface tension*area energy for atom 4: 6.791214455333E-03 283s Surface tension*area energy for atom 5: 7.108560925209E-03 283s Surface tension*area energy for atom 6: 1.700994289850E-01 283s Surface tension*area energy for atom 7: 1.373641482506E-01 283s Surface tension*area energy for atom 8: 1.700994289850E-01 283s Surface tension*area energy for atom 9: 1.376299286084E-01 283s Surface tension*area energy for atom 10: 1.373641482506E-01 283s Surface tension*area energy for atom 11: 1.694349780905E-01 283s Surface tension*area energy for atom 12: 1.700994289850E-01 283s Surface tension*area energy for atom 13: 1.375413351558E-01 283s Surface tension*area energy for atom 14: 1.374527417032E-01 283s Surface tension*area energy for atom 15: 1.701437257113E-01 283s Surface tension*area energy for atom 16: 1.694792748168E-01 283s Surface tension*area energy for atom 17: 1.374527417032E-01 283s 283s Total surface tension energy: 1.88529 kJ/mol 283s 283s Total solvent accessible volume: 267.435 A^3 283s 283s Total pressure*volume energy: 64.0239 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -5.793234697241E+00 283s WCA energy for atom 1: -5.784370526583E+00 283s WCA energy for atom 2: -5.791799130412E+00 283s WCA energy for atom 3: -5.788504399087E+00 283s WCA energy for atom 4: -5.797319672490E+00 283s WCA energy for atom 5: -5.787358035342E+00 283s WCA energy for atom 6: -1.523887929614E+00 283s WCA energy for atom 7: -1.413678912317E+00 283s WCA energy for atom 8: -1.521751604392E+00 283s WCA energy for atom 9: -1.414741802525E+00 283s WCA energy for atom 10: -1.413367854344E+00 283s WCA energy for atom 11: -1.523407238081E+00 283s WCA energy for atom 12: -1.523000623583E+00 283s WCA energy for atom 13: -1.413922068538E+00 283s WCA energy for atom 14: -1.416316744211E+00 283s WCA energy for atom 15: -1.524577474659E+00 283s WCA energy for atom 16: -1.523300410052E+00 283s WCA energy for atom 17: -1.414522566061E+00 283s 283s Total WCA energy: -52.3691 kJ/mol 283s 283s Total non-polar energy = 1.354016672221E+01 kJ/mol 283s ---------------------------------------- 283s CALCULATION #4 (solvated-cyclopentane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 9.490526193215E+00 283s SASA for atom 1: 9.512927120500E+00 283s SASA for atom 2: 2.299828534626E+00 283s SASA for atom 3: 1.919012770776E+00 283s SASA for atom 4: 2.307295510388E+00 283s SASA for atom 5: 2.325838699632E+01 283s SASA for atom 6: 2.325838699632E+01 283s SASA for atom 7: 2.045987617019E+01 283s SASA for atom 8: 2.067875411190E+01 283s SASA for atom 9: 2.028790064456E+01 283s SASA for atom 10: 1.897463299431E+01 283s SASA for atom 11: 2.048593306801E+01 283s SASA for atom 12: 2.070481100972E+01 283s 283s Total solvent accessible surface area: 193.638 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 8.066947264233E-02 283s Surface tension*area energy for atom 1: 8.085988052425E-02 283s Surface tension*area energy for atom 2: 1.954854254432E-02 283s Surface tension*area energy for atom 3: 1.631160855160E-02 283s Surface tension*area energy for atom 4: 1.961201183830E-02 283s Surface tension*area energy for atom 5: 1.976962894687E-01 283s Surface tension*area energy for atom 6: 1.976962894687E-01 283s Surface tension*area energy for atom 7: 1.739089474466E-01 283s Surface tension*area energy for atom 8: 1.757694099511E-01 283s Surface tension*area energy for atom 9: 1.724471554788E-01 283s Surface tension*area energy for atom 10: 1.612843804516E-01 283s Surface tension*area energy for atom 11: 1.741304310781E-01 283s Surface tension*area energy for atom 12: 1.759908935826E-01 283s 283s Total surface tension energy: 1.64593 kJ/mol 283s 283s Total solvent accessible volume: 217.998 A^3 283s 283s Total pressure*volume energy: 52.1887 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.343496616804E+00 283s WCA energy for atom 1: -6.327869601807E+00 283s WCA energy for atom 2: -6.334858040579E+00 283s WCA energy for atom 3: -6.296075406417E+00 283s WCA energy for atom 4: -6.345600816761E+00 283s WCA energy for atom 5: -1.663697465126E+00 283s WCA energy for atom 6: -1.662444032853E+00 283s WCA energy for atom 7: -1.572325104493E+00 283s WCA energy for atom 8: -1.604626551065E+00 283s WCA energy for atom 9: -1.586431484963E+00 283s WCA energy for atom 10: -1.554291291374E+00 283s WCA energy for atom 11: -1.574315220751E+00 283s WCA energy for atom 12: -1.604941679892E+00 283s 283s Total WCA energy: -44.471 kJ/mol 283s 283s Total non-polar energy = 9.363673200142E+00 kJ/mol 283s ---------------------------------------- 283s CALCULATION #5 (solvated-ethane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 5.995981536705E+00 283s SASA for atom 1: 5.966113633657E+00 283s SASA for atom 2: 2.121552620704E+01 283s SASA for atom 3: 2.124158310486E+01 283s SASA for atom 4: 2.125200586399E+01 283s SASA for atom 5: 2.123116034573E+01 283s SASA for atom 6: 2.125200586399E+01 283s SASA for atom 7: 2.127285138225E+01 283s 283s Total solvent accessible surface area: 139.427 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 5.096584306199E-02 283s Surface tension*area energy for atom 1: 5.071196588609E-02 283s Surface tension*area energy for atom 2: 1.803319727598E-01 283s Surface tension*area energy for atom 3: 1.805534563913E-01 283s Surface tension*area energy for atom 4: 1.806420498439E-01 283s Surface tension*area energy for atom 5: 1.804648629387E-01 283s Surface tension*area energy for atom 6: 1.806420498439E-01 283s Surface tension*area energy for atom 7: 1.808192367491E-01 283s 283s Total surface tension energy: 1.18513 kJ/mol 283s 283s Total solvent accessible volume: 140.346 A^3 283s 283s Total pressure*volume energy: 33.5988 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -7.360066353115E+00 283s WCA energy for atom 1: -7.355483516201E+00 283s WCA energy for atom 2: -1.776106201066E+00 283s WCA energy for atom 3: -1.773973940651E+00 283s WCA energy for atom 4: -1.775401936843E+00 283s WCA energy for atom 5: -1.773464835521E+00 283s WCA energy for atom 6: -1.774382856097E+00 283s WCA energy for atom 7: -1.772366599434E+00 283s 283s Total WCA energy: -25.3612 kJ/mol 283s 283s Total non-polar energy = 9.422717598546E+00 kJ/mol 283s ---------------------------------------- 283s CALCULATION #6 (solvated-hexane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 4.405515699447E+00 283s SASA for atom 1: 8.213673337951E-01 283s SASA for atom 2: 3.285469335181E-01 283s SASA for atom 3: 2.986790304710E-01 283s SASA for atom 4: 1.855251124959E+01 283s SASA for atom 5: 2.147609518526E+01 283s SASA for atom 6: 1.852645435176E+01 283s SASA for atom 7: 1.655655287639E+01 283s SASA for atom 8: 1.655134149682E+01 283s SASA for atom 9: 1.360170066332E+01 283s SASA for atom 10: 1.357043238593E+01 283s SASA for atom 11: 1.381536722546E+01 283s SASA for atom 12: 1.384142412329E+01 283s SASA for atom 13: 7.765654792245E-01 283s SASA for atom 14: 1.684839013200E+01 283s SASA for atom 15: 1.682233323417E+01 283s SASA for atom 16: 4.166572475070E+00 283s SASA for atom 17: 2.179398933870E+01 283s SASA for atom 18: 1.877660057086E+01 283s SASA for atom 19: 1.876096643216E+01 283s 283s Total solvent accessible surface area: 250.291 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 3.744688344530E-02 283s Surface tension*area energy for atom 1: 6.981622337259E-03 283s Surface tension*area energy for atom 2: 2.792648934903E-03 283s Surface tension*area energy for atom 3: 2.538771759003E-03 283s Surface tension*area energy for atom 4: 1.576963456215E-01 283s Surface tension*area energy for atom 5: 1.825468090747E-01 283s Surface tension*area energy for atom 6: 1.574748619900E-01 283s Surface tension*area energy for atom 7: 1.407306994493E-01 283s Surface tension*area energy for atom 8: 1.406864027230E-01 283s Surface tension*area energy for atom 9: 1.156144556382E-01 283s Surface tension*area energy for atom 10: 1.153486752804E-01 283s Surface tension*area energy for atom 11: 1.174306214164E-01 283s Surface tension*area energy for atom 12: 1.176521050479E-01 283s Surface tension*area energy for atom 13: 6.600806573408E-03 283s Surface tension*area energy for atom 14: 1.432113161220E-01 283s Surface tension*area energy for atom 15: 1.429898324905E-01 283s Surface tension*area energy for atom 16: 3.541586603809E-02 283s Surface tension*area energy for atom 17: 1.852489093789E-01 283s Surface tension*area energy for atom 18: 1.596011048523E-01 283s Surface tension*area energy for atom 19: 1.594682146734E-01 283s 283s Total surface tension energy: 2.12748 kJ/mol 283s 283s Total solvent accessible volume: 298.053 A^3 283s 283s Total pressure*volume energy: 71.3539 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.635406071935E+00 283s WCA energy for atom 1: -5.957247427848E+00 283s WCA energy for atom 2: -5.524801144538E+00 283s WCA energy for atom 3: -5.522294168859E+00 283s WCA energy for atom 4: -1.605314409440E+00 283s WCA energy for atom 5: -1.701051761776E+00 283s WCA energy for atom 6: -1.606669162773E+00 283s WCA energy for atom 7: -1.442505934938E+00 283s WCA energy for atom 8: -1.443059002759E+00 283s WCA energy for atom 9: -1.328947132810E+00 283s WCA energy for atom 10: -1.328906972440E+00 283s WCA energy for atom 11: -1.331566344214E+00 283s WCA energy for atom 12: -1.328041776815E+00 283s WCA energy for atom 13: -5.937562025661E+00 283s WCA energy for atom 14: -1.442277774427E+00 283s WCA energy for atom 15: -1.442777091510E+00 283s WCA energy for atom 16: -6.602262542378E+00 283s WCA energy for atom 17: -1.698172146664E+00 283s WCA energy for atom 18: -1.600970858835E+00 283s WCA energy for atom 19: -1.600841970217E+00 283s 283s Total WCA energy: -57.0807 kJ/mol 283s 283s Total non-polar energy = 1.640068943201E+01 kJ/mol 283s ---------------------------------------- 283s CALCULATION #7 (solvated-isobutane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 3.464676753463E+00 283s SASA for atom 1: 1.984493338158E+01 283s SASA for atom 2: 1.778643845361E+01 283s SASA for atom 3: 1.671289426332E+01 283s SASA for atom 4: 0.000000000000E+00 283s SASA for atom 5: 3.531879535319E+00 283s SASA for atom 6: 1.673895116114E+01 283s SASA for atom 7: 1.793756846098E+01 283s SASA for atom 8: 1.973549441072E+01 283s SASA for atom 9: 1.710895911022E+01 283s SASA for atom 10: 4.599657069253E+00 283s SASA for atom 11: 1.937069784121E+01 283s SASA for atom 12: 1.654613011726E+01 283s SASA for atom 13: 1.936548646165E+01 283s 283s Total solvent accessible surface area: 192.744 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 2.944975240444E-02 283s Surface tension*area energy for atom 1: 1.686819337434E-01 283s Surface tension*area energy for atom 2: 1.511847268556E-01 283s Surface tension*area energy for atom 3: 1.420596012382E-01 283s Surface tension*area energy for atom 4: 0.000000000000E+00 283s Surface tension*area energy for atom 5: 3.002097605021E-02 283s Surface tension*area energy for atom 6: 1.422810848697E-01 283s Surface tension*area energy for atom 7: 1.524693319183E-01 283s Surface tension*area energy for atom 8: 1.677517024912E-01 283s Surface tension*area energy for atom 9: 1.454261524369E-01 283s Surface tension*area energy for atom 10: 3.909708508865E-02 283s Surface tension*area energy for atom 11: 1.646509316503E-01 283s Surface tension*area energy for atom 12: 1.406421059967E-01 283s Surface tension*area energy for atom 13: 1.646066349240E-01 283s 283s Total surface tension energy: 1.63832 kJ/mol 283s 283s Total solvent accessible volume: 218.943 A^3 283s 283s Total pressure*volume energy: 52.415 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.381016335247E+00 283s WCA energy for atom 1: -1.612317964554E+00 283s WCA energy for atom 2: -1.588013719598E+00 283s WCA energy for atom 3: -1.532162371190E+00 283s WCA energy for atom 4: -5.987950445279E+00 283s WCA energy for atom 5: -6.393089030861E+00 283s WCA energy for atom 6: -1.533454887042E+00 283s WCA energy for atom 7: -1.587650918485E+00 283s WCA energy for atom 8: -1.614083521570E+00 283s WCA energy for atom 9: -1.442402031577E+00 283s WCA energy for atom 10: -6.408813541353E+00 283s WCA energy for atom 11: -1.605830214390E+00 283s WCA energy for atom 12: -1.529385873788E+00 283s WCA energy for atom 13: -1.605662490385E+00 283s 283s Total WCA energy: -40.8218 kJ/mol 283s 283s Total non-polar energy = 1.323144287435E+01 kJ/mol 283s ---------------------------------------- 283s CALCULATION #8 (solvated-methane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 1.231304303117E+01 283s SASA for atom 1: 2.323233009850E+01 283s SASA for atom 2: 2.345641941977E+01 283s SASA for atom 3: 2.377431357320E+01 283s SASA for atom 4: 2.264344420771E+01 283s 283s Total solvent accessible surface area: 105.42 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 1.046608657649E-01 283s Surface tension*area energy for atom 1: 1.974748058372E-01 283s Surface tension*area energy for atom 2: 1.993795650680E-01 283s Surface tension*area energy for atom 3: 2.020816653722E-01 283s Surface tension*area energy for atom 4: 1.924692757655E-01 283s 283s Total surface tension energy: 0.896066 kJ/mol 283s 283s Total solvent accessible volume: 95.985 A^3 283s 283s Total pressure*volume energy: 22.9788 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -8.133807570805E+00 283s WCA energy for atom 1: -1.962181541765E+00 283s WCA energy for atom 2: -1.964078319162E+00 283s WCA energy for atom 3: -1.963015006647E+00 283s WCA energy for atom 4: -1.957425549100E+00 283s 283s Total WCA energy: -15.9805 kJ/mol 283s 283s Total non-polar energy = 7.894367190329E+00 kJ/mol 283s ---------------------------------------- 283s CALCULATION #9 (solvated-neopentane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 2.441701074100E+00 283s SASA for atom 1: 1.663993494942E+01 283s SASA for atom 2: 1.715586152630E+01 283s SASA for atom 3: 1.645753666466E+01 283s SASA for atom 4: 0.000000000000E+00 283s SASA for atom 5: 2.389432243768E+00 283s SASA for atom 6: 1.638457735076E+01 283s SASA for atom 7: 1.667641460637E+01 283s SASA for atom 8: 1.721839808108E+01 283s SASA for atom 9: 2.419300146815E+00 283s SASA for atom 10: 1.640021148945E+01 283s SASA for atom 11: 1.666599184724E+01 283s SASA for atom 12: 1.719234118325E+01 283s SASA for atom 13: 2.449168049862E+00 283s SASA for atom 14: 1.723403221977E+01 283s SASA for atom 15: 1.639500010989E+01 283s SASA for atom 16: 1.663472356985E+01 283s 283s Total solvent accessible surface area: 210.755 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 2.075445912985E-02 283s Surface tension*area energy for atom 1: 1.414394470700E-01 283s Surface tension*area energy for atom 2: 1.458248229736E-01 283s Surface tension*area energy for atom 3: 1.398890616496E-01 283s Surface tension*area energy for atom 4: 0.000000000000E+00 283s Surface tension*area energy for atom 5: 2.031017407203E-02 283s Surface tension*area energy for atom 6: 1.392689074814E-01 283s Surface tension*area energy for atom 7: 1.417495241541E-01 283s Surface tension*area energy for atom 8: 1.463563836891E-01 283s Surface tension*area energy for atom 9: 2.056405124793E-02 283s Surface tension*area energy for atom 10: 1.394017976603E-01 283s Surface tension*area energy for atom 11: 1.416609307015E-01 283s Surface tension*area energy for atom 12: 1.461349000577E-01 283s Surface tension*area energy for atom 13: 2.081792842383E-02 283s Surface tension*area energy for atom 14: 1.464892738680E-01 283s Surface tension*area energy for atom 15: 1.393575009340E-01 283s Surface tension*area energy for atom 16: 1.413951503437E-01 283s 283s Total surface tension energy: 1.79141 kJ/mol 283s 283s Total solvent accessible volume: 251.127 A^3 283s 283s Total pressure*volume energy: 60.1198 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.011082520236E+00 283s WCA energy for atom 1: -1.497367782613E+00 283s WCA energy for atom 2: -1.498546483218E+00 283s WCA energy for atom 3: -1.492562171495E+00 283s WCA energy for atom 4: -5.447325863939E+00 283s WCA energy for atom 5: -6.004516149175E+00 283s WCA energy for atom 6: -1.492776531092E+00 283s WCA energy for atom 7: -1.496078170066E+00 283s WCA energy for atom 8: -1.501529655270E+00 283s WCA energy for atom 9: -5.996267554365E+00 283s WCA energy for atom 10: -1.492194267752E+00 283s WCA energy for atom 11: -1.496027211216E+00 283s WCA energy for atom 12: -1.500561393960E+00 283s WCA energy for atom 13: -6.000218612907E+00 283s WCA energy for atom 14: -1.500859921426E+00 283s WCA energy for atom 15: -1.492908499790E+00 283s WCA energy for atom 16: -1.494057174414E+00 283s 283s Total WCA energy: -47.4149 kJ/mol 283s 283s Total non-polar energy = 1.449633815052E+01 kJ/mol 283s ---------------------------------------- 283s CALCULATION #10 (solvated-pentane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 4.405515699447E+00 283s SASA for atom 1: 8.213673337951E-01 283s SASA for atom 2: 3.285469335181E-01 283s SASA for atom 3: 7.466975761774E-01 283s SASA for atom 4: 1.855251124959E+01 283s SASA for atom 5: 2.147609518526E+01 283s SASA for atom 6: 1.852645435176E+01 283s SASA for atom 7: 1.655655287639E+01 283s SASA for atom 8: 1.655134149682E+01 283s SASA for atom 9: 1.360170066332E+01 283s SASA for atom 10: 1.357043238593E+01 283s SASA for atom 11: 1.685881289113E+01 283s SASA for atom 12: 1.687444702982E+01 283s SASA for atom 13: 4.196440378117E+00 283s SASA for atom 14: 1.881308022781E+01 283s SASA for atom 15: 1.882350298694E+01 283s SASA for atom 16: 2.182004623652E+01 283s 283s Total solvent accessible surface area: 222.524 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 3.744688344530E-02 283s Surface tension*area energy for atom 1: 6.981622337259E-03 283s Surface tension*area energy for atom 2: 2.792648934903E-03 283s Surface tension*area energy for atom 3: 6.346929397508E-03 283s Surface tension*area energy for atom 4: 1.576963456215E-01 283s Surface tension*area energy for atom 5: 1.825468090747E-01 283s Surface tension*area energy for atom 6: 1.574748619900E-01 283s Surface tension*area energy for atom 7: 1.407306994493E-01 283s Surface tension*area energy for atom 8: 1.406864027230E-01 283s Surface tension*area energy for atom 9: 1.156144556382E-01 283s Surface tension*area energy for atom 10: 1.153486752804E-01 283s Surface tension*area energy for atom 11: 1.432999095746E-01 283s Surface tension*area energy for atom 12: 1.434327997535E-01 283s Surface tension*area energy for atom 13: 3.566974321399E-02 283s Surface tension*area energy for atom 14: 1.599111819364E-01 283s Surface tension*area energy for atom 15: 1.599997753890E-01 283s Surface tension*area energy for atom 16: 1.854703930104E-01 283s 283s Total surface tension energy: 1.89145 kJ/mol 283s 283s Total solvent accessible volume: 258.93 A^3 283s 283s Total pressure*volume energy: 61.9878 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.655804319869E+00 283s WCA energy for atom 1: -6.027315962813E+00 283s WCA energy for atom 2: -5.696430965386E+00 283s WCA energy for atom 3: -6.016749084714E+00 283s WCA energy for atom 4: -1.608595384643E+00 283s WCA energy for atom 5: -1.703300955380E+00 283s WCA energy for atom 6: -1.609931495887E+00 283s WCA energy for atom 7: -1.457107525189E+00 283s WCA energy for atom 8: -1.457741620594E+00 283s WCA energy for atom 9: -1.354235498709E+00 283s WCA energy for atom 10: -1.354106470090E+00 283s WCA energy for atom 11: -1.456736412636E+00 283s WCA energy for atom 12: -1.455995435596E+00 283s WCA energy for atom 1Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 283s *** PASSED *** 283s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 283s *** PASSED *** 283s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 283s *** PASSED *** 283s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 283s *** PASSED *** 283s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 283s *** PASSED *** 283s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 283s *** PASSED *** 283s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 283s *** PASSED *** 283s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 283s *** PASSED *** 283s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 283s *** PASSED *** 283s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 283s *** PASSED *** 283s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 283s *** PASSED *** 283s Elapsed time: 15.112469 seconds 283s -------------------------------------------------------------------------------- 283s Total elapsed time: 15.112469 seconds 283s Test results have been logged 283s -------------------------------------------------------------------------------- 283s -------------------------------------------------------------------------------- 283s Testing input file 1d7h-dmso-mol.in 283s 283s 3: -6.633650611186E+00 283s WCA energy for atom 14: -1.605996088477E+00 283s WCA energy for atom 15: -1.606549890103E+00 283s WCA energy for atom 16: -1.700042300035E+00 283s 283s Total WCA energy: -49.4003 kJ/mol 283s 283s Total non-polar energy = 1.447900211546E+01 kJ/mol 283s ---------------------------------------- 283s CALCULATION #11 (solvated-propane): APOLAR 283s 283s Solvent Accessible Surface Area (SASA) for each atom: 283s SASA for atom 0: 3.173464698754E+00 283s SASA for atom 1: 1.931858404557E+01 283s SASA for atom 2: 2.014198201675E+01 283s SASA for atom 3: 2.149694070352E+01 283s SASA for atom 4: 1.904078819252E+00 283s SASA for atom 5: 2.067354273233E+01 283s SASA for atom 6: 1.937590922077E+01 283s SASA for atom 7: 3.098794941136E+00 283s SASA for atom 8: 1.942802301642E+01 283s SASA for atom 9: 1.973028303116E+01 283s SASA for atom 10: 2.204934693736E+01 283s 283s Total solvent accessible surface area: 170.391 A^2 283s 283s Surface tension*area energies (gamma * SASA) for each atom: 283s Surface tension*area energy for atom 0: 2.697444993941E-02 283s Surface tension*area energy for atom 1: 1.642079643873E-01 283s Surface tension*area energy for atom 2: 1.712068471424E-01 283s Surface tension*area energy for atom 3: 1.827239959799E-01 283s Surface tension*area energy for atom 4: 1.618466996365E-02 283s Surface tension*area energy for atom 5: 1.757251132248E-01 283s Surface tension*area energy for atom 6: 1.646952283766E-01 283s Surface tension*area energy for atom 7: 2.633975699966E-02 283s Surface tension*area energy for atom 8: 1.651381956396E-01 283s Surface tension*area energy for atom 9: 1.677074057649E-01 283s Surface tension*area energy for atom 10: 1.874194489675E-01 283s 283s Total surface tension energy: 1.44832 kJ/mol 283s 283s Total solvent accessible volume: 183.573 A^3 283s 283s Total pressure*volume energy: 43.9474 kJ/mol 283s 283s WCA dispersion Energies for each atom: 283s WCA energy for atom 0: -6.818670105515E+00 283s WCA energy for atom 1: -1.641297645338E+00 283s WCA energy for atom 2: -1.649584120441E+00 283s WCA energy for atom 3: -1.711408141255E+00 283s WCA energy for atom 4: -6.624720142882E+00 283s WCA energy for atom 5: -1.610117050515E+00 283s WCA energy for atom 6: -1.596858009746E+00 283s WCA energy for atom 7: -6.816460624835E+00 283s WCA energy for atom 8: -1.642782751806E+00 283s WCA energy for atom 9: -1.645779566650E+00 283s WCA energy for atom 10: -1.714436154542E+00 283s 283s Total WCA energy: -33.4721 kJ/mol 283s 283s Total non-polar energy = 1.192358496286E+01 kJ/mol 283s ---------------------------------------- 283s PRINT STATEMENTS 283s 283s print APOL energy 1 (solvated-2-methylbutane) end 283s Global net APOL energy = 1.439739455792E+01 kJ/mol 283s 283s print APOL energy 2 (solvated-butane) end 283s Global net APOL energy = 1.208346456826E+01 kJ/mol 283s 283s print APOL energy 3 (solvated-cyclohexane) end 283s Global net APOL energy = 1.354016672221E+01 kJ/mol 283s 283s print APOL energy 4 (solvated-cyclopentane) end 283s Global net APOL energy = 9.363673200142E+00 kJ/mol 283s 283s print APOL energy 5 (solvated-ethane) end 283s Global net APOL energy = 9.422717598546E+00 kJ/mol 283s 283s print APOL energy 6 (solvated-hexane) end 283s Global net APOL energy = 1.640068943201E+01 kJ/mol 283s 283s print APOL energy 7 (solvated-isobutane) end 283s Global net APOL energy = 1.323144287435E+01 kJ/mol 283s 283s print APOL energy 8 (solvated-methane) end 283s Global net APOL energy = 7.894367190329E+00 kJ/mol 283s 283s print APOL energy 9 (solvated-neopentane) end 283s Global net APOL energy = 1.449633815052E+01 kJ/mol 283s 283s print APOL energy 10 (solvated-pentane) end 283s Global net APOL energy = 1.447900211546E+01 kJ/mol 283s 283s print APOL energy 11 (solvated-propane) end 283s Global net APOL energy = 1.192358496286E+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 11 molecules 283s Final memory usage: 0.001 MB total, 2.267 MB high water 283s 283s 283s Thanks for using APBS! 283s 293s Checking for intermediate energies in input file alkanes.out 293s EXPECTED COMPUTED: 11 293s EXPECTED EXPECTED: 11 293s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 293s 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'] 293s COMPUTED RESULT 14.39739455792 293s COMPUTED RESULT 12.08346456826 293s COMPUTED RESULT 13.54016672221 293s COMPUTED RESULT 9.363673200142 293s COMPUTED RESULT 9.422717598546 293s COMPUTED RESULT 16.40068943201 293s COMPUTED RESULT 13.23144287435 293s COMPUTED RESULT 7.894367190329 293s COMPUTED RESULT 14.49633815052 293s COMPUTED RESULT 14.47900211546 293s COMPUTED RESULT 11.92358496286 293s Running tests for FKBP section 293s BINARY: /usr/bin/apbs 293s INPUT: 1d7h-dmso-mol.in 293s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 293s asc_getToken: Error occurred (bailing out). 293s Vio_scanf: Format problem with input. 293s 293s 293s ---------------------------------------------------------------------- 293s APBS -- Adaptive Poisson-Boltzmann Solver 293s Version APBS 3.4.1 293s 293s Nathan A. Baker (nathan.baker@pnnl.gov) 293s Pacific Northwest National Laboratory 293s 293s Additional contributing authors listed in the code documentation. 293s 293s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 293s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 293s Northwest Division for the U.S. Department of Energy. 293s 293s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 293s Portions Copyright (c) 2002-2020, Nathan A. Baker. 293s Portions Copyright (c) 1999-2002, The Regents of the University of California. 293s Portions Copyright (c) 1995, Michael Holst. 293s All rights reserved. 293s 293s Redistribution and use in source and binary forms, with or without 293s modification, are permitted provided that the following conditions are met: 293s 293s * Redistributions of source code must retain the above copyright notice, this 293s list of conditions and the following disclaimer. 293s 293s * Redistributions in binary form must reproduce the above copyright notice, 293s this list of conditions and the following disclaimer in the documentation 293s and/or other materials provided with the distribution. 293s 293s * Neither the name of the developer nor the names of its contributors may be 293s used to endorse or promote products derived from this software without 293s specific prior written permission. 293s 293s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 293s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 293s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 293s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 293s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 293s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 293s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 293s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 293s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 293s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 293s ---------------------------------------------------------------------- 293s APBS uses FETK (the Finite Element ToolKit) to solve the 293s Poisson-Boltzmann equation numerically. FETK is a portable collection 293s of finite element modeling class libraries developed by the Michael Holst 293s research group and written in an object-oriented form of C. FEtk is 293s designed to solve general coupled systems of nonlinear partial differential 293s equations using adaptive finite element methods, inexact Newton methods, 293s and algebraic multilevel methods. More information about FEtk may be found 293s at . 293s ---------------------------------------------------------------------- 293s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 293s Aqua is a modified form of the Holst group PMG library 293s which has been modified by Patrice Koehl 293s for improved efficiency and 293s memory usage when solving the Poisson-Boltzmann equation. 293s ---------------------------------------------------------------------- 293s Please cite your use of APBS as: 293s 293s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 293s nanosystems: application to microtubules and the ribosome. Proc. 293s Natl. Acad. Sci. USA 98, 10037-10041 2001. 293s 293s 293s This executable compiled on Jan 3 2025 at 11:01:42 293s 293s Parsing input file 1d7h-dmso-mol.in... 293s rank 0 size 1... 293s Parsed input file. 293s Got paths for 3 molecules 293s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 293s asc_getToken: Error occurred (bailing out). 293s Vio_scanf: Format problem with input. 293s 1673 atoms 293s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 293s Net charge 9.91e-01 e 293s Reading PQR-format atom data from dmso-min.pqr. 293s asc_getToken: Error occurred (bailing out). 293s Vio_scanf: Format problem with input. 293s 10 atoms 293s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 293s Net charge 2.78e-17 e 293s Reading PQR-format atom data from 1d7h-min.pqr. 293s 1663 atoms 293s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 293s Net charge 9.91e-01 e 293s Preparing to run 12 PBE calculations. 293s ---------------------------------------- 293s CALCULATION #1 (complex-solv-coarse): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 30.4176 A 293s Current memory usage: 122.059 MB total, 122.059 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 1.500 x 1.500 x 1.500 293s Grid lengths: 96.000 x 96.000 x 96.000 293s Grid center: (25.875, 18.349, 19.112) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.060899690259E+04 kJ/mol 293s Calculating forces... 293s [focusFillBound()]: WARNING: 293s Unusually large potential values 293s detected on the focusing boundary! 293s Convergence not guaranteed for NPBE/NRPBE calculations! 293s 293s ---------------------------------------- 293s CALCULATION #2 (complex-solv-fine): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 30.4176 A 293s Current memory usage: 122.059 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.225 x 0.225 x 0.225 293s Grid lengths: 14.400 x 14.400 x 14.400 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 4.276523673491E+04 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #3 (complex-ref-coarse): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 4.87072 A 293s Current memory usage: 122.059 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 1.500 x 1.500 x 1.500 293s Grid lengths: 96.000 x 96.000 x 96.000 293s Grid center: (25.875, 18.349, 19.112) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 2.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.399234956777E+04 kJ/mol 293s Calculating forces... 293s [focusFillBound()]: WARNING: 293s Unusually large potential values 293s detected on the focusing boundary! 293s Convergence not guaranteed for NPBE/NRPBE calculations! 293s 293s ---------------------------------------- 293s CALCULATION #4 (complex-ref-fine): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 4.87072 A 293s Current memory usage: 122.059 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.225 x 0.225 x 0.225 293s Grid lengths: 14.400 x 14.400 x 14.400 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 1 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 2.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 4.610066575192E+04 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 30.4176 A 293s Current memory usage: 62.428 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 1.500 x 1.500 x 1.500 293s Grid lengths: 96.000 x 96.000 x 96.000 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 2 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 3.961107503213E+01 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #6 (dmso-solv-fine): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 30.4176 A 293s Current memory usage: 62.428 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.225 x 0.225 x 0.225 293s Grid lengths: 14.400 x 14.400 x 14.400 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 2 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 7.121048606059E+02 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 4.87072 A 293s Current memory usage: 62.428 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 1.500 x 1.500 x 1.500 293s Grid lengths: 96.000 x 96.000 x 96.000 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 2 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 2.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 6.751571424823E+01 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #8 (dmso-ref-fine): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 4.87072 A 293s Current memory usage: 62.428 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.225 x 0.225 x 0.225 293s Grid lengths: 14.400 x 14.400 x 14.400 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 2 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 2.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 7.339101343121E+02 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 30.4176 A 293s Current memory usage: 121.736 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 1.500 x 1.500 x 1.500 293s Grid lengths: 96.000 x 96.000 x 96.000 293s Grid center: (25.875, 18.349, 19.112) 293s Multigrid levels: 5 293s Molecule ID: 3 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.058410584089E+04 kJ/mol 293s Calculating forces... 293s [focusFillBound()]: WARNING: 293s Unusually large potential values 293s detected on the focusing boundary! 293s Convergence not guaranteed for NPBE/NRPBE calculations! 293s 293s ---------------------------------------- 293s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 30.4176 A 293s Current memory usage: 121.736 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.225 x 0.225 x 0.225 293s Grid lengths: 14.400 x 14.400 x 14.400 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 3 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 4.205385249581E+04 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 4.87072 A 293s Current memory usage: 121.736 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 1.500 x 1.500 x 1.500 293s Grid lengths: 96.000 x 96.000 x 96.000 293s Grid center: (25.875, 18.349, 19.112) 293s Multigrid levels: 5 293s Molecule ID: 3 293s Linearized traditional PBE 293s Multiple Debye-Huckel sphere boundary conditions 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 2.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.395961902233E+04 kJ/mol 293s Calculating forces... 293s [focusFillBound()]: WARNING: 293s Unusually large potential values 293s detected on the focusing boundary! 293s Convergence not guaranteed for NPBE/NRPBE calculations! 293s 293s ---------------------------------------- 293s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 4.87072 A 293s Current memory usage: 121.736 MB total, 221.696 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.225 x 0.225 x 0.225 293s Grid lengths: 14.400 x 14.400 x 14.400 293s Grid center: (17.751, 17.770, 20.492) 293s Multigrid levels: 5 293s Molecule ID: 3 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.010 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 2.000 293s Using "molecular" surface definition; no smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 300.000 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 4.538248433997E+04 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s PRINT STATEMENTS 293s 293s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 293s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 293s Global net ELEC energy = -3.335429017008E+03 kJ/mol 293s 293s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 293s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 293s Global net ELEC energy = -2.180527370616E+01 kJ/mol 293s 293s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 293s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 293s Global net ELEC energy = -3.328631844166E+03 kJ/mol 293s 293s 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 293s Local net energy (PE 0) = 1.500810086373E+01 kJ/mol 293s Global net ELEC energy = 1.500810086373E+01 kJ/mol 293s ---------------------------------------- 293s CLEANING UP AND SHUTTING DOWN... 293s Destroying force arrays. 293s No energy arrays to destroy. 293s Destroying multigrid structures. 293s Destroying finite element structures. 293s Destroying 3 molecules 293s Final memory usage: 0.001 MB total, 221.696 MB high water 293s 293s 293s Thanks for using APBS! 293s 293s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 293s *** PASSED *** 293s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 293s *** PASSED *** 293s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 293s *** PASSED *** 293s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 293s *** PASSED *** 293s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 293s *** PASSED *** 293s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 293s *** PASSED *** 293s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 293s *** PASSED *** 293s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 293s *** PASSED *** 293s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 293s *** PASSED *** 293s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 293s *** PASSED *** 293s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 293s *** PASSED *** 293s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 293s *** PASSED *** 293s Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) 293s *** PASSED *** 293s Elapsed time: 10.612093 seconds 293s -------------------------------------------------------------------------------- 293s -------------------------------------------------------------------------------- 293s Testing input file 1d7h-dmso-smol.in 293s 303s Checking for intermediate energies in input file 1d7h-dmso-mol.out 303s EXPECTED COMPUTED: 16 303s EXPECTED EXPECTED: 16 303s 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] 303s 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'] 303s COMPUTED RESULT 10608.99690259 303s COMPUTED RESULT 42765.23673491 303s COMPUTED RESULT 13992.34956777 303s COMPUTED RESULT 46100.66575192 303s COMPUTED RESULT 39.61107503213 303s COMPUTED RESULT 712.1048606059 303s COMPUTED RESULT 67.51571424823 303s COMPUTED RESULT 733.9101343121 303s COMPUTED RESULT 10584.10584089 303s COMPUTED RESULT 42053.85249581 303s COMPUTED RESULT 13959.61902233 303s COMPUTED RESULT 45382.48433997 303s COMPUTED RESULT -3335.429017008 303s COMPUTED RESULT -21.80527370616 303s COMPUTED RESULT -3328.631844166 303s COMPUTED RESULT 15.00810086373 303s BINARY: /usr/bin/apbs 303s INPUT: 1d7h-dmso-smol.in 303s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 303s asc_getToken: Error occurred (bailing out). 303s Vio_scanf: Format problem with input. 303s 303s 303s ---------------------------------------------------------------------- 303s APBS -- Adaptive Poisson-Boltzmann Solver 303s Version APBS 3.4.1 303s 303s Nathan A. Baker (nathan.baker@pnnl.gov) 303s Pacific Northwest National Laboratory 303s 303s Additional contributing authors listed in the code documentation. 303s 303s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 303s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 303s Northwest Division for the U.S. Department of Energy. 303s 303s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 303s Portions Copyright (c) 2002-2020, Nathan A. Baker. 303s Portions Copyright (c) 1999-2002, The Regents of the University of California. 303s Portions Copyright (c) 1995, Michael Holst. 303s All rights reserved. 303s 303s Redistribution and use in source and binary forms, with or without 303s modification, are permitted provided that the following conditions are met: 303s 303s * Redistributions of source code must retain the above copyright notice, this 303s list of conditions and the following disclaimer. 303s 303s * Redistributions in binary form must reproduce the above copyright notice, 303s this list of conditions and the following disclaimer in the documentation 303s and/or other materials provided with the distribution. 303s 303s * Neither the name of the developer nor the names of its contributors may be 303s used to endorse or promote products derived from this software without 303s specific prior written permission. 303s 303s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 303s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 303s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 303s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 303s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 303s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 303s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 303s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 303s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 303s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 303s ---------------------------------------------------------------------- 303s APBS uses FETK (the Finite Element ToolKit) to solve the 303s Poisson-Boltzmann equation numerically. FETK is a portable collection 303s of finite element modeling class libraries developed by the Michael Holst 303s research group and written in an object-oriented form of C. FEtk is 303s designed to solve general coupled systems of nonlinear partial differential 303s equations using adaptive finite element methods, inexact Newton methods, 303s and algebraic multilevel methods. More information about FEtk may be found 303s at . 303s ---------------------------------------------------------------------- 303s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 303s Aqua is a modified form of the Holst group PMG library 303s which has been modified by Patrice Koehl 303s for improved efficiency and 303s memory usage when solving the Poisson-Boltzmann equation. 303s ---------------------------------------------------------------------- 303s Please cite your use of APBS as: 303s 303s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 303s nanosystems: application to microtubules and the ribosome. Proc. 303s Natl. Acad. Sci. USA 98, 10037-10041 2001. 303s 303s 303s This executable compiled on Jan 3 2025 at 11:01:42 303s 303s Parsing input file 1d7h-dmso-smol.in... 303s rank 0 size 1... 303s Parsed input file. 303s Got paths for 3 molecules 303s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 303s asc_getToken: Error occurred (bailing out). 303s Vio_scanf: Format problem with input. 303s 1673 atoms 303s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 303s Net charge 9.91e-01 e 303s Reading PQR-format atom data from dmso-min.pqr. 303s asc_getToken: Error occurred (bailing out). 303s Vio_scanf: Format problem with input. 303s 10 atoms 303s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 303s Net charge 2.78e-17 e 303s Reading PQR-format atom data from 1d7h-min.pqr. 303s 1663 atoms 303s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 303s Net charge 9.91e-01 e 303s Preparing to run 12 PBE calculations. 303s ---------------------------------------- 303s CALCULATION #1 (complex-solv-coarse): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 30.4176 A 303s Current memory usage: 122.059 MB total, 122.059 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 1.500 x 1.500 x 1.500 303s Grid lengths: 96.000 x 96.000 x 96.000 303s Grid center: (25.875, 18.349, 19.112) 303s Multigrid levels: 5 303s Molecule ID: 1 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 1.074948704824E+04 kJ/mol 303s Calculating forces... 303s [focusFillBound()]: WARNING: 303s Unusually large potential values 303s detected on the focusing boundary! 303s Convergence not guaranteed for NPBE/NRPBE calculations! 303s 303s ---------------------------------------- 303s CALCULATION #2 (complex-solv-fine): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 30.4176 A 303s Current memory usage: 122.059 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.225 x 0.225 x 0.225 303s Grid lengths: 14.400 x 14.400 x 14.400 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 1 303s Linearized traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 4.289487256481E+04 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #3 (complex-ref-coarse): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 4.87072 A 303s Current memory usage: 122.059 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 1.500 x 1.500 x 1.500 303s Grid lengths: 96.000 x 96.000 x 96.000 303s Grid center: (25.875, 18.349, 19.112) 303s Multigrid levels: 5 303s Molecule ID: 1 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 2.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 1.399234956777E+04 kJ/mol 303s Calculating forces... 303s [focusFillBound()]: WARNING: 303s Unusually large potential values 303s detected on the focusing boundary! 303s Convergence not guaranteed for NPBE/NRPBE calculations! 303s 303s ---------------------------------------- 303s CALCULATION #4 (complex-ref-fine): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 4.87072 A 303s Current memory usage: 122.059 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.225 x 0.225 x 0.225 303s Grid lengths: 14.400 x 14.400 x 14.400 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 1 303s Linearized traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 2.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 4.610066575192E+04 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 30.4176 A 303s Current memory usage: 62.428 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 1.500 x 1.500 x 1.500 303s Grid lengths: 96.000 x 96.000 x 96.000 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 2 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 3.719709905887E+01 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #6 (dmso-solv-fine): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 30.4176 A 303s Current memory usage: 62.428 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.225 x 0.225 x 0.225 303s Grid lengths: 14.400 x 14.400 x 14.400 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 2 303s Linearized traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 7.125747080979E+02 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 4.87072 A 303s Current memory usage: 62.428 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 1.500 x 1.500 x 1.500 303s Grid lengths: 96.000 x 96.000 x 96.000 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 2 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 2.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 6.751571424823E+01 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #8 (dmso-ref-fine): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 4.87072 A 303s Current memory usage: 62.428 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.225 x 0.225 x 0.225 303s Grid lengths: 14.400 x 14.400 x 14.400 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 2 303s Linearized traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 2.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 7.339101343121E+02 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 30.4176 A 303s Current memory usage: 121.736 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 1.500 x 1.500 x 1.500 303s Grid lengths: 96.000 x 96.000 x 96.000 303s Grid center: (25.875, 18.349, 19.112) 303s Multigrid levels: 5 303s Molecule ID: 3 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 1.071654753674E+04 kJ/mol 303s Calculating forces... 303s [focusFillBound()]: WARNING: 303s Unusually large potential values 303s detected on the focusing boundary! 303s Convergence not guaranteed for NPBE/NRPBE calculations! 303s 303s ---------------------------------------- 303s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 30.4176 A 303s Current memory usage: 121.736 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.225 x 0.225 x 0.225 303s Grid lengths: 14.400 x 14.400 x 14.400 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 3 303s Linearized traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 78.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 4.218178203716E+04 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 4.87072 A 303s Current memory usage: 121.736 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 1.500 x 1.500 x 1.500 303s Grid lengths: 96.000 x 96.000 x 96.000 303s Grid center: (25.875, 18.349, 19.112) 303s Multigrid levels: 5 303s Molecule ID: 3 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 2.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 1.395961902233E+04 kJ/mol 303s Calculating forces... 303s [focusFillBound()]: WARNING: 303s Unusually large potential values 303s detected on the focusing boundary! 303s Convergence not guaranteed for NPBE/NRPBE calculations! 303s 303s ---------------------------------------- 303s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 303s Debye length: 4.87072 A 303s Current memory usage: 121.736 MB total, 221.696 MB high water 303s Using linear spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.225 x 0.225 x 0.225 303s Grid lengths: 14.400 x 14.400 x 14.400 303s Grid center: (17.751, 17.770, 20.492) 303s Multigrid levels: 5 303s Molecule ID: 3 303s Linearized traditional PBE 303s Boundary conditions from focusing 303s 2 ion species (0.010 M ionic strength): 303s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 303s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 303s Solute dielectric: 2.000 303s Solvent dielectric: 2.000 303s Using "molecular" surface definition;harmonic average smoothing 303s Solvent probe radius: 0.000 A 303s Temperature: 300.000 K 303s Electrostatic energies will be calculated 303s Total electrostatic energy = 4.538248433997E+04 kJ/mol 303s Calculating forces... 303s ---------------------------------------- 303s PRINT STATEMENTS 303s 303s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 303s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 303s Global net ELEC energy = -3.205793187109E+03 kJ/mol 303s 303s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 303s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 303s Global net ELEC energy = -2.133542621421E+01 kJ/mol 303s 303s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 303s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 303s Global net ELEC energy = -3.200702302816E+03 kJ/mol 303s 303s 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 303s Local net energy (PE 0) = 1.624454192074E+01 kJ/mol 303s Global net ELEC energy = 1.624454192074E+01 kJ/mol 303s ---------------------------------------- 303s CLEANING UP AND SHUTTING DOWN... 303s Destroying force arrays. 303s No energy arrays to destroy. 303s Destroying multigrid structures. 303s Destroying finite element structures. 303s Destroying 3 molecules 303s Final memory usage: 0.001 MB total, 221.696 MB high water 303s 303s 303s Thanks for using APBS! 303s 303s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 303s *** PASSED *** 303s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 303s *** PASSED *** 303s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 303s *** PASSED *** 303s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 303s *** PASSED *** 303s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 303s *** PASSED *** 303s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 303s *** PASSED *** 303s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 303s *** PASSED *** 303s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 303s *** PASSED *** 303s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 303s *** PASSED *** 303s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 303s *** PASSED *** 303s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 303s *** PASSED *** 303s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 303s *** PASSED *** 303s Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) 303s *** PASSED *** 303s Elapsed time: 9.871447 seconds 303s -------------------------------------------------------------------------------- 303s -------------------------------------------------------------------------------- 303s Testing input file 1d7i-dss-mol.in 303s 313s Checking for intermediate energies in input file 1d7h-dmso-smol.out 313s EXPECTED COMPUTED: 16 313s EXPECTED EXPECTED: 16 313s 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] 313s 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'] 313s COMPUTED RESULT 10749.48704824 313s COMPUTED RESULT 42894.87256481 313s COMPUTED RESULT 13992.34956777 313s COMPUTED RESULT 46100.66575192 313s COMPUTED RESULT 37.19709905887 313s COMPUTED RESULT 712.5747080979 313s COMPUTED RESULT 67.51571424823 313s COMPUTED RESULT 733.9101343121 313s COMPUTED RESULT 10716.54753674 313s COMPUTED RESULT 42181.78203716 313s COMPUTED RESULT 13959.61902233 313s COMPUTED RESULT 45382.48433997 313s COMPUTED RESULT -3205.793187109 313s COMPUTED RESULT -21.33542621421 313s COMPUTED RESULT -3200.702302816 313s COMPUTED RESULT 16.24454192074 313s BINARY: /usr/bin/apbs 313s INPUT: 1d7i-dss-mol.in 313s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 313s asc_getToken: Error occurred (bailing out). 313s Vio_scanf: Format problem with input. 313s 313s 313s ---------------------------------------------------------------------- 313s APBS -- Adaptive Poisson-Boltzmann Solver 313s Version APBS 3.4.1 313s 313s Nathan A. Baker (nathan.baker@pnnl.gov) 313s Pacific Northwest National Laboratory 313s 313s Additional contributing authors listed in the code documentation. 313s 313s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 313s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 313s Northwest Division for the U.S. Department of Energy. 313s 313s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 313s Portions Copyright (c) 2002-2020, Nathan A. Baker. 313s Portions Copyright (c) 1999-2002, The Regents of the University of California. 313s Portions Copyright (c) 1995, Michael Holst. 313s All rights reserved. 313s 313s Redistribution and use in source and binary forms, with or without 313s modification, are permitted provided that the following conditions are met: 313s 313s * Redistributions of source code must retain the above copyright notice, this 313s list of conditions and the following disclaimer. 313s 313s * Redistributions in binary form must reproduce the above copyright notice, 313s this list of conditions and the following disclaimer in the documentation 313s and/or other materials provided with the distribution. 313s 313s * Neither the name of the developer nor the names of its contributors may be 313s used to endorse or promote products derived from this software without 313s specific prior written permission. 313s 313s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 313s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 313s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 313s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 313s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 313s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 313s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 313s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 313s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 313s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 313s ---------------------------------------------------------------------- 313s APBS uses FETK (the Finite Element ToolKit) to solve the 313s Poisson-Boltzmann equation numerically. FETK is a portable collection 313s of finite element modeling class libraries developed by the Michael Holst 313s research group and written in an object-oriented form of C. FEtk is 313s designed to solve general coupled systems of nonlinear partial differential 313s equations using adaptive finite element methods, inexact Newton methods, 313s and algebraic multilevel methods. More information about FEtk may be found 313s at . 313s ---------------------------------------------------------------------- 313s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 313s Aqua is a modified form of the Holst group PMG library 313s which has been modified by Patrice Koehl 313s for improved efficiency and 313s memory usage when solving the Poisson-Boltzmann equation. 313s ---------------------------------------------------------------------- 313s Please cite your use of APBS as: 313s 313s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 313s nanosystems: application to microtubules and the ribosome. Proc. 313s Natl. Acad. Sci. USA 98, 10037-10041 2001. 313s 313s 313s This executable compiled on Jan 3 2025 at 11:01:42 313s 313s Parsing input file 1d7i-dss-mol.in... 313s rank 0 size 1... 313s Parsed input file. 313s Got paths for 3 molecules 313s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 313s asc_getToken: Error occurred (bailing out). 313s Vio_scanf: Format problem with input. 313s 1677 atoms 313s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 313s Net charge 9.91e-01 e 313s Reading PQR-format atom data from dss-min.pqr. 313s asc_getToken: Error occurred (bailing out). 313s Vio_scanf: Format problem with input. 313s 14 atoms 313s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 313s Net charge -8.33e-17 e 313s Reading PQR-format atom data from 1d7i-min.pqr. 313s 1663 atoms 313s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 313s Net charge 9.91e-01 e 313s Preparing to run 12 PBE calculations. 313s ---------------------------------------- 313s CALCULATION #1 (complex-solv-coarse): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 30.4176 A 313s Current memory usage: 122.425 MB total, 122.425 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 1.500 x 1.500 x 1.500 313s Grid lengths: 96.000 x 96.000 x 96.000 313s Grid center: (25.264, 18.988, 19.122) 313s Multigrid levels: 5 313s Molecule ID: 1 313s Linearized traditional PBE 313s Multiple Debye-Huckel sphere boundary conditions 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 9.160578033846E+03 kJ/mol 313s Calculating forces... 313s [focusFillBound()]: WARNING: 313s Unusually large potential values 313s detected on the focusing boundary! 313s Convergence not guaranteed for NPBE/NRPBE calculations! 313s 313s ---------------------------------------- 313s CALCULATION #2 (complex-solv-fine): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 30.4176 A 313s Current memory usage: 122.425 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 0.225 x 0.225 x 0.225 313s Grid lengths: 14.400 x 14.400 x 14.400 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 1 313s Linearized traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 3.955701871716E+04 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #3 (complex-ref-coarse): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 4.87072 A 313s Current memory usage: 122.425 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 1.500 x 1.500 x 1.500 313s Grid lengths: 96.000 x 96.000 x 96.000 313s Grid center: (25.264, 18.988, 19.122) 313s Multigrid levels: 5 313s Molecule ID: 1 313s Linearized traditional PBE 313s Multiple Debye-Huckel sphere boundary conditions 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 2.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 1.264965939588E+04 kJ/mol 313s Calculating forces... 313s [focusFillBound()]: WARNING: 313s Unusually large potential values 313s detected on the focusing boundary! 313s Convergence not guaranteed for NPBE/NRPBE calculations! 313s 313s ---------------------------------------- 313s CALCULATION #4 (complex-ref-fine): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 4.87072 A 313s Current memory usage: 122.425 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 0.225 x 0.225 x 0.225 313s Grid lengths: 14.400 x 14.400 x 14.400 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 1 313s Linearized traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 2.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 4.301801664829E+04 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #5 (dss-solv-coarse): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 30.4176 A 313s Current memory usage: 62.528 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 1.500 x 1.500 x 1.500 313s Grid lengths: 96.000 x 96.000 x 96.000 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 2 313s Linearized traditional PBE 313s Multiple Debye-Huckel sphere boundary conditions 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 9.431133325426E+01 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #6 (dss-solv-fine): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 30.4176 A 313s Current memory usage: 62.528 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 0.225 x 0.225 x 0.225 313s Grid lengths: 14.400 x 14.400 x 14.400 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 2 313s Linearized traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 1.677348113184E+03 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #7 (dss-ref-coarse): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 4.87072 A 313s Current memory usage: 62.528 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 1.500 x 1.500 x 1.500 313s Grid lengths: 96.000 x 96.000 x 96.000 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 2 313s Linearized traditional PBE 313s Multiple Debye-Huckel sphere boundary conditions 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 2.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 1.171079106781E+02 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #8 (dss-ref-fine): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 4.87072 A 313s Current memory usage: 62.528 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 0.225 x 0.225 x 0.225 313s Grid lengths: 14.400 x 14.400 x 14.400 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 2 313s Linearized traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 2.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 1.697869784185E+03 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 30.4176 A 313s Current memory usage: 121.977 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 1.500 x 1.500 x 1.500 313s Grid lengths: 96.000 x 96.000 x 96.000 313s Grid center: (25.264, 18.988, 19.122) 313s Multigrid levels: 5 313s Molecule ID: 3 313s Linearized traditional PBE 313s Multiple Debye-Huckel sphere boundary conditions 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 9.040108332204E+03 kJ/mol 313s Calculating forces... 313s [focusFillBound()]: WARNING: 313s Unusually large potential values 313s detected on the focusing boundary! 313s Convergence not guaranteed for NPBE/NRPBE calculations! 313s 313s ---------------------------------------- 313s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 30.4176 A 313s Current memory usage: 121.977 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 0.225 x 0.225 x 0.225 313s Grid lengths: 14.400 x 14.400 x 14.400 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 3 313s Linearized traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 78.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 3.787747796627E+04 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 4.87072 A 313s Current memory usage: 121.977 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 1.500 x 1.500 x 1.500 313s Grid lengths: 96.000 x 96.000 x 96.000 313s Grid center: (25.264, 18.988, 19.122) 313s Multigrid levels: 5 313s Molecule ID: 3 313s Linearized traditional PBE 313s Multiple Debye-Huckel sphere boundary conditions 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 2.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 1.252495566243E+04 kJ/mol 313s Calculating forces... 313s [focusFillBound()]: WARNING: 313s Unusually large potential values 313s detected on the focusing boundary! 313s Convergence not guaranteed for NPBE/NRPBE calculations! 313s 313s ---------------------------------------- 313s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 313s Setting up problem... 313s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 313s Debye length: 4.87072 A 313s Current memory usage: 121.977 MB total, 222.305 MB high water 313s Using linear spline charge discretization. 313s Grid dimensions: 65 x 65 x 65 313s Grid spacings: 0.225 x 0.225 x 0.225 313s Grid lengths: 14.400 x 14.400 x 14.400 313s Grid center: (17.340, 19.211, 20.503) 313s Multigrid levels: 5 313s Molecule ID: 3 313s Linearized traditional PBE 313s Boundary conditions from focusing 313s 2 ion species (0.010 M ionic strength): 313s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 313s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 313s Solute dielectric: 2.000 313s Solvent dielectric: 2.000 313s Using "molecular" surface definition; no smoothing 313s Solvent probe radius: 0.000 A 313s Temperature: 300.000 K 313s Electrostatic energies will be calculated 313s Total electrostatic energy = 4.133237922574E+04 kJ/mol 313s Calculating forces... 313s ---------------------------------------- 313s PRINT STATEMENTS 313s 313s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 313s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 313s Global net ELEC energy = -3.460997931137E+03 kJ/mol 313s 313s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 313s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 313s Global net ELEC energy = -2.052167100108E+01 kJ/mol 313s 313s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 313s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 313s Global net ELEC energy = -3.454901259473E+03 kJ/mol 313s 313s 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 313s Local net energy (PE 0) = 1.442499933664E+01 kJ/mol 313s Global net ELEC energy = 1.442499933664E+01 kJ/mol 313s ---------------------------------------- 313s CLEANING UP AND SHUTTING DOWN... 313s Destroying force arrays. 313s No energy arrays to destroy. 313s Destroying multigrid structures. 313s Destroying finite element structures. 313s Destroying 3 molecules 313s Final memory usage: 0.001 MB total, 222.305 MB high water 313s 313s 313s Thanks for using APBS! 313s 313s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 313s *** PASSED *** 313s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 313s *** PASSED *** 313s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 313s *** PASSED *** 313s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 313s *** PASSED *** 313s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 313s *** PASSED *** 313s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 313s *** PASSED *** 313s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 313s *** PASSED *** 313s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 313s *** PASSED *** 313s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 313s *** PASSED *** 313s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 313s *** PASSED *** 313s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 313s *** PASSED *** 313s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 313s *** PASSED *** 313s Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) 313s *** PASSED *** 313s Elapsed time: 10.2304 seconds 313s -------------------------------------------------------------------------------- 313s -------------------------------------------------------------------------------- 313s Testing input file 1d7i-dss-smol.in 313s 323s Checking for intermediate energies in input file 1d7i-dss-mol.out 323s EXPECTED COMPUTED: 16 323s EXPECTED EXPECTED: 16 323s 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] 323s 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'] 323s COMPUTED RESULT 9160.578033846 323s COMPUTED RESULT 39557.01871716 323s COMPUTED RESULT 12649.65939588 323s COMPUTED RESULT 43018.01664829 323s COMPUTED RESULT 94.31133325426 323s COMPUTED RESULT 1677.348113184 323s COMPUTED RESULT 117.1079106781 323s COMPUTED RESULT 1697.869784185 323s COMPUTED RESULT 9040.108332204 323s COMPUTED RESULT 37877.47796627 323s COMPUTED RESULT 12524.95566243 323s COMPUTED RESULT 41332.37922574 323s COMPUTED RESULT -3460.997931137 323s COMPUTED RESULT -20.52167100108 323s COMPUTED RESULT -3454.901259473 323s COMPUTED RESULT 14.42499933664 323s BINARY: /usr/bin/apbs 323s INPUT: 1d7i-dss-smol.in 323s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 323s asc_getToken: Error occurred (bailing out). 323s Vio_scanf: Format problem with input. 323s 323s 323s ---------------------------------------------------------------------- 323s APBS -- Adaptive Poisson-Boltzmann Solver 323s Version APBS 3.4.1 323s 323s Nathan A. Baker (nathan.baker@pnnl.gov) 323s Pacific Northwest National Laboratory 323s 323s Additional contributing authors listed in the code documentation. 323s 323s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 323s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 323s Northwest Division for the U.S. Department of Energy. 323s 323s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 323s Portions Copyright (c) 2002-2020, Nathan A. Baker. 323s Portions Copyright (c) 1999-2002, The Regents of the University of California. 323s Portions Copyright (c) 1995, Michael Holst. 323s All rights reserved. 323s 323s Redistribution and use in source and binary forms, with or without 323s modification, are permitted provided that the following conditions are met: 323s 323s * Redistributions of source code must retain the above copyright notice, this 323s list of conditions and the following disclaimer. 323s 323s * Redistributions in binary form must reproduce the above copyright notice, 323s this list of conditions and the following disclaimer in the documentation 323s and/or other materials provided with the distribution. 323s 323s * Neither the name of the developer nor the names of its contributors may be 323s used to endorse or promote products derived from this software without 323s specific prior written permission. 323s 323s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 323s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 323s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 323s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 323s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 323s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 323s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 323s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 323s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 323s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 323s ---------------------------------------------------------------------- 323s APBS uses FETK (the Finite Element ToolKit) to solve the 323s Poisson-Boltzmann equation numerically. FETK is a portable collection 323s of finite element modeling class libraries developed by the Michael Holst 323s research group and written in an object-oriented form of C. FEtk is 323s designed to solve general coupled systems of nonlinear partial differential 323s equations using adaptive finite element methods, inexact Newton methods, 323s and algebraic multilevel methods. More information about FEtk may be found 323s at . 323s ---------------------------------------------------------------------- 323s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 323s Aqua is a modified form of the Holst group PMG library 323s which has been modified by Patrice Koehl 323s for improved efficiency and 323s memory usage when solving the Poisson-Boltzmann equation. 323s ---------------------------------------------------------------------- 323s Please cite your use of APBS as: 323s 323s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 323s nanosystems: application to microtubules and the ribosome. Proc. 323s Natl. Acad. Sci. USA 98, 10037-10041 2001. 323s 323s 323s This executable compiled on Jan 3 2025 at 11:01:42 323s 323s Parsing input file 1d7i-dss-smol.in... 323s rank 0 size 1... 323s Parsed input file. 323s Got paths for 3 molecules 323s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 323s asc_getToken: Error occurred (bailing out). 323s Vio_scanf: Format problem with input. 323s 1677 atoms 323s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 323s Net charge 9.91e-01 e 323s Reading PQR-format atom data from dss-min.pqr. 323s asc_getToken: Error occurred (bailing out). 323s Vio_scanf: Format problem with input. 323s 14 atoms 323s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 323s Net charge -8.33e-17 e 323s Reading PQR-format atom data from 1d7i-min.pqr. 323s 1663 atoms 323s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 323s Net charge 9.91e-01 e 323s Preparing to run 12 PBE calculations. 323s ---------------------------------------- 323s CALCULATION #1 (complex-solv-coarse): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 30.4176 A 323s Current memory usage: 122.425 MB total, 122.425 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 1.500 x 1.500 x 1.500 323s Grid lengths: 96.000 x 96.000 x 96.000 323s Grid center: (25.264, 18.988, 19.122) 323s Multigrid levels: 5 323s Molecule ID: 1 323s Linearized traditional PBE 323s Multiple Debye-Huckel sphere boundary conditions 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 78.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 9.634884642408E+03 kJ/mol 323s Calculating forces... 323s [focusFillBound()]: WARNING: 323s Unusually large potential values 323s detected on the focusing boundary! 323s Convergence not guaranteed for NPBE/NRPBE calculations! 323s 323s ---------------------------------------- 323s CALCULATION #2 (complex-solv-fine): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 30.4176 A 323s Current memory usage: 122.425 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 0.225 x 0.225 x 0.225 323s Grid lengths: 14.400 x 14.400 x 14.400 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 1 323s Linearized traditional PBE 323s Boundary conditions from focusing 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 78.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 4.003177540425E+04 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s CALCULATION #3 (complex-ref-coarse): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 4.87072 A 323s Current memory usage: 122.425 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 1.500 x 1.500 x 1.500 323s Grid lengths: 96.000 x 96.000 x 96.000 323s Grid center: (25.264, 18.988, 19.122) 323s Multigrid levels: 5 323s Molecule ID: 1 323s Linearized traditional PBE 323s Multiple Debye-Huckel sphere boundary conditions 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 2.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 1.264965939588E+04 kJ/mol 323s Calculating forces... 323s [focusFillBound()]: WARNING: 323s Unusually large potential values 323s detected on the focusing boundary! 323s Convergence not guaranteed for NPBE/NRPBE calculations! 323s 323s ---------------------------------------- 323s CALCULATION #4 (complex-ref-fine): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 4.87072 A 323s Current memory usage: 122.425 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 0.225 x 0.225 x 0.225 323s Grid lengths: 14.400 x 14.400 x 14.400 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 1 323s Linearized traditional PBE 323s Boundary conditions from focusing 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 2.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 4.301801664829E+04 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s CALCULATION #5 (dss-solv-coarse): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 30.4176 A 323s Current memory usage: 62.528 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 1.500 x 1.500 x 1.500 323s Grid lengths: 96.000 x 96.000 x 96.000 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 2 323s Linearized traditional PBE 323s Multiple Debye-Huckel sphere boundary conditions 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 78.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 7.942232645345E+01 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s CALCULATION #6 (dss-solv-fine): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 30.4176 A 323s Current memory usage: 62.528 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 0.225 x 0.225 x 0.225 323s Grid lengths: 14.400 x 14.400 x 14.400 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 2 323s Linearized traditional PBE 323s Boundary conditions from focusing 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 78.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 1.677798535473E+03 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s CALCULATION #7 (dss-ref-coarse): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 4.87072 A 323s Current memory usage: 62.528 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 1.500 x 1.500 x 1.500 323s Grid lengths: 96.000 x 96.000 x 96.000 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 2 323s Linearized traditional PBE 323s Multiple Debye-Huckel sphere boundary conditions 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 2.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 1.171079106781E+02 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s CALCULATION #8 (dss-ref-fine): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 4.87072 A 323s Current memory usage: 62.528 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 0.225 x 0.225 x 0.225 323s Grid lengths: 14.400 x 14.400 x 14.400 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 2 323s Linearized traditional PBE 323s Boundary conditions from focusing 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 2.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 1.697869784185E+03 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 30.4176 A 323s Current memory usage: 121.977 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 1.500 x 1.500 x 1.500 323s Grid lengths: 96.000 x 96.000 x 96.000 323s Grid center: (25.264, 18.988, 19.122) 323s Multigrid levels: 5 323s Molecule ID: 3 323s Linearized traditional PBE 323s Multiple Debye-Huckel sphere boundary conditions 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 78.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 9.507068451372E+03 kJ/mol 323s Calculating forces... 323s [focusFillBound()]: WARNING: 323s Unusually large potential values 323s detected on the focusing boundary! 323s Convergence not guaranteed for NPBE/NRPBE calculations! 323s 323s ---------------------------------------- 323s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 30.4176 A 323s Current memory usage: 121.977 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 0.225 x 0.225 x 0.225 323s Grid lengths: 14.400 x 14.400 x 14.400 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 3 323s Linearized traditional PBE 323s Boundary conditions from focusing 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 78.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 3.835075772299E+04 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 4.87072 A 323s Current memory usage: 121.977 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 1.500 x 1.500 x 1.500 323s Grid lengths: 96.000 x 96.000 x 96.000 323s Grid center: (25.264, 18.988, 19.122) 323s Multigrid levels: 5 323s Molecule ID: 3 323s Linearized traditional PBE 323s Multiple Debye-Huckel sphere boundary conditions 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 2.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 1.252495566243E+04 kJ/mol 323s Calculating forces... 323s [focusFillBound()]: WARNING: 323s Unusually large potential values 323s detected on the focusing boundary! 323s Convergence not guaranteed for NPBE/NRPBE calculations! 323s 323s ---------------------------------------- 323s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 323s Setting up problem... 323s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 323s Debye length: 4.87072 A 323s Current memory usage: 121.977 MB total, 222.305 MB high water 323s Using linear spline charge discretization. 323s Grid dimensions: 65 x 65 x 65 323s Grid spacings: 0.225 x 0.225 x 0.225 323s Grid lengths: 14.400 x 14.400 x 14.400 323s Grid center: (17.340, 19.211, 20.503) 323s Multigrid levels: 5 323s Molecule ID: 3 323s Linearized traditional PBE 323s Boundary conditions from focusing 323s 2 ion species (0.010 M ionic strength): 323s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 323s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 323s Solute dielectric: 2.000 323s Solvent dielectric: 2.000 323s Using "molecular" surface definition;harmonic average smoothing 323s Solvent probe radius: 0.000 A 323s Temperature: 300.000 K 323s Electrostatic energies will be calculated 323s Total electrostatic energy = 4.133237922574E+04 kJ/mol 323s Calculating forces... 323s ---------------------------------------- 323s PRINT STATEMENTS 323s 323s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 323s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 323s Global net ELEC energy = -2.986241244040E+03 kJ/mol 323s 323s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 323s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 323s Global net ELEC energy = -2.007124871262E+01 kJ/mol 323s 323s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 323s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 323s Global net ELEC energy = -2.981621502756E+03 kJ/mol 323s 323s 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 323s Local net energy (PE 0) = 1.545150742843E+01 kJ/mol 323s Global net ELEC energy = 1.545150742843E+01 kJ/mol 323s ---------------------------------------- 323s CLEANING UP AND SHUTTING DOWN... 323s Destroying force arrays. 323s No energy arrays to destroy. 323s Destroying multigrid structures. 323s Destroying finite element structures. 323s Destroying 3 molecules 323s Final memory usage: 0.001 MB total, 222.305 MB high water 323s 323s 323s Thanks for using APBS! 323s 323s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 323s *** PASSED *** 323s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 323s *** PASSED *** 323s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 323s *** PASSED *** 323s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 323s *** PASSED *** 323s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 323s *** PASSED *** 323s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 323s *** PASSED *** 323s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 323s *** PASSED *** 323s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 323s *** PASSED *** 323s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 323s *** PASSED *** 323s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 323s *** PASSED *** 323s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 323s *** PASSED *** 323s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 323s *** PASSED *** 323s Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) 323s *** PASSED *** 323s Elapsed time: 9.919785 seconds 323s -------------------------------------------------------------------------------- 323s Total elapsed time: 40.633725 seconds 323s Test results have been logged 323s -------------------------------------------------------------------------------- 323s -------------------------------------------------------------------------------- 323s Testing input file apbs-mol.in 323s 332s Checking for intermediate energies in input file 1d7i-dss-smol.out 332s EXPECTED COMPUTED: 16 332s EXPECTED EXPECTED: 16 332s 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] 332s 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'] 332s COMPUTED RESULT 9634.884642408 332s COMPUTED RESULT 40031.77540425 332s COMPUTED RESULT 12649.65939588 332s COMPUTED RESULT 43018.01664829 332s COMPUTED RESULT 79.42232645345 332s COMPUTED RESULT 1677.798535473 332s COMPUTED RESULT 117.1079106781 332s COMPUTED RESULT 1697.869784185 332s COMPUTED RESULT 9507.068451372 332s COMPUTED RESULT 38350.75772299 332s COMPUTED RESULT 12524.95566243 332s COMPUTED RESULT 41332.37922574 332s COMPUTED RESULT -2986.24124404 332s COMPUTED RESULT -20.07124871262 332s COMPUTED RESULT -2981.621502756 332s COMPUTED RESULT 15.45150742843 332s Running tests for hca-bind section 332s BINARY: /usr/bin/apbs 332s INPUT: apbs-mol.in 332s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 332s asc_getToken: Error occurred (bailing out). 332s Vio_scanf: Format problem with input. 332s 332s 332s ---------------------------------------------------------------------- 332s APBS -- Adaptive Poisson-Boltzmann Solver 332s Version APBS 3.4.1 332s 332s Nathan A. Baker (nathan.baker@pnnl.gov) 332s Pacific Northwest National Laboratory 332s 332s Additional contributing authors listed in the code documentation. 332s 332s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 332s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 332s Northwest Division for the U.S. Department of Energy. 332s 332s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 332s Portions Copyright (c) 2002-2020, Nathan A. Baker. 332s Portions Copyright (c) 1999-2002, The Regents of the University of California. 332s Portions Copyright (c) 1995, Michael Holst. 332s All rights reserved. 332s 332s Redistribution and use in source and binary forms, with or without 332s modification, are permitted provided that the following conditions are met: 332s 332s * Redistributions of source code must retain the above copyright notice, this 332s list of conditions and the following disclaimer. 332s 332s * Redistributions in binary form must reproduce the above copyright notice, 332s this list of conditions and the following disclaimer in the documentation 332s and/or other materials provided with the distribution. 332s 332s * Neither the name of the developer nor the names of its contributors may be 332s used to endorse or promote products derived from this software without 332s specific prior written permission. 332s 332s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 332s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 332s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 332s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 332s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 332s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 332s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 332s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 332s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 332s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 332s ---------------------------------------------------------------------- 332s APBS uses FETK (the Finite Element ToolKit) to solve the 332s Poisson-Boltzmann equation numerically. FETK is a portable collection 332s of finite element modeling class libraries developed by the Michael Holst 332s research group and written in an object-oriented form of C. FEtk is 332s designed to solve general coupled systems of nonlinear partial differential 332s equations using adaptive finite element methods, inexact Newton methods, 332s and algebraic multilevel methods. More information about FEtk may be found 332s at . 332s ---------------------------------------------------------------------- 332s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 332s Aqua is a modified form of the Holst group PMG library 332s which has been modified by Patrice Koehl 332s for improved efficiency and 332s memory usage when solving the Poisson-Boltzmann equation. 332s ---------------------------------------------------------------------- 332s Please cite your use of APBS as: 332s 332s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 332s nanosystems: application to microtubules and the ribosome. Proc. 332s Natl. Acad. Sci. USA 98, 10037-10041 2001. 332s 332s 332s This executable compiled on Jan 3 2025 at 11:01:42 332s 332s Parsing input file apbs-mol.in... 332s rank 0 size 1... 332s Parsed input file. 332s Got paths for 3 molecules 332s Reading PQR-format atom data from acet.pqr. 332s asc_getToken: Error occurred (bailing out). 332s Vio_scanf: Format problem with input. 332s 18 atoms 332s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 332s Net charge -1.00e+00 e 332s Reading PQR-format atom data from hca.pqr. 332s asc_getToken: Error occurred (bailing out). 332s Vio_scanf: Format problem with input. 332s 2482 atoms 332s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 332s Net charge 1.00e+00 e 332s Reading PQR-format atom data from complex.pqr. 332s 2500 atoms 332s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 332s Net charge -1.02e-14 e 332s Preparing to run 9 PBE calculations. 332s ---------------------------------------- 332s CALCULATION #1 (acet): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 62.727 MB total, 62.727 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 1.500 x 1.500 x 1.500 332s Grid lengths: 96.000 x 96.000 x 96.000 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 1 332s Linearized traditional PBE 332s Single Debye-Huckel sphere boundary conditions 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 2.213600726771E+02 kJ/mol 332s Calculating forces... 332s ---------------------------------------- 332s CALCULATION #2 (acet): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 62.727 MB total, 123.701 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 0.581 x 0.581 x 0.581 332s Grid lengths: 37.181 x 37.181 x 37.181 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 1 332s Linearized traditional PBE 332s Boundary conditions from focusing 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 1.825764811255E+03 kJ/mol 332s Calculating forces... 332s ---------------------------------------- 332s CALCULATION #3 (acet): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 62.727 MB total, 123.701 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 0.225 x 0.225 x 0.225 332s Grid lengths: 14.400 x 14.400 x 14.400 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 1 332s Linearized traditional PBE 332s Boundary conditions from focusing 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 6.458471211905E+03 kJ/mol 332s Calculating forces... 332s ---------------------------------------- 332s CALCULATION #4 (hca): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 146.516 MB total, 146.516 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 1.500 x 1.500 x 1.500 332s Grid lengths: 96.000 x 96.000 x 96.000 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 2 332s Linearized traditional PBE 332s Single Debye-Huckel sphere boundary conditions 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 2.093606095527E+04 kJ/mol 332s Calculating forces... 332s [focusFillBound()]: WARNING: 332s Unusually large potential values 332s detected on the focusing boundary! 332s Convergence not guaranteed for NPBE/NRPBE calculations! 332s 332s ---------------------------------------- 332s CALCULATION #5 (hca): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 146.516 MB total, 245.092 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 0.581 x 0.581 x 0.581 332s Grid lengths: 37.181 x 37.181 x 37.181 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 2 332s Linearized traditional PBE 332s Boundary conditions from focusing 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 1.515433544464E+05 kJ/mol 332s Calculating forces... 332s [focusFillBound()]: WARNING: 332s Unusually large potential values 332s detected on the focusing boundary! 332s Convergence not guaranteed for NPBE/NRPBE calculations! 332s 332s ---------------------------------------- 332s CALCULATION #6 (hca): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 146.516 MB total, 245.092 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 0.225 x 0.225 x 0.225 332s Grid lengths: 14.400 x 14.400 x 14.400 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 2 332s Linearized traditional PBE 332s Boundary conditions from focusing 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 1.786369323561E+05 kJ/mol 332s Calculating forces... 332s ---------------------------------------- 332s CALCULATION #7 (complex): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 146.926 MB total, 245.092 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 1.500 x 1.500 x 1.500 332s Grid lengths: 96.000 x 96.000 x 96.000 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 3 332s Linearized traditional PBE 332s Single Debye-Huckel sphere boundary conditions 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 2.105322784838E+04 kJ/mol 332s Calculating forces... 332s [focusFillBound()]: WARNING: 332s Unusually large potential values 332s detected on the focusing boundary! 332s Convergence not guaranteed for NPBE/NRPBE calculations! 332s 332s ---------------------------------------- 332s CALCULATION #8 (complex): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 146.926 MB total, 245.725 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 0.581 x 0.581 x 0.581 332s Grid lengths: 37.181 x 37.181 x 37.181 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 3 332s Linearized traditional PBE 332s Boundary conditions from focusing 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 1.533304996252E+05 kJ/mol 332s Calculating forces... 332s [focusFillBound()]: WARNING: 332s Unusually large potential values 332s detected on the focusing boundary! 332s Convergence not guaranteed for NPBE/NRPBE calculations! 332s 332s ---------------------------------------- 332s CALCULATION #9 (complex): MULTIGRID 332s Setting up problem... 332s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 332s Debye length: 0 A 332s Current memory usage: 146.926 MB total, 245.725 MB high water 332s Using linear spline charge discretization. 332s Grid dimensions: 65 x 65 x 65 332s Grid spacings: 0.225 x 0.225 x 0.225 332s Grid lengths: 14.400 x 14.400 x 14.400 332s Grid center: (-6.028, 3.898, 15.179) 332s Multigrid levels: 5 332s Molecule ID: 3 332s Linearized traditional PBE 332s Boundary conditions from focusing 332s 2 ion species (0.000 M ionic strength): 332s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 332s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 332s Solute dielectric: 2.000 332s Solvent dielectric: 78.540 332s Using "molecular" surface definition; no smoothing 332s Solvent probe radius: 0.000 A 332s Temperature: 298.150 K 332s Electrostatic energies will be calculated 332s Total electrostatic energy = 1.850429388099E+05 kJ/mol 332s Calculating forces... 332s ---------------------------------------- 332s PRINT STATEMENTS 332s 332s print energy 3 (complex) - 1 (acet) - 2 (hca) end 332s Local net energy (PE 0) = -5.246475812684E+01 kJ/mol 332s Global net ELEC energy = -5.246475812684E+01 kJ/mol 332s ---------------------------------------- 332s CLEANING UP AND SHUTTING DOWN... 332s Destroying force arrays. 332s No energy arrays to destroy. 332s Destroying multigrid structures. 332s Destroying finite element structures. 332s Destroying 3 molecules 332s Final memory usage: 0.001 MB total, 245.725 MB high water 332s 332s 332s Thanks for using APBS! 332s 332s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 332s *** PASSED *** 332s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 332s *** PASSED *** 332s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 332s *** PASSED *** 332s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 332s *** PASSED *** 332s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 332s *** PASSED *** 332s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 332s *** PASSED *** 332s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 332s *** PASSED *** 332s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 332s *** PASSED *** 332s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 332s *** PASSED *** 332s Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) 332s *** PASSED *** 332s Elapsed time: 8.879184 seconds 332s -------------------------------------------------------------------------------- 332s -------------------------------------------------------------------------------- 332s Testing input file apbs-smol.in 332s 341s Checking for intermediate energies in input file apbs-mol.out 341s EXPECTED COMPUTED: 10 341s EXPECTED EXPECTED: 10 341s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] 341s 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'] 341s COMPUTED RESULT 221.3600726771 341s COMPUTED RESULT 1825.764811255 341s COMPUTED RESULT 6458.471211905 341s COMPUTED RESULT 20936.06095527 341s COMPUTED RESULT 151543.3544464 341s COMPUTED RESULT 178636.9323561 341s COMPUTED RESULT 21053.22784838 341s COMPUTED RESULT 153330.4996252 341s COMPUTED RESULT 185042.9388099 341s COMPUTED RESULT -52.46475812684 341s BINARY: /usr/bin/apbs 341s INPUT: apbs-smol.in 341s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 341s asc_getToken: Error occurred (bailing out). 341s Vio_scanf: Format problem with input. 341s 341s 341s ---------------------------------------------------------------------- 341s APBS -- Adaptive Poisson-Boltzmann Solver 341s Version APBS 3.4.1 341s 341s Nathan A. Baker (nathan.baker@pnnl.gov) 341s Pacific Northwest National Laboratory 341s 341s Additional contributing authors listed in the code documentation. 341s 341s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 341s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 341s Northwest Division for the U.S. Department of Energy. 341s 341s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 341s Portions Copyright (c) 2002-2020, Nathan A. Baker. 341s Portions Copyright (c) 1999-2002, The Regents of the University of California. 341s Portions Copyright (c) 1995, Michael Holst. 341s All rights reserved. 341s 341s Redistribution and use in source and binary forms, with or without 341s modification, are permitted provided that the following conditions are met: 341s 341s * Redistributions of source code must retain the above copyright notice, this 341s list of conditions and the following disclaimer. 341s 341s * Redistributions in binary form must reproduce the above copyright notice, 341s this list of conditions and the following disclaimer in the documentation 341s and/or other materials provided with the distribution. 341s 341s * Neither the name of the developer nor the names of its contributors may be 341s used to endorse or promote products derived from this software without 341s specific prior written permission. 341s 341s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 341s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 341s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 341s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 341s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 341s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 341s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 341s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 341s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 341s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 341s ---------------------------------------------------------------------- 341s APBS uses FETK (the Finite Element ToolKit) to solve the 341s Poisson-Boltzmann equation numerically. FETK is a portable collection 341s of finite element modeling class libraries developed by the Michael Holst 341s research group and written in an object-oriented form of C. FEtk is 341s designed to solve general coupled systems of nonlinear partial differential 341s equations using adaptive finite element methods, inexact Newton methods, 341s and algebraic multilevel methods. More information about FEtk may be found 341s at . 341s ---------------------------------------------------------------------- 341s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 341s Aqua is a modified form of the Holst group PMG library 341s which has been modified by Patrice Koehl 341s for improved efficiency and 341s memory usage when solving the Poisson-Boltzmann equation. 341s ---------------------------------------------------------------------- 341s Please cite your use of APBS as: 341s 341s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 341s nanosystems: application to microtubules and the ribosome. Proc. 341s Natl. Acad. Sci. USA 98, 10037-10041 2001. 341s 341s 341s This executable compiled on Jan 3 2025 at 11:01:42 341s 341s Parsing input file apbs-smol.in... 341s rank 0 size 1... 341s Parsed input file. 341s Got paths for 3 molecules 341s Reading PQR-format atom data from acet.pqr. 341s asc_getToken: Error occurred (bailing out). 341s Vio_scanf: Format problem with input. 341s 18 atoms 341s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 341s Net charge -1.00e+00 e 341s Reading PQR-format atom data from hca.pqr. 341s asc_getToken: Error occurred (bailing out). 341s Vio_scanf: Format problem with input. 341s 2482 atoms 341s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 341s Net charge 1.00e+00 e 341s Reading PQR-format atom data from complex.pqr. 341s 2500 atoms 341s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 341s Net charge -1.02e-14 e 341s Preparing to run 9 PBE calculations. 341s ---------------------------------------- 341s CALCULATION #1 (acet): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 62.727 MB total, 62.727 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 1.500 x 1.500 x 1.500 341s Grid lengths: 96.000 x 96.000 x 96.000 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 1 341s Linearized traditional PBE 341s Single Debye-Huckel sphere boundary conditions 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 1.884888131017E+02 kJ/mol 341s Calculating forces... 341s ---------------------------------------- 341s CALCULATION #2 (acet): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 62.727 MB total, 123.701 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 0.581 x 0.581 x 0.581 341s Grid lengths: 37.181 x 37.181 x 37.181 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 1 341s Linearized traditional PBE 341s Boundary conditions from focusing 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 1.820045922544E+03 kJ/mol 341s Calculating forces... 341s ---------------------------------------- 341s CALCULATION #3 (acet): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 62.727 MB total, 123.701 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 0.225 x 0.225 x 0.225 341s Grid lengths: 14.400 x 14.400 x 14.400 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 1 341s Linearized traditional PBE 341s Boundary conditions from focusing 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 6.460002606908E+03 kJ/mol 341s Calculating forces... 341s ---------------------------------------- 341s CALCULATION #4 (hca): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 146.516 MB total, 146.516 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 1.500 x 1.500 x 1.500 341s Grid lengths: 96.000 x 96.000 x 96.000 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 2 341s Linearized traditional PBE 341s Single Debye-Huckel sphere boundary conditions 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 2.189161497021E+04 kJ/mol 341s Calculating forces... 341s [focusFillBound()]: WARNING: 341s Unusually large potential values 341s detected on the focusing boundary! 341s Convergence not guaranteed for NPBE/NRPBE calculations! 341s 341s ---------------------------------------- 341s CALCULATION #5 (hca): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 146.516 MB total, 245.092 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 0.581 x 0.581 x 0.581 341s Grid lengths: 37.181 x 37.181 x 37.181 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 2 341s Linearized traditional PBE 341s Boundary conditions from focusing 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 1.520000494925E+05 kJ/mol 341s Calculating forces... 341s [focusFillBound()]: WARNING: 341s Unusually large potential values 341s detected on the focusing boundary! 341s Convergence not guaranteed for NPBE/NRPBE calculations! 341s 341s ---------------------------------------- 341s CALCULATION #6 (hca): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 146.516 MB total, 245.092 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 0.225 x 0.225 x 0.225 341s Grid lengths: 14.400 x 14.400 x 14.400 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 2 341s Linearized traditional PBE 341s Boundary conditions from focusing 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 1.790436191580E+05 kJ/mol 341s Calculating forces... 341s ---------------------------------------- 341s CALCULATION #7 (complex): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 146.926 MB total, 245.092 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 1.500 x 1.500 x 1.500 341s Grid lengths: 96.000 x 96.000 x 96.000 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 3 341s Linearized traditional PBE 341s Single Debye-Huckel sphere boundary conditions 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 2.195842512312E+04 kJ/mol 341s Calculating forces... 341s [focusFillBound()]: WARNING: 341s Unusually large potential values 341s detected on the focusing boundary! 341s Convergence not guaranteed for NPBE/NRPBE calculations! 341s 341s ---------------------------------------- 341s CALCULATION #8 (complex): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 146.926 MB total, 245.725 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 0.581 x 0.581 x 0.581 341s Grid lengths: 37.181 x 37.181 x 37.181 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 3 341s Linearized traditional PBE 341s Boundary conditions from focusing 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 1.537771604355E+05 kJ/mol 341s Calculating forces... 341s [focusFillBound()]: WARNING: 341s Unusually large potential values 341s detected on the focusing boundary! 341s Convergence not guaranteed for NPBE/NRPBE calculations! 341s 341s ---------------------------------------- 341s CALCULATION #9 (complex): MULTIGRID 341s Setting up problem... 341s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 341s Debye length: 0 A 341s Current memory usage: 146.926 MB total, 245.725 MB high water 341s Using linear spline charge discretization. 341s Grid dimensions: 65 x 65 x 65 341s Grid spacings: 0.225 x 0.225 x 0.225 341s Grid lengths: 14.400 x 14.400 x 14.400 341s Grid center: (-6.028, 3.898, 15.179) 341s Multigrid levels: 5 341s Molecule ID: 3 341s Linearized traditional PBE 341s Boundary conditions from focusing 341s 2 ion species (0.000 M ionic strength): 341s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 341s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 341s Solute dielectric: 2.000 341s Solvent dielectric: 78.540 341s Using "molecular" surface definition;harmonic average smoothing 341s Solvent probe radius: 0.000 A 341s Temperature: 298.150 K 341s Electrostatic energies will be calculated 341s Total electrostatic energy = 1.854495619747E+05 kJ/mol 341s Calculating forces... 341s ---------------------------------------- 341s PRINT STATEMENTS 341s 341s print energy 3 (complex) - 1 (acet) - 2 (hca) end 341s Local net energy (PE 0) = -5.405979017059E+01 kJ/mol 341s Global net ELEC energy = -5.405979017059E+01 kJ/mol 341s ---------------------------------------- 341s CLEANING UP AND SHUTTING DOWN... 341s Destroying force arrays. 341s No energy arrays to destroy. 341s Destroying multigrid structures. 341s Destroying finite element structures. 341s Destroying 3 molecules 341s Final memory usage: 0.001 MB total, 245.725 MB high water 341s 341s 341s Thanks for using APBS! 341s 341s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 341s *** PASSED *** 341s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 341s *** PASSED *** 341s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 341s *** PASSED *** 341s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 341s *** PASSED *** 341s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 341s *** PASSED *** 341s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 341s *** PASSED *** 341s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 341s *** PASSED *** 341s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 341s *** PASSED *** 341s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 341s *** PASSED *** 341s Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) 341s *** PASSED *** 341s Elapsed time: 8.350059 seconds 341s -------------------------------------------------------------------------------- 341s Total elapsed time: 17.229243 seconds 341s Test results have been logged 341s -------------------------------------------------------------------------------- 341s -------------------------------------------------------------------------------- 341s Testing input file apbs-mol.in 341s 343s Checking for intermediate energies in input file apbs-smol.out 343s EXPECTED COMPUTED: 10 343s EXPECTED EXPECTED: 10 343s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] 343s 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'] 343s COMPUTED RESULT 188.4888131017 343s COMPUTED RESULT 1820.045922544 343s COMPUTED RESULT 6460.002606908 343s COMPUTED RESULT 21891.61497021 343s COMPUTED RESULT 152000.0494925 343s COMPUTED RESULT 179043.619158 343s COMPUTED RESULT 21958.42512312 343s COMPUTED RESULT 153777.1604355 343s COMPUTED RESULT 185449.5619747 343s COMPUTED RESULT -54.05979017059 343s Running tests for ionize section 343s BINARY: /usr/bin/apbs 343s INPUT: apbs-mol.in 343s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 343s asc_getToken: Error occurred (bailing out). 343s Vio_scanf: Format problem with input. 343s 343s 343s ---------------------------------------------------------------------- 343s APBS -- Adaptive Poisson-Boltzmann Solver 343s Version APBS 3.4.1 343s 343s Nathan A. Baker (nathan.baker@pnnl.gov) 343s Pacific Northwest National Laboratory 343s 343s Additional contributing authors listed in the code documentation. 343s 343s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 343s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 343s Northwest Division for the U.S. Department of Energy. 343s 343s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 343s Portions Copyright (c) 2002-2020, Nathan A. Baker. 343s Portions Copyright (c) 1999-2002, The Regents of the University of California. 343s Portions Copyright (c) 1995, Michael Holst. 343s All rights reserved. 343s 343s Redistribution and use in source and binary forms, with or without 343s modification, are permitted provided that the following conditions are met: 343s 343s * Redistributions of source code must retain the above copyright notice, this 343s list of conditions and the following disclaimer. 343s 343s * Redistributions in binary form must reproduce the above copyright notice, 343s this list of conditions and the following disclaimer in the documentation 343s and/or other materials provided with the distribution. 343s 343s * Neither the name of the developer nor the names of its contributors may be 343s used to endorse or promote products derived from this software without 343s specific prior written permission. 343s 343s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 343s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 343s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 343s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 343s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 343s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 343s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 343s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 343s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 343s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 343s ---------------------------------------------------------------------- 343s APBS uses FETK (the Finite Element ToolKit) to solve the 343s Poisson-Boltzmann equation numerically. FETK is a portable collection 343s of finite element modeling class libraries developed by the Michael Holst 343s research group and written in an object-oriented form of C. FEtk is 343s designed to solve general coupled systems of nonlinear partial differential 343s equations using adaptive finite element methods, inexact Newton methods, 343s and algebraic multilevel methods. More information about FEtk may be found 343s at . 343s ---------------------------------------------------------------------- 343s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 343s Aqua is a modified form of the Holst group PMG library 343s which has been modified by Patrice Koehl 343s for improved efficiency and 343s memory usage when solving the Poisson-Boltzmann equation. 343s ---------------------------------------------------------------------- 343s Please cite your use of APBS as: 343s 343s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 343s nanosystems: application to microtubules and the ribosome. Proc. 343s Natl. Acad. Sci. USA 98, 10037-10041 2001. 343s 343s 343s This executable compiled on Jan 3 2025 at 11:01:42 343s 343s Parsing input file apbs-mol.in... 343s rank 0 size 1... 343s Parsed input file. 343s Got paths for 3 molecules 343s Reading PQR-format atom data from acetic-acid.pqr. 343s asc_getToken: Error occurred (bailing out). 343s Vio_scanf: Format problem with input. 343s 8 atoms 343s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 343s Net charge -1.67e-16 e 343s Reading PQR-format atom data from acetate.pqr. 343s asc_getToken: Error occurred (bailing out). 343s Vio_scanf: Format problem with input. 343s 8 atoms 343s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 343s Net charge -1.00e+00 e 343s Reading PQR-format atom data from proton.pqr. 343s 1 atoms 343s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 343s Net charge 1.00e+00 e 343s Preparing to run 12 PBE calculations. 343s ---------------------------------------- 343s CALCULATION #1 (acetic-solv): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 7.76163 A 343s Current memory usage: 61.598 MB total, 61.598 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.188 x 0.188 x 0.188 343s Grid lengths: 12.000 x 12.000 x 12.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 1 343s Linearized traditional PBE 343s Multiple Debye-Huckel sphere boundary conditions 343s 2 ion species (0.150 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 78.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 5.823898055191E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #2 (acetic-solv): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 7.76163 A 343s Current memory usage: 61.598 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.094 x 0.094 x 0.094 343s Grid lengths: 6.000 x 6.000 x 6.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 1 343s Linearized traditional PBE 343s Boundary conditions from focusing 343s 2 ion species (0.150 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 78.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 9.793274462353E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #3 (acetic-ref): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 0 A 343s Current memory usage: 61.422 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.188 x 0.188 x 0.188 343s Grid lengths: 12.000 x 12.000 x 12.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 1 343s Linearized traditional PBE 343s Multiple Debye-Huckel sphere boundary conditions 343s 2 ion species (0.000 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 343s 2.000 A-radius, -1.000 e-Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 343s *** PASSED *** 343s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 343s *** PASSED *** 343s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 343s *** PASSED *** 343s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 343s *** PASSED *** 343s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 343s *** PASSED *** 343s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 343s *** PASSED *** 343s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 343s *** PASSED *** 343s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 343s *** PASSED *** 343s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 343s *** PASSED *** 343s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 343s *** PASSED *** 343s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 343s *** PASSED *** 343s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 343s *** PASSED *** 343s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 343s *** PASSED *** 343s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 343s *** PASSED *** 343s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 343s *** PASSED *** 343s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 343s *** PASSED *** 343s Elapsed time: 2.271691 seconds 343s -------------------------------------------------------------------------------- 343s -------------------------------------------------------------------------------- 343s Testing input file apbs-smol.in 343s 343s charge, 0.000 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 2.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 5.846917564309E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #4 (acetic-ref): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 0 A 343s Current memory usage: 61.422 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.094 x 0.094 x 0.094 343s Grid lengths: 6.000 x 6.000 x 6.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 1 343s Linearized traditional PBE 343s Boundary conditions from focusing 343s 2 ion species (0.000 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 2.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 9.815953282539E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #5 (acetate-solv): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 7.76163 A 343s Current memory usage: 61.598 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.188 x 0.188 x 0.188 343s Grid lengths: 12.000 x 12.000 x 12.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 2 343s Linearized traditional PBE 343s Multiple Debye-Huckel sphere boundary conditions 343s 2 ion species (0.150 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 78.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 8.219846763777E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #6 (acetate-solv): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 7.76163 A 343s Current memory usage: 61.598 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.094 x 0.094 x 0.094 343s Grid lengths: 6.000 x 6.000 x 6.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 2 343s Linearized traditional PBE 343s Boundary conditions from focusing 343s 2 ion species (0.150 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 78.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 1.392741988698E+04 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #7 (acetate-ref): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 0 A 343s Current memory usage: 61.422 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.188 x 0.188 x 0.188 343s Grid lengths: 12.000 x 12.000 x 12.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 2 343s Linearized traditional PBE 343s Multiple Debye-Huckel sphere boundary conditions 343s 2 ion species (0.000 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 2.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 8.420373979905E+03 kJ/mol 343s Calculating forces... 343s [focusFillBound()]: WARNING: 343s Unusually large potential values 343s detected on the focusing boundary! 343s Convergence not guaranteed for NPBE/NRPBE calculations! 343s 343s ---------------------------------------- 343s CALCULATION #8 (acetate-ref): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 0 A 343s Current memory usage: 61.422 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.094 x 0.094 x 0.094 343s Grid lengths: 6.000 x 6.000 x 6.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 2 343s Linearized traditional PBE 343s Boundary conditions from focusing 343s 2 ion species (0.000 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 2.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 1.412716615065E+04 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #9 (proton-solv): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 7.76163 A 343s Current memory usage: 61.412 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.188 x 0.188 x 0.188 343s Grid lengths: 12.000 x 12.000 x 12.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 3 343s Linearized traditional PBE 343s Multiple Debye-Huckel sphere boundary conditions 343s 2 ion species (0.150 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 78.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 3.862359524598E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #10 (proton-solv): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 7.76163 A 343s Current memory usage: 61.412 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.094 x 0.094 x 0.094 343s Grid lengths: 6.000 x 6.000 x 6.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 3 343s Linearized traditional PBE 343s Boundary conditions from focusing 343s 2 ion species (0.150 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 78.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 6.288156251610E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s CALCULATION #11 (proton-ref): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 0 A 343s Current memory usage: 61.373 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.188 x 0.188 x 0.188 343s Grid lengths: 12.000 x 12.000 x 12.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 3 343s Linearized traditional PBE 343s Multiple Debye-Huckel sphere boundary conditions 343s 2 ion species (0.000 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 2.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 4.162533113906E+03 kJ/mol 343s Calculating forces... 343s [focusFillBound()]: WARNING: 343s Unusually large potential values 343s detected on the focusing boundary! 343s Convergence not guaranteed for NPBE/NRPBE calculations! 343s 343s ---------------------------------------- 343s CALCULATION #12 (proton-ref): MULTIGRID 343s Setting up problem... 343s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 343s Debye length: 0 A 343s Current memory usage: 61.373 MB total, 122.404 MB high water 343s Using linear spline charge discretization. 343s Grid dimensions: 65 x 65 x 65 343s Grid spacings: 0.094 x 0.094 x 0.094 343s Grid lengths: 6.000 x 6.000 x 6.000 343s Grid center: (0.000, -0.154, 1.287) 343s Multigrid levels: 5 343s Molecule ID: 3 343s Linearized traditional PBE 343s Boundary conditions from focusing 343s 2 ion species (0.000 M ionic strength): 343s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 343s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 343s Solute dielectric: 2.000 343s Solvent dielectric: 2.000 343s Using "molecular" surface definition; no smoothing 343s Solvent probe radius: 0.000 A 343s Temperature: 293.000 K 343s Electrostatic energies will be calculated 343s Total electrostatic energy = 6.585616091973E+03 kJ/mol 343s Calculating forces... 343s ---------------------------------------- 343s PRINT STATEMENTS 343s 343s print energy 1 (acetic-solv) - 2 (acetic-ref) end 343s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 343s Global net ELEC energy = -2.267882018629E+01 kJ/mol 343s 343s print energy 3 (acetate-solv) - 4 (acetate-ref) end 343s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 343s Global net ELEC energy = -1.997462636633E+02 kJ/mol 343s 343s print energy 5 (proton-solv) - 6 (proton-ref) end 343s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 343s Global net ELEC energy = -2.974598403628E+02 kJ/mol 343s 343s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 343s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 343s Global net ELEC energy = -4.745272838398E+02 kJ/mol 343s ---------------------------------------- 343s CLEANING UP AND SHUTTING DOWN... 343s Destroying force arrays. 343s No energy arrays to destroy. 343s Destroying multigrid structures. 343s Destroying finite element structures. 343s Destroying 3 molecules 343s Final memory usage: 0.001 MB total, 122.404 MB high water 343s 343s 343s Thanks for using APBS! 343s 345s Checking for intermediate energies in input file apbs-mol.out 345s EXPECTED COMPUTED: 16 345s EXPECTED EXPECTED: 16 345s 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] 345s 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'] 345s COMPUTED RESULT 5823.898055191 345s COMPUTED RESULT 9793.274462353 345s COMPUTED RESULT 5846.917564309 345s COMPUTED RESULT 9815.953282539 345s COMPUTED RESULT 8219.846763777 345s COMPUTED RESULT 13927.41988698 345s COMPUTED RESULT 8420.373979905 345s COMPUTED RESULT 14127.16615065 345s COMPUTED RESULT 3862.359524598 345s COMPUTED RESULT 6288.15625161 345s COMPUTED RESULT 4162.533113906 345s COMPUTED RESULT 6585.616091973 345s COMPUTED RESULT -22.67882018629 345s COMPUTED RESULT -199.7462636633 345s COMPUTED RESULT -297.4598403628 345s COMPUTED RESULT -474.5272838398 345s BINARY: /usr/bin/apbs 345s INPUT: apbs-smol.in 345s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 345s asc_getToken: Error occurred (bailing out). 345s Vio_scanf: Format problem with input. 345s 345s 345s ---------------------------------------------------------------------- 345s APBS -- Adaptive Poisson-Boltzmann Solver 345s Version APBS 3.4.1 345s 345s Nathan A. Baker (nathan.baker@pnnl.gov) 345s Pacific Northwest National Laboratory 345s 345s Additional contributing authors listed in the code documentation. 345s 345s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 345s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 345s Northwest Division for the U.S. Department of Energy. 345s 345s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 345s Portions Copyright (c) 2002-2020, Nathan A. Baker. 345s Portions Copyright (c) 1999-2002, The Regents of the University of California. 345s Portions Copyright (c) 1995, Michael Holst. 345s All rights reserved. 345s 345s Redistribution and use in source and binary forms, with or without 345s modification, are permitted provided that the following conditions are met: 345s 345s * Redistributions of source code must retain the above copyright notice, this 345s list of conditions and the following disclaimer. 345s 345s * Redistributions in binary form must reproduce the above copyright notice, 345s this list of conditions and the following disclaimer in the documentation 345s and/or other materials provided with the distribution. 345s 345s * Neither the name of the developer nor the names of its contributors may be 345s used to endorse or promote products derived from this software without 345s specific prior written permission. 345s 345s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 345s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 345s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 345s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 345s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 345s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 345s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 345s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 345s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 345s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 345s ---------------------------------------------------------------------- 345s APBS uses FETK (the Finite Element ToolKit) to solve the 345s Poisson-Boltzmann equation numerically. FETK is a portable collection 345s of finite element modeling class libraries developed by the Michael Holst 345s research group and written in an object-oriented form of C. FEtk is 345s designed to solve general coupled systems of nonlinear partial differential 345s equations using adaptive finite element methods, inexact Newton methods, 345s and algebraic multilevel methods. More information about FEtk may be found 345s at . 345s ---------------------------------------------------------------------- 345s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 345s Aqua is a modified form of the Holst group PMG library 345s which has been modified by Patrice Koehl 345s for improved efficiency and 345s memory usage when solving the Poisson-Boltzmann equation. 345s ---------------------------------------------------------------------- 345s Please cite your use of APBS as: 345s 345s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 345s nanosystems: application to microtubules and the ribosome. Proc. 345s Natl. Acad. Sci. USA 98, 10037-10041 2001. 345s 345s 345s This executable compiled on Jan 3 2025 at 11:01:42 345s 345s Parsing input file apbs-smol.in... 345s rank 0 size 1... 345s Parsed input file. 345s Got paths for 3 molecules 345s Reading PQR-format atom data from acetic-acid.pqr. 345s asc_getToken: Error occurred (bailing out). 345s Vio_scanf: Format problem with input. 345s 8 atoms 345s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 345s Net charge -1.67e-16 e 345s Reading PQR-format atom data from acetate.pqr. 345s asc_getToken: Error occurred (bailing out). 345s Vio_scanf: Format problem with input. 345s 8 atoms 345s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 345s Net charge -1.00e+00 e 345s Reading PQR-format atom data from proton.pqr. 345s 1 atoms 345s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 345s Net charge 1.00e+00 e 345s Preparing to run 12 PBE calculations. 345s ---------------------------------------- 345s CALCULATION #1 (acetic-solv): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 7.76163 A 345s Current memory usage: 61.598 MB total, 61.598 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.188 x 0.188 x 0.188 345s Grid lengths: 12.000 x 12.000 x 12.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 1 345s Linearized traditional PBE 345s Multiple Debye-Huckel sphere boundary conditions 345s 2 ion species (0.150 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 78.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 5.824172730822E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #2 (acetic-solv): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 7.76163 A 345s Current memory usage: 61.598 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.094 x 0.094 x 0.094 345s Grid lengths: 6.000 x 6.000 x 6.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 1 345s Linearized traditional PBE 345s Boundary conditions from focusing 345s 2 ion species (0.150 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 78.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 9.793622759239E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #3 (acetic-ref): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 0 A 345s Current memory usage: 61.422 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.188 x 0.188 x 0.188 345s Grid lengths: 12.000 x 12.000 x 12.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 1 345s Linearized traditional PBE 345s Multiple Debye-Huckel sphere boundary conditions 345s 2 ion species (0.000 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 2.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 5.846917564309E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #4 (acetic-ref): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 0 A 345s Current memory usage: 61.422 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.094 x 0.094 x 0.094 345s Grid lengths: 6.000 x 6.000 x 6.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 1 345s Linearized traditional PBE 345s Boundary conditions from focusing 345s 2 ion species (0.000 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 2.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 9.815953282539E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #5 (acetate-solv): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 7.76163 A 345s Current memory usage: 61.598 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.188 x 0.188 x 0.188 345s Grid lengths: 12.000 x 12.000 x 12.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 2 345s Linearized traditional PBE 345s Multiple Debye-Huckel sphere boundary conditions 345s 2 ion species (0.150 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 78.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 8.221328580569E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #6 (acetate-solv): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 7.76163 A 345s Current memory usage: 61.598 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.094 x 0.094 x 0.094 345s Grid lengths: 6.000 x 6.000 x 6.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 2 345s Linearized traditional PBE 345s Boundary conditions from focusing 345s 2 ion species (0.150 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 78.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 1.392867783119E+04 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #7 (acetate-ref): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 0 A 345s Current memory usage: 61.422 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.188 x 0.188 x 0.188 345s Grid lengths: 12.000 x 12.000 x 12.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 2 345s Linearized traditional PBE 345s Multiple Debye-Huckel sphere boundary conditions 345s 2 ion species (0.000 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 2.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 8.420373979905E+03 kJ/mol 345s Calculating forces... 345s [focusFillBound()]: WARNING: 345s Unusually large potential values 345s detected on the focusing boundary! 345s Convergence not guaranteed for NPBE/NRPBE calculations! 345s 345s ---------------------------------------- 345s CALCULATION #8 (acetate-ref): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 0 A 345s Current memory usage: 61.422 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.094 x 0.094 x 0.094 345s Grid lengths: 6.000 x 6.000 x 6.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 2 345s Linearized traditional PBE 345s Boundary conditions from focusing 345s 2 ion species (0.000 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 2.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 1.412716615065E+04 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #9 (proton-solv): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 7.76163 A 345s Current memory usage: 61.412 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.188 x 0.188 x 0.188 345s Grid lengths: 12.000 x 12.000 x 12.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 3 345s Linearized traditional PBE 345s Multiple Debye-Huckel sphere boundary conditions 345s 2 ion species (0.150 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 78.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 3.863066835285E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #10 (proton-solv): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 7.76163 A 345s Current memory usage: 61.412 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.094 x 0.094 x 0.094 345s Grid lengths: 6.000 x 6.000 x 6.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 3 345s Linearized traditional PBE 345s Boundary conditions from focusing 345s 2 ion species (0.150 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 78.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 6.289649216644E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s CALCULATION #11 (proton-ref): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 0 A 345s Current memory usage: 61.373 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.188 x 0.188 x 0.188 345s Grid lengths: 12.000 x 12.000 x 12.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 3 345s Linearized traditional PBE 345s Multiple Debye-Huckel sphere boundary conditions 345s 2 ion species (0.000 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 2.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 4.162533113906E+03 kJ/mol 345s Calculating forces... 345s [focusFillBound()]: WARNING: 345s Unusually large potential values 345s detected on the focusing boundary! 345s Convergence not guaranteed for NPBE/NRPBE calculations! 345s 345s ---------------------------------------- 345s CALCULATION #12 (proton-ref): MULTIGRID 345s Setting up problem... 345s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 345s Debye length: 0 A 345s Current memory usage: 61.373 MB total, 122.404 MB high water 345s Using linear spline charge discretization. 345s Grid dimensions: 65 x 65 x 65 345s Grid spacings: 0.094 x 0.094 x 0.094 345s Grid lengths: 6.000 x 6.000 x 6.000 345s Grid center: (0.000, -0.154, 1.287) 345s Multigrid levels: 5 345s Molecule ID: 3 345s Linearized traditional PBE 345s Boundary conditions from focusing 345s 2 ion species (0.000 M ionic strength): 345s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 345s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 345s Solute dielectric: 2.000 345s Solvent dielectric: 2.000 345s Using "molecular" surface definition;harmonic average smoothing 345s Solvent probe radius: 0.000 A 345s Temperature: 293.000 K 345s Electrostatic energies will be calculated 345s Total electrostatic energy = 6.585616091973E+03 kJ/mol 345s Calculating forces... 345s ---------------------------------------- 345s PRINT STATEMENTS 345s 345s print energy 1 (acetic-solv) - 2 (acetic-ref) end 345s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 345s Global net ELEC energy = -2.233052329981E+01 kJ/mol 345s 345s print energy 3 (acetate-solv) - 4 (acetate-ref) end 345s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 345s Global net ELEC energy = -1.984883194538E+02 kJ/mol 345s 345s print energy 5 (proton-solv) - 6 (proton-ref) end 345s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 345s Global net ELEC energy = -2.959668753288E+02 kJ/mol 345s 345s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 345s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 345s Global net ELEC energy = -4.721246714828E+02 kJ/mol 345s ---------------------------------------- 345s CLEANING UP AND SHUTTING DOWN... 345s Destroying force arrays. 345s No energy arrays to destroy. 345s Destroying multigrid structures. 345s Destroying finite element structures. 345s Destroying 3 molecules 345s Final memory usage: 0.001 MB total, 122.404 MB high water 345s 345s 345s Thanks for using APBS! 345s 345s Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 345s *** PASSED *** 345s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 345s *** PASSED *** 345s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 345s *** PASSED *** 345s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 345s *** PASSED *** 345s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 345s *** PASSED *** 345s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 345s *** PASSED *** 345s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 345s *** PASSED *** 345s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 345s *** PASSED *** 345s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 345s *** PASSED *** 345s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 345s *** PASSED *** 345s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 345s *** PASSED *** 345s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 345s *** PASSED *** 345s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 345s *** PASSED *** 345s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 345s *** PASSED *** 345s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 345s *** PASSED *** 345s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 345s *** PASSED *** 345s Elapsed time: 1.923479 seconds 345s -------------------------------------------------------------------------------- 345s Total elapsed time: 4.19517 seconds 345s Test results have been logged 345s -------------------------------------------------------------------------------- 345s -------------------------------------------------------------------------------- 345s Testing input file ion-pmf.in 345s 353s Checking for intermediate energies in input file apbs-smol.out 353s EXPECTED COMPUTED: 16 353s EXPECTED EXPECTED: 16 353s 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] 353s 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'] 353s COMPUTED RESULT 5824.172730822 353s COMPUTED RESULT 9793.622759239 353s COMPUTED RESULT 5846.917564309 353s COMPUTED RESULT 9815.953282539 353s COMPUTED RESULT 8221.328580569 353s COMPUTED RESULT 13928.67783119 353s COMPUTED RESULT 8420.373979905 353s COMPUTED RESULT 14127.16615065 353s COMPUTED RESULT 3863.066835285 353s COMPUTED RESULT 6289.649216644 353s COMPUTED RESULT 4162.533113906 353s COMPUTED RESULT 6585.616091973 353s COMPUTED RESULT -22.33052329981 353s COMPUTED RESULT -198.4883194538 353s COMPUTED RESULT -295.9668753288 353s COMPUTED RESULT -472.1246714828 353s Running tests for ion-pmf section 353s BINARY: /usr/bin/apbs 353s INPUT: ion-pmf.in 353s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 353s asc_getToken: Error occurred (bailing out). 353s Vio_scanf: Format problem with input. 353s asc_getToken: Error occurred (bailing out). 353s Vio_scanf: Format problem with input. 353s 353s 353s ---------------------------------------------------------------------- 353s APBS -- Adaptive Poisson-Boltzmann Solver 353s Version APBS 3.4.1 353s 353s Nathan A. Baker (nathan.baker@pnnl.gov) 353s Pacific Northwest National Laboratory 353s 353s Additional contributing authors listed in the code documentation. 353s 353s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 353s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 353s Northwest Division for the U.S. Department of Energy. 353s 353s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 353s Portions Copyright (c) 2002-2020, Nathan A. Baker. 353s Portions Copyright (c) 1999-2002, The Regents of the University of California. 353s Portions Copyright (c) 1995, Michael Holst. 353s All rights reserved. 353s 353s Redistribution and use in source and binary forms, with or without 353s modification, are permitted provided that the following conditions are met: 353s 353s * Redistributions of source code must retain the above copyright notice, this 353s list of conditions and the following disclaimer. 353s 353s * Redistributions in binary form must reproduce the above copyright notice, 353s this list of conditions and the following disclaimer in the documentation 353s and/or other materials provided with the distribution. 353s 353s * Neither the name of the developer nor the names of its contributors may be 353s used to endorse or promote products derived from this software without 353s specific prior written permission. 353s 353s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 353s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 353s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 353s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 353s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 353s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 353s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 353s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 353s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 353s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 353s ---------------------------------------------------------------------- 353s APBS uses FETK (the Finite Element ToolKit) to solve the 353s Poisson-Boltzmann equation numerically. FETK is a portable collection 353s of finite element modeling class libraries developed by the Michael Holst 353s research group and written in an object-oriented form of C. FEtk is 353s designed to solve general coupled systems of nonlinear partial differential 353s equations using adaptive finite element methods, inexact Newton methods, 353s and algebraic multilevel methods. More information about FEtk may be found 353s at . 353s ---------------------------------------------------------------------- 353s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 353s Aqua is a modified form of the Holst group PMG library 353s which has been modified by Patrice Koehl 353s for improved efficiency and 353s memory usage when solving the Poisson-Boltzmann equation. 353s ---------------------------------------------------------------------- 353s Please cite your use of APBS as: 353s 353s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 353s nanosystems: application to microtubules and the ribosome. Proc. 353s Natl. Acad. Sci. USA 98, 10037-10041 2001. 353s 353s 353s This executable compiled on Jan 3 2025 at 11:01:42 353s 353s Parsing input file ion-pmf.in... 353s rank 0 size 1... 353s Parsed input file. 353s Reading parameter data from parm.dat. 353s Got paths for 1 molecules 353s Reading PDB-format atom data from ion-pmf.pdb. 353s Vpmg_ibForce: No force for zero ionic strength! 353s Vpmg_ibForce: No force for zero ionic strength! 353s 2 atoms 353s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 353s Net charge 2.00e+00 e 353s Preparing to run 3 PBE calculations. 353s ---------------------------------------- 353s CALCULATION #1 (solv): MULTIGRID 353s Setting up problem... 353s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 353s Debye length: 0 A 353s Current memory usage: 61.106 MB total, 61.106 MB high water 353s Using cubic spline charge discretization. 353s Grid dimensions: 65 x 65 x 65 353s Grid spacings: 0.210 x 0.210 x 0.210 353s Grid lengths: 13.440 x 13.440 x 13.440 353s Grid center: (0.000, 0.000, 0.000) 353s Multigrid levels: 5 353s Molecule ID: 1 353s Linearized traditional PBE 353s Multiple Debye-Huckel sphere boundary conditions 353s 0 ion species (0.000 M ionic strength): 353s Solute dielectric: 1.000 353s Solvent dielectric: 78.540 353s Using spline-based surface definition;window = 0.300 353s Temperature: 298.150 K 353s Electrostatic energies will be calculated 353s All-atom solvent forces will be calculated 353s Total electrostatic energy = 7.839535983197E+03 kJ/mol 353s Calculating forces... 353s Printing per-atom forces for molecule 1 (kJ/mol/A) 353s Legend: 353s tot n -- total force for atom n 353s qf n -- fixed charge force for atom n 353s db n -- dielectric boundary force for atom n 353s ib n -- ionic boundary force for atom n 353s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 353s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 353s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 353s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 353s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 353s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 353s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 353s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 353s Vpmg_ibForce: No force for zero ionic strength! 353s Vpmg_ibForce: No force for zero ionic strength! 353s ---------------------------------------- 353s CALCULATION #2 (ref): MULTIGRID 353s Setting up problem... 353s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 353s Debye length: 0 A 353s Current memory usage: 61.106 MB total, 61.155 MB high water 353s Using cubic spline charge discretization. 353s Grid dimensions: 65 x 65 x 65 353s Grid spacings: 0.210 x 0.210 x 0.210 353s Grid lengths: 13.440 x 13.440 x 13.440 353s Grid center: (0.000, 0.000, 0.000) 353s Multigrid levels: 5 353s Molecule ID: 1 353s Linearized traditional PBE 353s Multiple Debye-Huckel sphere boundary conditions 353s 0 ion species (0.000 M ionic strength): 353s Solute dielectric: 1.000 353s Solvent dielectric: 1.000 353s Using spline-based surface definition;window = 0.300 353s Temperature: 298.150 K 353s Electrostatic energies will be calculated 353s All-atom solvent forces will be calculated 353s Total electrostatic energy = 8.964727588811E+03 kJ/mol 353s Calculating forces... 353s Printing per-atom forces for molecule 1 (kJ/mol/A) 353s Legend: 353s tot n -- total force for atom n 353s qf n -- fixed charge force for atom n 353s db n -- dielectric boundary force for atom n 353s ib n -- ionic boundary force for atom n 353s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 353s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 353s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 353s mgF db 0 0.000e+00 0.000e+00 0.000e+00 353s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 353s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 353s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 353s mgF db 1 0.000e+00 0.000e+00 0.000e+00 353s ---------------------------------------- 353s CALCULATION #3 (asolv): APOLAR 353s Printing per atom forces (kJ/mol/A) 353s Legend: 353s tot n -- Total force for atom n 353s sasa n -- SASA force for atom n 353s sav n -- SAV force for atom n 353s wca n -- WCA force for atom n 353s 353s gamma 0.000720 353s pressure 0.000000 353s bconc 0.033000 353s 353s tot 0 2.715e-02 9.130e-07 9.128e-07 353s sasa 0 -1.100e+01 0.000e+00 0.000e+00 353s sav 0 0.000e+00 0.000e+00 0.000e+00 353s wca 0 -5.827e-01 -2.767e-05 -2.766e-05 353s tot 1 -2.723e-02 9.131e-07 9.134e-07 353s sasa 1 1.112e+01 0.000e+00 0.000e+00 353s sav 1 0.000e+00 0.000e+00 0.000e+00 353s wca 1 5.827e-01 -2.767e-05 -2.768e-05 353s 353s 353s Solvent Accessible Surface Area (SASA) for each atom: 353s SASA for atom 0: 1.153275282828E+02 353s SASA for atom 1: 1.153114143344E+02 353s 353s Total solvent accessible surface area: 230.639 A^2 353s 353s Surface tension*area energies (gamma * SASA) for each atom: 353s Surface tension*area energy for atom 0: 8.303582036361E-02 353s Surface tension*area energy for atom 1: 8.302421832080E-02 353s 353s Total surface tension energy: 0.16606 kJ/mol 353s 353s Total solvent accessible volume: 0 A^3 353s 353s Total pressure*volume energy: 0 kJ/mol 353s 353s WCA dispersion Energies for each atom: 353s WCA energy for atom 0: -6.909718345777E+00 353s WCA energy for atom 1: -6.909411348230E+00 353s 353s Total WCA energy: -13.8191 kJ/mol 353s 353s Total non-polar energy = -1.365306965532E+01 kJ/mol 353s ---------------------------------------- 353s PRINT STATEMENTS 353s 353s print energy 1 (solv) - 2 (ref) end 353s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 353s Global net ELEC energy = -1.125191605614E+03 kJ/mol 353s print force 1 (solv) - 2 (ref) end 353s Printing per-atom forces (kJ/mol/A). 353s Legend: 353s tot n -- Total force for atom n 353s qf n -- Fixed charge force for atom n 353s db n -- Dielectric boundary force for atom n 353s ib n -- Ionic boundary force for atom n 353s tot all -- Total force for system 353s qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 353s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 353s db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 353s tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 353s qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 353s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 353s db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 353s tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 353s tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 353s 353s print APOL energy 1 (asolv) end 353s Global net APOL energy = -1.365306965532E+01 kJ/mol 353s 353s print APOL force 1 (asolv) end 353s Printing per atom forces (kJ/mol/A) 353s Legend: 353s tot n -- Total force for atom n 353s sasa n -- SASA force for atom n 353s sav n -- SAV force for atom n 353s wca n -- WCA force for atom n 353s tot all -- Total force for system 353s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 353s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 353s wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 353s tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 353s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 353s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 353s wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 353s tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 353s tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 353s ---------------------------------------- 353s CLEANING UP AND SHUTTING DOWN... 353s Destroying force arrays. 353s No energy arrays to destroy. 353s Destroying multigrid structures. 353s Destroying finite element structures. 353s Destroying 1 molecules 353s Final memory usage: 60.711 MB total, 62.250 MB high water 353s 353s 353s Thanks for using APBS! 353s 353s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 353s *** PASSED *** 353s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 353s *** PASSED *** 353s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 353s *** PASSED *** 353s Elapsed time: 8.681402 seconds 353s -------------------------------------------------------------------------------- 353s Total elapsed time: 8.681402 seconds 353s Test results have been logged 353s -------------------------------------------------------------------------------- 353s -------------------------------------------------------------------------------- 353s Testing input file apbs-mol-vdw.in 353s 364s Checking for intermediate energies in input file ion-pmf.out 364s EXPECTED COMPUTED: 4 364s EXPECTED EXPECTED: 4 364s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] 364s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 364s COMPUTED RESULT 7839.535983197 364s COMPUTED RESULT 8964.727588811 364s COMPUTED RESULT -1125.191605614 364s COMPUTED RESULT -13.65306965532 364s Running tests for pka-lig section 364s BINARY: /usr/bin/apbs 364s INPUT: apbs-mol-vdw.in 364s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 364s asc_getToken: Error occurred (bailing out). 364s Vio_scanf: Format problem with input. 364s 364s 364s ---------------------------------------------------------------------- 364s APBS -- Adaptive Poisson-Boltzmann Solver 364s Version APBS 3.4.1 364s 364s Nathan A. Baker (nathan.baker@pnnl.gov) 364s Pacific Northwest National Laboratory 364s 364s Additional contributing authors listed in the code documentation. 364s 364s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 364s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 364s Northwest Division for the U.S. Department of Energy. 364s 364s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 364s Portions Copyright (c) 2002-2020, Nathan A. Baker. 364s Portions Copyright (c) 1999-2002, The Regents of the University of California. 364s Portions Copyright (c) 1995, Michael Holst. 364s All rights reserved. 364s 364s Redistribution and use in source and binary forms, with or without 364s modification, are permitted provided that the following conditions are met: 364s 364s * Redistributions of source code must retain the above copyright notice, this 364s list of conditions and the following disclaimer. 364s 364s * Redistributions in binary form must reproduce the above copyright notice, 364s this list of conditions and the following disclaimer in the documentation 364s and/or other materials provided with the distribution. 364s 364s * Neither the name of the developer nor the names of its contributors may be 364s used to endorse or promote products derived from this software without 364s specific prior written permission. 364s 364s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 364s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 364s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 364s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 364s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 364s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 364s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 364s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 364s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 364s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 364s ---------------------------------------------------------------------- 364s APBS uses FETK (the Finite Element ToolKit) to solve the 364s Poisson-Boltzmann equation numerically. FETK is a portable collection 364s of finite element modeling class libraries developed by the Michael Holst 364s research group and written in an object-oriented form of C. FEtk is 364s designed to solve general coupled systems of nonlinear partial differential 364s equations using adaptive finite element methods, inexact Newton methods, 364s and algebraic multilevel methods. More information about FEtk may be found 364s at . 364s ---------------------------------------------------------------------- 364s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 364s Aqua is a modified form of the Holst group PMG library 364s which has been modified by Patrice Koehl 364s for improved efficiency and 364s memory usage when solving the Poisson-Boltzmann equation. 364s ---------------------------------------------------------------------- 364s Please cite your use of APBS as: 364s 364s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 364s nanosystems: application to microtubules and the ribosome. Proc. 364s Natl. Acad. Sci. USA 98, 10037-10041 2001. 364s 364s 364s This executable compiled on Jan 3 2025 at 11:01:42 364s 364s Parsing input file apbs-mol-vdw.in... 364s rank 0 size 1... 364s Parsed input file. 364s Got paths for 3 molecules 364s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 364s asc_getToken: Error occurred (bailing out). 364s Vio_scanf: Format problem with input. 364s 47 atoms 364s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 364s Net charge 1.11e-16 e 364s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 364s asc_getToken: Error occurred (bailing out). 364s Vio_scanf: Format problem with input. 364s 3423 atoms 364s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 364s Net charge 1.00e+00 e 364s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 364s 3470 atoms 364s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 364s Net charge 1.00e+00 e 364s Preparing to run 6 PBE calculations. 364s ---------------------------------------- 364s CALCULATION #1 (lig-coarse): MULTIGRID 364s Setting up problem... 364s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 364s Debye length: 0 A 364s Current memory usage: 204.292 MB total, 204.292 MB high water 364s Using linear spline charge discretization. 364s Grid dimensions: 97 x 97 x 97 364s Grid spacings: 0.729 x 0.729 x 0.729 364s Grid lengths: 70.000 x 70.000 x 70.000 364s Grid center: (28.969, -32.507, 27.022) 364s Multigrid levels: 4 364s Molecule ID: 1 364s Linearized traditional PBE 364s Single Debye-Huckel sphere boundary conditions 364s 2 ion species (0.000 M ionic strength): 364s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 364s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 364s Solute dielectric: 2.000 364s Solvent dielectric: 78.000 364s Using "molecular" surface definition; no smoothing 364s Solvent probe radius: 0.000 A 364s Temperature: 298.150 K 364s Electrostatic energies will be calculated 364s Total electrostatic energy = 2.224988750664E+03 kJ/mol 364s Calculating forces... 364s ---------------------------------------- 364s CALCULATION #2 (lig-fine): MULTIGRID 364s Setting up problem... 364s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 364s Debye length: 0 A 364s Current memory usage: 204.292 MB total, 406.001 MB high water 364s Using linear spline charge discretization. 364s Grid dimensions: 97 x 97 x 97 364s Grid spacings: 0.250 x 0.250 x 0.250 364s Grid lengths: 24.000 x 24.000 x 24.000 364s Grid center: (24.822, -33.153, 21.545) 364s Multigrid levels: 4 364s Molecule ID: 1 364s Linearized traditional PBE 364s Boundary conditions from focusing 364s 2 ion species (0.000 M ionic strength): 364s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 364s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 364s Solute dielectric: 2.000 364s Solvent dielectric: 78.000 364s Using "molecular" surface definition; no smoothing 364s Solvent probe radius: 0.000 A 364s Temperature: 298.150 K 364s Electrostatic energies will be calculated 364s Total electrostatic energy = 1.049695084686E+04 kJ/mol 364s Calculating forces... 364s ---------------------------------------- 364s CALCULATION #3 (pka-coarse): MULTIGRID 364s Setting up problem... 364s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 364s Debye length: 0 A 364s Current memory usage: 291.151 MB total, 406.001 MB high water 364s Using linear spline charge discretization. 364s Grid dimensions: 97 x 97 x 97 364s Grid spacings: 0.729 x 0.729 x 0.729 364s Grid lengths: 70.000 x 70.000 x 70.000 364s Grid center: (28.969, -32.507, 27.022) 364s Multigrid levels: 4 364s Molecule ID: 2 364s Linearized traditional PBE 364s Single Debye-Huckel sphere boundary conditions 364s 2 ion species (0.000 M ionic strength): 364s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 364s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 364s Solute dielectric: 2.000 364s Solvent dielectric: 78.000 364s Using "molecular" surface definition; no smoothing 364s Solvent probe radius: 0.000 A 364s Temperature: 298.150 K 364s Electrostatic energies will be calculated 364s Total electrostatic energy = 1.818450789522E+05 kJ/mol 364s Calculating forces... 364s [focusFillBound()]: WARNING: 364s Unusually large potential values 364s detected on the focusing boundary! 364s Convergence not guaranteed for NPBE/NRPBE calculations! 364s 364s ---------------------------------------- 364s CALCULATION #4 (pka-fine): MULTIGRID 364s Setting up problem... 364s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 364s Debye length: 0 A 364s Current memory usage: 291.151 MB total, 533.426 MB high water 364s Using linear spline charge discretization. 364s Grid dimensions: 97 x 97 x 97 364s Grid spacings: 0.250 x 0.250 x 0.250 364s Grid lengths: 24.000 x 24.000 x 24.000 364s Grid center: (24.822, -33.153, 21.545) 364s Multigrid levels: 4 364s Molecule ID: 2 364s Linearized traditional PBE 364s Boundary conditions from focusing 364s 2 ion species (0.000 M ionic strength): 364s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 364s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 364s Solute dielectric: 2.000 364s Solvent dielectric: 78.000 364s Using "molecular" surface definition; no smoothing 364s Solvent probe radius: 0.000 A 364s Temperature: 298.150 K 364s Electrostatic energies will be calculated 364s Total electrostatic energy = 3.008254338259E+05 kJ/mol 364s Calculating forces... 364s ---------------------------------------- 364s CALCULATION #5 (complex-coarse): MULTIGRID 364s Setting up problem... 364s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 364s Debye length: 0 A 364s Current memory usage: 292.063 MB total, 533.426 MB high water 364s Using linear spline charge discretization. 364s Grid dimensions: 97 x 97 x 97 364s Grid spacings: 0.729 x 0.729 x 0.729 364s Grid lengths: 70.000 x 70.000 x 70.000 364s Grid center: (28.969, -32.507, 27.022) 364s Multigrid levels: 4 364s Molecule ID: 3 364s Linearized traditional PBE 364s Single Debye-Huckel sphere boundary conditions 364s 2 ion species (0.000 M ionic strength): 364s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 364s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 364s Solute dielectric: 2.000 364s Solvent dielectric: 78.000 364s Using "molecular" surface definition; no smoothing 364s Solvent probe radius: 0.000 A 364s Temperature: 298.150 K 364s Electrostatic energies will be calculated 364s Total electrostatic energy = 1.840918409896E+05 kJ/mol 364s Calculating forces... 364s [focusFillBound()]: WARNING: 364s Unusually large potential values 364s detected on the focusing boundary! 364s Convergence not guaranteed for NPBE/NRPBE calculations! 364s 364s ---------------------------------------- 364s CALCULATION #6 (complex-fine): MULTIGRID 364s Setting up problem... 364s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 364s Debye length: 0 A 364s Current memory usage: 292.063 MB total, 534.806 MB high water 364s Using linear spline charge discretization. 364s Grid dimensions: 97 x 97 x 97 364s Grid spacings: 0.250 x 0.250 x 0.250 364s Grid lengths: 24.000 x 24.000 x 24.000 364s Grid center: (24.822, -33.153, 21.545) 364s Multigrid levels: 4 364s Molecule ID: 3 364s Linearized traditional PBE 364s Boundary conditions from focusing 364s 2 ion species (0.000 M ionic strength): 364s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 364s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 364s Solute dielectric: 2.000 364s Solvent dielectric: 78.000 364s Using "molecular" surface definition; no smoothing 364s Solvent probe radius: 0.000 A 364s Temperature: 298.150 K 364s Electrostatic energies will be calculated 364s Total electrostatic energy = 3.113304681884E+05 kJ/mol 364s Calculating forces... 364s ---------------------------------------- 364s PRINT STATEMENTS 364s 364s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 364s Local net energy (PE 0) = 8.083515648803E+00 kJ/mol 364s Global net ELEC energy = 8.083515648803E+00 kJ/mol 364s ---------------------------------------- 364s CLEANING UP AND SHUTTING DOWN... 364s Destroying force arrays. 364s No energy arrays to destroy. 364s Destroying multigrid structures. 364s Destroying finite element structures. 364s Destroying 3 molecules 364s Final memory usage: 0.001 MB total, 534.806 MB high water 364s 364s 364s Thanks for using APBS! 364s 364s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 364s *** PASSED *** 364s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 364s *** PASSED *** 364s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 364s *** PASSED *** 364s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 364s *** PASSED *** 364s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 364s *** PASSED *** 364s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 364s *** PASSED *** 364s Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) 364s *** PASSED *** 364s Elapsed time: 11.096872 seconds 364s -------------------------------------------------------------------------------- 364s -------------------------------------------------------------------------------- 364s Testing input file apbs-smol-vdw.in 364s 374s Checking for intermediate energies in input file apbs-mol-vdw.out 374s EXPECTED COMPUTED: 7 374s EXPECTED EXPECTED: 7 374s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] 374s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 374s COMPUTED RESULT 2224.988750664 374s COMPUTED RESULT 10496.95084686 374s COMPUTED RESULT 181845.0789522 374s COMPUTED RESULT 300825.4338259 374s COMPUTED RESULT 184091.8409896 374s COMPUTED RESULT 311330.4681884 374s COMPUTED RESULT 8.083515648803 374s BINARY: /usr/bin/apbs 374s INPUT: apbs-smol-vdw.in 374s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 374s asc_getToken: Error occurred (bailing out). 374s Vio_scanf: Format problem with input. 374s 374s 374s ---------------------------------------------------------------------- 374s APBS -- Adaptive Poisson-Boltzmann Solver 374s Version APBS 3.4.1 374s 374s Nathan A. Baker (nathan.baker@pnnl.gov) 374s Pacific Northwest National Laboratory 374s 374s Additional contributing authors listed in the code documentation. 374s 374s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 374s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 374s Northwest Division for the U.S. Department of Energy. 374s 374s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 374s Portions Copyright (c) 2002-2020, Nathan A. Baker. 374s Portions Copyright (c) 1999-2002, The Regents of the University of California. 374s Portions Copyright (c) 1995, Michael Holst. 374s All rights reserved. 374s 374s Redistribution and use in source and binary forms, with or without 374s modification, are permitted provided that the following conditions are met: 374s 374s * Redistributions of source code must retain the above copyright notice, this 374s list of conditions and the following disclaimer. 374s 374s * Redistributions in binary form must reproduce the above copyright notice, 374s this list of conditions and the following disclaimer in the documentation 374s and/or other materials provided with the distribution. 374s 374s * Neither the name of the developer nor the names of its contributors may be 374s used to endorse or promote products derived from this software without 374s specific prior written permission. 374s 374s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 374s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 374s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 374s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 374s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 374s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 374s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 374s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 374s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 374s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 374s ---------------------------------------------------------------------- 374s APBS uses FETK (the Finite Element ToolKit) to solve the 374s Poisson-Boltzmann equation numerically. FETK is a portable collection 374s of finite element modeling class libraries developed by the Michael Holst 374s research group and written in an object-oriented form of C. FEtk is 374s designed to solve general coupled systems of nonlinear partial differential 374s equations using adaptive finite element methods, inexact Newton methods, 374s and algebraic multilevel methods. More information about FEtk may be found 374s at . 374s ---------------------------------------------------------------------- 374s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 374s Aqua is a modified form of the Holst group PMG library 374s which has been modified by Patrice Koehl 374s for improved efficiency and 374s memory usage when solving the Poisson-Boltzmann equation. 374s ---------------------------------------------------------------------- 374s Please cite your use of APBS as: 374s 374s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 374s nanosystems: application to microtubules and the ribosome. Proc. 374s Natl. Acad. Sci. USA 98, 10037-10041 2001. 374s 374s 374s This executable compiled on Jan 3 2025 at 11:01:42 374s 374s Parsing input file apbs-smol-vdw.in... 374s rank 0 size 1... 374s Parsed input file. 374s Got paths for 3 molecules 374s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 374s asc_getToken: Error occurred (bailing out). 374s Vio_scanf: Format problem with input. 374s 47 atoms 374s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 374s Net charge 1.11e-16 e 374s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 374s asc_getToken: Error occurred (bailing out). 374s Vio_scanf: Format problem with input. 374s 3423 atoms 374s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 374s Net charge 1.00e+00 e 374s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 374s 3470 atoms 374s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 374s Net charge 1.00e+00 e 374s Preparing to run 6 PBE calculations. 374s ---------------------------------------- 374s CALCULATION #1 (lig-coarse): MULTIGRID 374s Setting up problem... 374s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 374s Debye length: 0 A 374s Current memory usage: 204.292 MB total, 204.292 MB high water 374s Using linear spline charge discretization. 374s Grid dimensions: 97 x 97 x 97 374s Grid spacings: 0.729 x 0.729 x 0.729 374s Grid lengths: 70.000 x 70.000 x 70.000 374s Grid center: (28.969, -32.507, 27.022) 374s Multigrid levels: 4 374s Molecule ID: 1 374s Linearized traditional PBE 374s Single Debye-Huckel sphere boundary conditions 374s 2 ion species (0.000 M ionic strength): 374s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 374s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 374s Solute dielectric: 2.000 374s Solvent dielectric: 78.000 374s Using "molecular" surface definition;harmonic average smoothing 374s Solvent probe radius: 0.000 A 374s Temperature: 298.150 K 374s Electrostatic energies will be calculated 374s Total electrostatic energy = 2.226793167046E+03 kJ/mol 374s Calculating forces... 374s ---------------------------------------- 374s CALCULATION #2 (lig-fine): MULTIGRID 374s Setting up problem... 374s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 374s Debye length: 0 A 374s Current memory usage: 204.292 MB total, 406.001 MB high water 374s Using linear spline charge discretization. 374s Grid dimensions: 97 x 97 x 97 374s Grid spacings: 0.250 x 0.250 x 0.250 374s Grid lengths: 24.000 x 24.000 x 24.000 374s Grid center: (24.822, -33.153, 21.545) 374s Multigrid levels: 4 374s Molecule ID: 1 374s Linearized traditional PBE 374s Boundary conditions from focusing 374s 2 ion species (0.000 M ionic strength): 374s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 374s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 374s Solute dielectric: 2.000 374s Solvent dielectric: 78.000 374s Using "molecular" surface definition;harmonic average smoothing 374s Solvent probe radius: 0.000 A 374s Temperature: 298.150 K 374s Electrostatic energies will be calculated 374s Total electrostatic energy = 1.050504485887E+04 kJ/mol 374s Calculating forces... 374s ---------------------------------------- 374s CALCULATION #3 (pka-coarse): MULTIGRID 374s Setting up problem... 374s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 374s Debye length: 0 A 374s Current memory usage: 291.151 MB total, 406.001 MB high water 374s Using linear spline charge discretization. 374s Grid dimensions: 97 x 97 x 97 374s Grid spacings: 0.729 x 0.729 x 0.729 374s Grid lengths: 70.000 x 70.000 x 70.000 374s Grid center: (28.969, -32.507, 27.022) 374s Multigrid levels: 4 374s Molecule ID: 2 374s Linearized traditional PBE 374s Single Debye-Huckel sphere boundary conditions 374s 2 ion species (0.000 M ionic strength): 374s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 374s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 374s Solute dielectric: 2.000 374s Solvent dielectric: 78.000 374s Using "molecular" surface definition;harmonic average smoothing 374s Solvent probe radius: 0.000 A 374s Temperature: 298.150 K 374s Electrostatic energies will be calculated 374s Total electrostatic energy = 1.827976621645E+05 kJ/mol 374s Calculating forces... 374s [focusFillBound()]: WARNING: 374s Unusually large potential values 374s detected on the focusing boundary! 374s Convergence not guaranteed for NPBE/NRPBE calculations! 374s 374s ---------------------------------------- 374s CALCULATION #4 (pka-fine): MULTIGRID 374s Setting up problem... 374s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 374s Debye length: 0 A 374s Current memory usage: 291.151 MB total, 533.426 MB high water 374s Using linear spline charge discretization. 374s Grid dimensions: 97 x 97 x 97 374s Grid spacings: 0.250 x 0.250 x 0.250 374s Grid lengths: 24.000 x 24.000 x 24.000 374s Grid center: (24.822, -33.153, 21.545) 374s Multigrid levels: 4 374s Molecule ID: 2 374s Linearized traditional PBE 374s Boundary conditions from focusing 374s 2 ion species (0.000 M ionic strength): 374s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 374s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 374s Solute dielectric: 2.000 374s Solvent dielectric: 78.000 374s Using "molecular" surface definition;harmonic average smoothing 374s Solvent probe radius: 0.000 A 374s Temperature: 298.150 K 374s Electrostatic energies will be calculated 374s Total electrostatic energy = 3.017228546773E+05 kJ/mol 374s Calculating forces... 374s ---------------------------------------- 374s CALCULATION #5 (complex-coarse): MULTIGRID 374s Setting up problem... 374s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 374s Debye length: 0 A 374s Current memory usage: 292.063 MB total, 533.426 MB high water 374s Using linear spline charge discretization. 374s Grid dimensions: 97 x 97 x 97 374s Grid spacings: 0.729 x 0.729 x 0.729 374s Grid lengths: 70.000 x 70.000 x 70.000 374s Grid center: (28.969, -32.507, 27.022) 374s Multigrid levels: 4 374s Molecule ID: 3 374s Linearized traditional PBE 374s Single Debye-Huckel sphere boundary conditions 374s 2 ion species (0.000 M ionic strength): 374s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 374s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 374s Solute dielectric: 2.000 374s Solvent dielectric: 78.000 374s Using "molecular" surface definition;harmonic average smoothing 374s Solvent probe radius: 0.000 A 374s Temperature: 298.150 K 374s Electrostatic energies will be calculated 374s Total electrostatic energy = 1.850819075387E+05 kJ/mol 374s Calculating forces... 374s [focusFillBound()]: WARNING: 374s Unusually large potential values 374s detected on the focusing boundary! 374s Convergence not guaranteed for NPBE/NRPBE calculations! 374s 374s ---------------------------------------- 374s CALCULATION #6 (complex-fine): MULTIGRID 374s Setting up problem... 374s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 374s Debye length: 0 A 374s Current memory usage: 292.063 MB total, 534.806 MB high water 374s Using linear spline charge discretization. 374s Grid dimensions: 97 x 97 x 97 374s Grid spacings: 0.250 x 0.250 x 0.250 374s Grid lengths: 24.000 x 24.000 x 24.000 374s Grid center: (24.822, -33.153, 21.545) 374s Multigrid levels: 4 374s Molecule ID: 3 374s Linearized traditional PBE 374s Boundary conditions from focusing 374s 2 ion species (0.000 M ionic strength): 374s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 374s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 374s Solute dielectric: 2.000 374s Solvent dielectric: 78.000 374s Using "molecular" surface definition;harmonic average smoothing 374s Solvent probe radius: 0.000 A 374s Temperature: 298.150 K 374s Electrostatic energies will be calculated 374s Total electrostatic energy = 3.122488625388E+05 kJ/mol 374s Calculating forces... 374s ---------------------------------------- 374s PRINT STATEMENTS 374s 374s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 374s Local net energy (PE 0) = 2.096300255720E+01 kJ/mol 374s Global net ELEC energy = 2.096300255720E+01 kJ/mol 374s ---------------------------------------- 374s CLEANING UP AND SHUTTING DOWN... 374s Destroying force arrays. 374s No energy arrays to destroy. 374s Destroying multigrid structures. 374s Destroying finite element structures. 374s Destroying 3 molecules 374s Final memory usage: 0.001 MB total, 534.806 MB high water 374s 374s 374s Thanks for using APBS! 374s 374s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 374s *** PASSED *** 374s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 374s *** PASSED *** 374s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 374s *** PASSED *** 374s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 374s *** PASSED *** 374s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 374s *** PASSED *** 374s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 374s *** PASSED *** 374s Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) 374s *** PASSED *** 374s Elapsed time: 9.859554 seconds 374s -------------------------------------------------------------------------------- 374s -------------------------------------------------------------------------------- 374s Testing input file apbs-mol-surf.in 374s 384s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 384s Checking for intermediate energies in input file apbs-smol-vdw.out 384s EXPECTED COMPUTED: 7 384s EXPECTED EXPECTED: 7 384s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] 384s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 384s COMPUTED RESULT 2226.793167046 384s COMPUTED RESULT 10505.04485887 384s COMPUTED RESULT 182797.6621645 384s COMPUTED RESULT 301722.8546773 384s COMPUTED RESULT 185081.9075387 384s COMPUTED RESULT 312248.8625388 384s COMPUTED RESULT 20.9630025572 384s BINARY: /usr/bin/apbs 384s INPUT: apbs-mol-surf.in 384s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 384s asc_getToken: Error occurred (bailing out). 384s Vio_scanf: Format problem with input. 384s 384s 384s ---------------------------------------------------------------------- 384s APBS -- Adaptive Poisson-Boltzmann Solver 384s Version APBS 3.4.1 384s 384s Nathan A. Baker (nathan.baker@pnnl.gov) 384s Pacific Northwest National Laboratory 384s 384s Additional contributing authors listed in the code documentation. 384s 384s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 384s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 384s Northwest Division for the U.S. Department of Energy. 384s 384s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 384s Portions Copyright (c) 2002-2020, Nathan A. Baker. 384s Portions Copyright (c) 1999-2002, The Regents of the University of California. 384s Portions Copyright (c) 1995, Michael Holst. 384s All rights reserved. 384s 384s Redistribution and use in source and binary forms, with or without 384s modification, are permitted provided that the following conditions are met: 384s 384s * Redistributions of source code must retain the above copyright notice, this 384s list of conditions and the following disclaimer. 384s 384s * Redistributions in binary form must reproduce the above copyright notice, 384s this list of conditions and the following disclaimer in the documentation 384s and/or other materials provided with the distribution. 384s 384s * Neither the name of the developer nor the names of its contributors may be 384s used to endorse or promote products derived from this software without 384s specific prior written permission. 384s 384s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 384s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 384s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 384s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 384s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 384s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 384s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 384s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 384s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 384s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 384s ---------------------------------------------------------------------- 384s APBS uses FETK (the Finite Element ToolKit) to solve the 384s Poisson-Boltzmann equation numerically. FETK is a portable collection 384s of finite element modeling class libraries developed by the Michael Holst 384s research group and written in an object-oriented form of C. FEtk is 384s designed to solve general coupled systems of nonlinear partial differential 384s equations using adaptive finite element methods, inexact Newton methods, 384s and algebraic multilevel methods. More information about FEtk may be found 384s at . 384s ---------------------------------------------------------------------- 384s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 384s Aqua is a modified form of the Holst group PMG library 384s which has been modified by Patrice Koehl 384s for improved efficiency and 384s memory usage when solving the Poisson-Boltzmann equation. 384s ---------------------------------------------------------------------- 384s Please cite your use of APBS as: 384s 384s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 384s nanosystems: application to microtubules and the ribosome. Proc. 384s Natl. Acad. Sci. USA 98, 10037-10041 2001. 384s 384s 384s This executable compiled on Jan 3 2025 at 11:01:42 384s 384s Parsing input file apbs-mol-surf.in... 384s rank 0 size 1... 384s Parsed input file. 384s Got paths for 3 molecules 384s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 384s asc_getToken: Error occurred (bailing out). 384s Vio_scanf: Format problem with input. 384s 47 atoms 384s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 384s Net charge 1.11e-16 e 384s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 384s asc_getToken: Error occurred (bailing out). 384s Vio_scanf: Format problem with input. 384s 3423 atoms 384s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 384s Net charge 1.00e+00 e 384s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 384s 3470 atoms 384s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 384s Net charge 1.00e+00 e 384s Preparing to run 6 PBE calculations. 384s ---------------------------------------- 384s CALCULATION #1 (lig-coarse): MULTIGRID 384s Setting up problem... 384s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 384s Debye length: 0 A 384s Current memory usage: 203.877 MB total, 203.877 MB high water 384s Using linear spline charge discretization. 384s Grid dimensions: 97 x 97 x 97 384s Grid spacings: 0.729 x 0.729 x 0.729 384s Grid lengths: 70.000 x 70.000 x 70.000 384s Grid center: (28.969, -32.507, 27.022) 384s Multigrid levels: 4 384s Molecule ID: 1 384s Linearized traditional PBE 384s Single Debye-Huckel sphere boundary conditions 384s 2 ion species (0.000 M ionic strength): 384s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 384s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 384s Solute dielectric: 2.000 384s Solvent dielectric: 78.000 384s Using "molecular" surface definition; no smoothing 384s Solvent probe radius: 1.400 A 384s Temperature: 298.150 K 384s Electrostatic energies will be calculated 384s Total electrostatic energy = 2.244350164274E+03 kJ/mol 384s Calculating forces... 384s ---------------------------------------- 384s CALCULATION #2 (lig-fine): MULTIGRID 384s Setting up problem... 384s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 384s Debye length: 0 A 384s Current memory usage: 203.877 MB total, 405.586 MB high water 384s Using linear spline charge discretization. 384s Grid dimensions: 97 x 97 x 97 384s Grid spacings: 0.250 x 0.250 x 0.250 384s Grid lengths: 24.000 x 24.000 x 24.000 384s Grid center: (24.822, -33.153, 21.545) 384s Multigrid levels: 4 384s Molecule ID: 1 384s Linearized traditional PBE 384s Boundary conditions from focusing 384s 2 ion species (0.000 M ionic strength): 384s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 384s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 384s Solute dielectric: 2.000 384s Solvent dielectric: 78.000 384s Using "molecular" surface definition; no smoothing 384s Solvent probe radius: 1.400 A 384s Temperature: 298.150 K 384s Electrostatic energies will be calculated 384s Total electrostatic energy = 1.052149475373E+04 kJ/mol 384s Calculating forces... 384s ---------------------------------------- 384s CALCULATION #3 (pka-coarse): MULTIGRID 384s Setting up problem... 384s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 384s Debye length: 0 A 384s Current memory usage: 251.521 MB total, 405.586 MB high water 384s Using linear spline charge discretization. 384s Grid dimensions: 97 x 97 x 97 384s Grid spacings: 0.729 x 0.729 x 0.729 384s Grid lengths: 70.000 x 70.000 x 70.000 384s Grid center: (28.969, -32.507, 27.022) 384s Multigrid levels: 4 384s Molecule ID: 2 384s Linearized traditional PBE 384s Single Debye-Huckel sphere boundary conditions 384s 2 ion species (0.000 M ionic strength): 384s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 384s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 384s Solute dielectric: 2.000 384s Solvent dielectric: 78.000 384s Using "molecular" surface definition; no smoothing 384s Solvent probe radius: 1.400 A 384s Temperature: 298.150 K 384s Electrostatic energies will be calculated 384s Total electrostatic energy = 1.862615690066E+05 kJ/mol 384s Calculating forces... 384s [focusFillBound()]: WARNING: 384s Unusually large potential values 384s detected on the focusing boundary! 384s Convergence not guaranteed for NPBE/NRPBE calculations! 384s 384s ---------------------------------------- 384s CALCULATION #4 (pka-fine): MULTIGRID 384s Setting up problem... 384s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 384s Debye length: 0 A 384s Current memory usage: 251.521 MB total, 493.795 MB high water 384s Using linear spline charge discretization. 384s Grid dimensions: 97 x 97 x 97 384s Grid spacings: 0.250 x 0.250 x 0.250 384s Grid lengths: 24.000 x 24.000 x 24.000 384s Grid center: (24.822, -33.153, 21.545) 384s Multigrid levels: 4 384s Molecule ID: 2 384s Linearized traditional PBE 384s Boundary conditions from focusing 384s 2 ion species (0.000 M ionic strength): 384s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 384s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 384s Solute dielectric: 2.000 384s Solvent dielectric: 78.000 384s Using "molecular" surface definition; no smoothing 384s Solvent probe radius: 1.400 A 384s Temperature: 298.150 K 384s Electrostatic energies will be calculated 384s Total electrostatic energy = 3.051810884053E+05 kJ/mol 384s Calculating forces... 384s ---------------------------------------- 384s CALCULATION #5 (complex-coarse): MULTIGRID 384s Setting up problem... 384s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 384s Debye length: 0 A 384s Current memory usage: 251.858 MB total, 493.795 MB high water 384s Using linear spline charge discretization. 384s Grid dimensions: 97 x 97 x 97 384s Grid spacings: 0.729 x 0.729 x 0.729 384s Grid lengths: 70.000 x 70.000 x 70.000 384s Grid center: (28.969, -32.507, 27.022) 384s Multigrid levels: 4 384s Molecule ID: 3 384s Linearized traditional PBE 384s Single Debye-Huckel sphere boundary conditions 384s 2 ion species (0.000 M ionic strength): 384s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 384s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 384s Solute dielectric: 2.000 384s Solvent dielectric: 78.000 384s Using "molecular" surface definition; no smoothing 384s Solvent probe radius: 1.400 A 384s Temperature: 298.150 K 384s Electrostatic energies will be calculated 384s Total electrostatic energy = 1.886625455219E+05 kJ/mol 384s Calculating forces... 384s [focusFillBound()]: WARNING: 384s Unusually large potential values 384s detected on the focusing boundary! 384s Convergence not guaranteed for NPBE/NRPBE calculations! 384s 384s ---------------------------------------- 384s CALCULATION #6 (complex-fine): MULTIGRID 384s Setting up problem... 384s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 384s Debye length: 0 A 384s Current memory usage: 251.858 MB total, 494.601 MB high water 384s Using linear spline charge discretization. 384s Grid dimensions: 97 x 97 x 97 384s Grid spacings: 0.250 x 0.250 x 0.250 384s Grid lengths: 24.000 x 24.000 x 24.000 384s Grid center: (24.822, -33.153, 21.545) 384s Multigrid levels: 4 384s Molecule ID: 3 384s Linearized traditional PBE 384s Boundary conditions from focusing 384s 2 ion species (0.000 M ionic strength): 384s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 384s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 384s Solute dielectric: 2.000 384s Solvent dielectric: 78.000 384s Using "molecular" surface definition; no smoothing 384s Solvent probe radius: 1.400 A 384s Temperature: 298.150 K 384s Electrostatic energies will be calculated 384s Total electrostatic energy = 3.158218439277E+05 kJ/mol 384s Calculating forces... 384s ---------------------------------------- 384s PRINT STATEMENTS 384s 384s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 384s Local net energy (PE 0) = 1.192607686582E+02 kJ/mol 384s Global net ELEC energy = 1.192607686582E+02 kJ/mol 384s ---------------------------------------- 384s CLEANING UP AND SHUTTING DOWN... 384s Destroying force arrays. 384s No energy arrays to destroy. 384s Destroying multigrid structures. 384s Destroying finite element structures. 384s Destroying 3 molecules 384s Final memory usage: 0.001 MB total, 494.601 MB high water 384s 384s 384s Thanks for using APBS! 384s 384s *** PASSED *** 384s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 384s *** PASSED *** 384s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 384s *** PASSED *** 384s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 384s *** PASSED *** 384s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 384s *** PASSED *** 384s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 384s *** PASSED *** 384s Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) 384s *** PASSED *** 384s Elapsed time: 9.869753 seconds 384s -------------------------------------------------------------------------------- 384s -------------------------------------------------------------------------------- 384s Testing input file apbs-smol-surf.in 384s 393s Checking for intermediate energies in input file apbs-mol-surf.out 393s EXPECTED COMPUTED: 7 393s EXPECTED EXPECTED: 7 393s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] 393s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 393s COMPUTED RESULT 2244.350164274 393s COMPUTED RESULT 10521.49475373 393s COMPUTED RESULT 186261.5690066 393s COMPUTED RESULT 305181.0884053 393s COMPUTED RESULT 188662.5455219 393s COMPUTED RESULT 315821.8439277 393s COMPUTED RESULT 119.2607686582 393s BINARY: /usr/bin/apbs 393s INPUT: apbs-smol-surf.in 393s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 393s asc_getToken: Error occurred (bailing out). 393s Vio_scanf: Format problem with input. 393s 393s 393s ---------------------------------------------------------------------- 393s APBS -- Adaptive Poisson-Boltzmann Solver 393s Version APBS 3.4.1 393s 393s Nathan A. Baker (nathan.baker@pnnl.gov) 393s Pacific Northwest National Laboratory 393s 393s Additional contributing authors listed in the code documentation. 393s 393s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 393s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 393s Northwest Division for the U.S. Department of Energy. 393s 393s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 393s Portions Copyright (c) 2002-2020, Nathan A. Baker. 393s Portions Copyright (c) 1999-2002, The Regents of the University of California. 393s Portions Copyright (c) 1995, Michael Holst. 393s All rights reserved. 393s 393s Redistribution and use in source and binary forms, with or without 393s modification, are permitted provided that the following conditions are met: 393s 393s * Redistributions of source code must retain the above copyright notice, this 393s list of conditions and the following disclaimer. 393s 393s * Redistributions in binary form must reproduce the above copyright notice, 393s this list of conditions and the following disclaimer in the documentation 393s and/or other materials provided with the distribution. 393s 393s * Neither the name of the developer nor the names of its contributors may be 393s used to endorse or promote products derived from this software without 393s specific prior written permission. 393s 393s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 393s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 393s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 393s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 393s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 393s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 393s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 393s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 393s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 393s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 393s ---------------------------------------------------------------------- 393s APBS uses FETK (the Finite Element ToolKit) to solve the 393s Poisson-Boltzmann equation numerically. FETK is a portable collection 393s of finite element modeling class libraries developed by the Michael Holst 393s research group and written in an object-oriented form of C. FEtk is 393s designed to solve general coupled systems of nonlinear partial differential 393s equations using adaptive finite element methods, inexact Newton methods, 393s and algebraic multilevel methods. More information about FEtk may be found 393s at . 393s ---------------------------------------------------------------------- 393s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 393s Aqua is a modified form of the Holst group PMG library 393s which has been modified by Patrice Koehl 393s for improved efficiency and 393s memory usage when solving the Poisson-Boltzmann equation. 393s ---------------------------------------------------------------------- 393s Please cite your use of APBS as: 393s 393s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 393s nanosystems: application to microtubules and the ribosome. Proc. 393s Natl. Acad. Sci. USA 98, 10037-10041 2001. 393s 393s 393s This executable compiled on Jan 3 2025 at 11:01:42 393s 393s Parsing input file apbs-smol-surf.in... 393s rank 0 size 1... 393s Parsed input file. 393s Got paths for 3 molecules 393s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 393s asc_getToken: Error occurred (bailing out). 393s Vio_scanf: Format problem with input. 393s 47 atoms 393s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 393s Net charge 1.11e-16 e 393s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 393s asc_getToken: Error occurred (bailing out). 393s Vio_scanf: Format problem with input. 393s 3423 atoms 393s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 393s Net charge 1.00e+00 e 393s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 393s 3470 atoms 393s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 393s Net charge 1.00e+00 e 393s Preparing to run 6 PBE calculations. 393s ---------------------------------------- 393s CALCULATION #1 (lig-coarse): MULTIGRID 393s Setting up problem... 393s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 393s Debye length: 0 A 393s Current memory usage: 203.877 MB total, 203.877 MB high water 393s Using linear spline charge discretization. 393s Grid dimensions: 97 x 97 x 97 393s Grid spacings: 0.729 x 0.729 x 0.729 393s Grid lengths: 70.000 x 70.000 x 70.000 393s Grid center: (28.969, -32.507, 27.022) 393s Multigrid levels: 4 393s Molecule ID: 1 393s Linearized traditional PBE 393s Single Debye-Huckel sphere boundary conditions 393s 2 ion species (0.000 M ionic strength): 393s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 393s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 393s Solute dielectric: 2.000 393s Solvent dielectric: 78.000 393s Using "molecular" surface definition;harmonic average smoothing 393s Solvent probe radius: 1.400 A 393s Temperature: 298.150 K 393s Electrostatic energies will be calculated 393s Total electrostatic energy = 2.251466789420E+03 kJ/mol 393s Calculating forces... 393s ---------------------------------------- 393s CALCULATION #2 (lig-fine): MULTIGRID 393s Setting up problem... 393s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 393s Debye length: 0 A 393s Current memory usage: 203.877 MB total, 405.586 MB high water 393s Using linear spline charge discretization. 393s Grid dimensions: 97 x 97 x 97 393s Grid spacings: 0.250 x 0.250 x 0.250 393s Grid lengths: 24.000 x 24.000 x 24.000 393s Grid center: (24.822, -33.153, 21.545) 393s Multigrid levels: 4 393s Molecule ID: 1 393s Linearized traditional PBE 393s Boundary conditions from focusing 393s 2 ion species (0.000 M ionic strength): 393s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 393s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 393s Solute dielectric: 2.000 393s Solvent dielectric: 78.000 393s Using "molecular" surface definition;harmonic average smoothing 393s Solvent probe radius: 1.400 A 393s Temperature: 298.150 K 393s Electrostatic energies will be calculated 393s Total electrostatic energy = 1.052814502873E+04 kJ/mol 393s Calculating forces... 393s ---------------------------------------- 393s CALCULATION #3 (pka-coarse): MULTIGRID 393s Setting up problem... 393s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 393s Debye length: 0 A 393s Current memory usage: 251.521 MB total, 405.586 MB high water 393s Using linear spline charge discretization. 393s Grid dimensions: 97 x 97 x 97 393s Grid spacings: 0.729 x 0.729 x 0.729 393s Grid lengths: 70.000 x 70.000 x 70.000 393s Grid center: (28.969, -32.507, 27.022) 393s Multigrid levels: 4 393s Molecule ID: 2 393s Linearized traditional PBE 393s Single Debye-Huckel sphere boundary conditions 393s 2 ion species (0.000 M ionic strength): 393s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 393s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 393s Solute dielectric: 2.000 393s Solvent dielectric: 78.000 393s Using "molecular" surface definition;harmonic average smoothing 393s Solvent probe radius: 1.400 A 393s Temperature: 298.150 K 393s Electrostatic energies will be calculated 393s Total electrostatic energy = 1.864071689626E+05 kJ/mol 393s Calculating forces... 393s [focusFillBound()]: WARNING: 393s Unusually large potential values 393s detected on the focusing boundary! 393s Convergence not guaranteed for NPBE/NRPBE calculations! 393s 393s ---------------------------------------- 393s CALCULATION #4 (pka-fine): MULTIGRID 393s Setting up problem... 393s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 393s Debye length: 0 A 393s Current memory usage: 251.521 MB total, 493.795 MB high water 393s Using linear spline charge discretization. 393s Grid dimensions: 97 x 97 x 97 393s Grid spacings: 0.250 x 0.250 x 0.250 393s Grid lengths: 24.000 x 24.000 x 24.000 393s Grid center: (24.822, -33.153, 21.545) 393s Multigrid levels: 4 393s Molecule ID: 2 393s Linearized traditional PBE 393s Boundary conditions from focusing 393s 2 ion species (0.000 M ionic strength): 393s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 393s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 393s Solute dielectric: 2.000 393s Solvent dielectric: 78.000 393s Using "molecular" surface definition;harmonic average smoothing 393s Solvent probe radius: 1.400 A 393s Temperature: 298.150 K 393s Electrostatic energies will be calculated 393s Total electrostatic energy = 3.053319953673E+05 kJ/mol 393s Calculating forces... 393s ---------------------------------------- 393s CALCULATION #5 (complex-coarse): MULTIGRID 393s Setting up problem... 393s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 393s Debye length: 0 A 393s Current memory usage: 251.858 MB total, 493.795 MB high water 393s Using linear spline charge discretization. 393s Grid dimensions: 97 x 97 x 97 393s Grid spacings: 0.729 x 0.729 x 0.729 393s Grid lengths: 70.000 x 70.000 x 70.000 393s Grid center: (28.969, -32.507, 27.022) 393s Multigrid levels: 4 393s Molecule ID: 3 393s Linearized traditional PBE 393s Single Debye-Huckel sphere boundary conditions 393s 2 ion species (0.000 M ionic strength): 393s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 393s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 393s Solute dielectric: 2.000 393s Solvent dielectric: 78.000 393s Using "molecular" surface definition;harmonic average smoothing 393s Solvent probe radius: 1.400 A 393s Temperature: 298.150 K 393s Electrostatic energies will be calculated 393s Total electrostatic energy = 1.888027142979E+05 kJ/mol 393s Calculating forces... 393s [focusFillBound()]: WARNING: 393s Unusually large potential values 393s detected on the focusing boundary! 393s Convergence not guaranteed for NPBE/NRPBE calculations! 393s 393s ---------------------------------------- 393s CALCULATION #6 (complex-fine): MULTIGRID 393s Setting up problem... 393s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 393s Debye length: 0 A 393s Current memory usage: 251.858 MB total, 494.601 MB high water 393s Using linear spline charge discretization. 393s Grid dimensions: 97 x 97 x 97 393s Grid spacings: 0.250 x 0.250 x 0.250 393s Grid lengths: 24.000 x 24.000 x 24.000 393s Grid center: (24.822, -33.153, 21.545) 393s Multigrid levels: 4 393s Molecule ID: 3 393s Linearized traditional PBE 393s Boundary conditions from focusing 393s 2 ion species (0.000 M ionic strength): 393s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 393s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 393s Solute dielectric: 2.000 393s Solvent dielectric: 78.000 393s Using "molecular" surface definition;harmonic average smoothing 393s Solvent probe radius: 1.400 A 393s Temperature: 298.150 K 393s Electrostatic energies will be calculated 393s Total electrostatic energy = 3.159690177241E+05 kJ/mol 393s Calculating forces... 393s ---------------------------------------- 393s PRINT STATEMENTS 393s 393s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 393s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 393s Global net ELEC energy = 1.088773280806E+02 kJ/mol 393s ---------------------------------------- 393s CLEANING UP AND SHUTTING DOWN... 393s Destroying force arrays. 393s No energy arrays to destroy. 393s Destroying multigrid structures. 393s Destroying finite element structures. 393s Destroying 3 molecules 393s Final memory usage: 0.001 MB total, 494.601 MB high water 393s 393s 393s Thanks for using APBS! 393s 393s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 393s *** PASSED *** 393s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 393s *** PASSED *** 393s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 393s *** PASSED *** 393s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 393s *** PASSED *** 393s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 393s *** PASSED *** 393s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 393s *** PASSED *** 393s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 393s *** PASSED *** 393s Elapsed time: 9.080143 seconds 393s -------------------------------------------------------------------------------- 393s Total elapsed time: 39.906322 seconds 393s Test results have been logged 393s -------------------------------------------------------------------------------- 393s -------------------------------------------------------------------------------- 393s Testing input file complex-0_1.in 393s 394s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 394s *** PASSED *** 394s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 394s *** PASSED *** 394s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 394s *** PASSED *** 394s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 394s *** PASSED *** 394s Elapsed time: 0.389134 seconds 394s -------------------------------------------------------------------------------- 394s -------------------------------------------------------------------------------- 394s Testing input file complex-0_2.in 394s 394s Checking for intermediate energies in input file apbs-smol-surf.out 394s EXPECTED COMPUTED: 7 394s EXPECTED EXPECTED: 7 394s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 394s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 394s COMPUTED RESULT 2251.46678942 394s COMPUTED RESULT 10528.14502873 394s COMPUTED RESULT 186407.1689626 394s COMPUTED RESULT 305331.9953673 394s COMPUTED RESULT 188802.7142979 394s COMPUTED RESULT 315969.0177241 394s COMPUTED RESULT 108.8773280806 394s Running tests for point-pmf section 394s BINARY: /usr/bin/apbs 394s INPUT: complex-0_1.in 394s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 394s 394s ---------------------------------------------------------------------- 394s APBS -- Adaptive Poisson-Boltzmann Solver 394s Version APBS 3.4.1 394s 394s Nathan A. Baker (nathan.baker@pnnl.gov) 394s Pacific Northwest National Laboratory 394s 394s Additional contributing authors listed in the code documentation. 394s 394s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 394s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 394s Northwest Division for the U.S. Department of Energy. 394s 394s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 394s Portions Copyright (c) 2002-2020, Nathan A. Baker. 394s Portions Copyright (c) 1999-2002, The Regents of the University of California. 394s Portions Copyright (c) 1995, Michael Holst. 394s All rights reserved. 394s 394s Redistribution and use in source and binary forms, with or without 394s modification, are permitted provided that the following conditions are met: 394s 394s * Redistributions of source code must retain the above copyright notice, this 394s list of conditions and the following disclaimer. 394s 394s * Redistributions in binary form must reproduce the above copyright notice, 394s this list of conditions and the following disclaimer in the documentation 394s and/or other materials provided with the distribution. 394s 394s * Neither the name of the developer nor the names of its contributors may be 394s used to endorse or promote products derived from this software without 394s specific prior written permission. 394s 394s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 394s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 394s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 394s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 394s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 394s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 394s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 394s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 394s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 394s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 394s ---------------------------------------------------------------------- 394s APBS uses FETK (the Finite Element ToolKit) to solve the 394s Poisson-Boltzmann equation numerically. FETK is a portable collection 394s of finite element modeling class libraries developed by the Michael Holst 394s research group and written in an object-oriented form of C. FEtk is 394s designed to solve general coupled systems of nonlinear partial differential 394s equations using adaptive finite element methods, inexact Newton methods, 394s and algebraic multilevel methods. More information about FEtk may be found 394s at . 394s ---------------------------------------------------------------------- 394s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 394s Aqua is a modified form of the Holst group PMG library 394s which has been modified by Patrice Koehl 394s for improved efficiency and 394s memory usage when solving the Poisson-Boltzmann equation. 394s ---------------------------------------------------------------------- 394s Please cite your use of APBS as: 394s 394s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 394s nanosystems: application to microtubules and the ribosome. Proc. 394s Natl. Acad. Sci. USA 98, 10037-10041 2001. 394s 394s 394s This executable compiled on Jan 3 2025 at 11:01:42 394s 394s Parsing input file complex-0_1.in... 394s rank 0 size 1... 394s Parsed input file. 394s Got paths for 3 molecules 394s Reading PQR-format atom data from mol0.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 1 atoms 394s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 394s Net charge 1.00e+00 e 394s Reading PQR-format atom data from mol1.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 1 atoms 394s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 394s Net charge 1.00e+00 e 394s Reading PQR-format atom data from complex-0_1.pqr. 394s 2 atoms 394s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 394s Net charge 2.00e+00 e 394s Preparing to run 3 PBE calculations. 394s ---------------------------------------- 394s CALCULATION #1 (point1): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.060 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 1 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 9.776035707281E+01 kJ/mol 394s Fixed charge energy = 97.7604 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 96.5336 kJ/mol 394s Per-atom energies: 394s Atom 0: 9.776035707281E+01 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #2 (point2): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.067 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 2 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 8.975920687031E+01 kJ/mol 394s Fixed charge energy = 89.7592 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 88.6151 kJ/mol 394s Per-atom energies: 394s Atom 0: 8.975920687031E+01 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #3 (complex): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.067 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 3 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 2.058277719334E+02 kJ/mol 394s Fixed charge energy = 205.828 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 201.106 kJ/mol 394s Per-atom energies: 394s Atom 0: 1.069144350786E+02 kJ/mol 394s Atom 1: 9.891333685475E+01 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s PRINT STATEMENTS 394s 394s print energy 3 (complex) - 1 (point1) - 2 (point2) end 394s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 394s Global net ELEC energy = 1.830820799027E+01 kJ/mol 394s ---------------------------------------- 394s CLEANING UP AND SHUTTING DOWN... 394s Destroying force arrays. 394s No energy arrays to destroy. 394s Destroying multigrid structures. 394s Destroying finite element structures. 394s Destroying 3 molecules 394s Final memory usage: 0.001 MB total, 61.067 MB high water 394s 394s 394s Thanks for using APBS! 394s 394s Checking for intermediate energies in input file complex-0_1.out 394s EXPECTED COMPUTED: 13 394s EXPECTED EXPECTED: 13 394s 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] 394s 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'] 394s COMPUTED RESULT 97.76035707281 394s COMPUTED RESULT 89.75920687031 394s COMPUTED RESULT 205.8277719334 394s COMPUTED RESULT 0.0 394s COMPUTED RESULT 0.0 394s COMPUTED RESULT 0.0 394s COMPUTED RESULT 97.7604 394s COMPUTED RESULT 89.7592 394s COMPUTED RESULT 205.828 394s COMPUTED RESULT 96.5336 394s COMPUTED RESULT 88.6151 394s COMPUTED RESULT 201.106 394s COMPUTED RESULT 18.30820799027 394s BINARY: /usr/bin/apbs 394s INPUT: complex-0_2.in 394s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 394s 394s ---------------------------------------------------------------------- 394s APBS -- Adaptive Poisson-Boltzmann Solver 394s Version APBS 3.4.1 394s 394s Nathan A. Baker (nathan.baker@pnnl.gov) 394s Pacific Northwest National Laboratory 394s 394s Additional contributing authors listed in the code documentation. 394s 394s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 394s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 394s Northwest Division for the U.S. Department of Energy. 394s 394s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 394s Portions Copyright (c) 2002-2020, Nathan A. Baker. 394s Portions Copyright (c) 1999-2002, The Regents of the University of California. 394s Portions Copyright (c) 1995, Michael Holst. 394s All rights reserved. 394s 394s Redistribution and use in source and binary forms, with or without 394s modification, are permitted provided that the following conditions are met: 394s 394s * Redistributions of source code must retain the above copyright notice, this 394s list of conditions and the following disclaimer. 394s 394s * Redistributions in binary form must reproduce the above copyright notice, 394s this list of conditions and the following disclaimer in the documentation 394s and/or other materials provided with the distribution. 394s 394s * Neither the name of the developer nor the names of its contributors may be 394s used to endorse or promote products derived from this software without 394s specific prior written permission. 394s 394s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 394s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 394s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 394s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 394s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 394s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 394s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 394s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 394s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 394s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 394s ---------------------------------------------------------------------- 394s APBS uses FETK (the Finite Element ToolKit) to solve the 394s Poisson-Boltzmann equation numerically. FETK is a portable collection 394s of finite element modeling class libraries developed by the Michael Holst 394s research group and written in an object-oriented form of C. FEtk is 394s designed to solve general coupled systems of nonlinear partial differential 394s equations using adaptive finite element methods, inexact Newton methods, 394s and algebraic multilevel methods. More information about FEtk may be found 394s at . 394s ---------------------------------------------------------------------- 394s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 394s Aqua is a modified form of the Holst group PMG library 394s which has been modified by Patrice Koehl 394s for improved efficiency and 394s memory usage when solving the Poisson-Boltzmann equation. 394s ---------------------------------------------------------------------- 394s Please cite your use of APBS as: 394s 394s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 394s nanosystems: application to microtubules and the ribosome. Proc. 394s Natl. Acad. Sci. USA 98, 10037-10041 2001. 394s 394s 394s This executable compiled on Jan 3 2025 at 11:01:42 394s 394s Parsing input file complex-0_2.in... 394s rank 0 size 1... 394s Parsed input file. 394s Got paths for 3 molecules 394s Reading PQR-format atom data from mol0.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 1 atoms 394s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 394s Net charge 1.00e+00 e 394s Reading PQR-format atom data from mol2.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 1 atoms 394s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 394s Net charge 1.00e+00 e 394s Reading PQR-format atom data from complex-0_2.pqr. 394s 2 atoms 394s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 394s Net charge 2.00e+00 e 394s Preparing to run 3 PBE calculations. 394s ---------------------------------------- 394s CALCULATION #1 (point1): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.060 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 1 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 9.776035707281E+01 kJ/mol 394s Fixed charge energy = 97.7604 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 96.5336 kJ/mol 394s Per-atom energies: 394s Atom 0: 9.776035707281E+01 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #2 (point2): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.067 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 2 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 1.017611498797E+02 kJ/mol 394s Fixed charge energy = 101.761 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 100.656 kJ/mol 394s Per-atom energies: 394s Atom 0: 1.017611498797E+02 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #3 (complex): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.068 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 3 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 394s *** PASSED *** 394s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 394s *** PASSED *** 394s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 394s *** PASSED *** 394s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) 394s *** PASSED *** 394s Elapsed time: 0.392971 seconds 394s -------------------------------------------------------------------------------- 394s -------------------------------------------------------------------------------- 394s Testing input file complex-0_3.in 394s 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 2.084282010393E+02 kJ/mol 394s Fixed charge energy = 208.428 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 203.83 kJ/mol 394s Per-atom energies: 394s Atom 0: 1.022136878480E+02 kJ/mol 394s Atom 1: 1.062145131913E+02 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s PRINT STATEMENTS 394s 394s print energy 3 (complex) - 1 (point1) - 2 (point2) end 394s Local net energy (PE 0) = 8.906694086751E+00 kJ/mol 394s Global net ELEC energy = 8.906694086751E+00 kJ/mol 394s ---------------------------------------- 394s CLEANING UP AND SHUTTING DOWN... 394s Destroying force arrays. 394s No energy arrays to destroy. 394s Destroying multigrid structures. 394s Destroying finite element structures. 394s Destroying 3 molecules 394s Final memory usage: 0.001 MB total, 61.068 MB high water 394s 394s 394s Thanks for using APBS! 394s 394s Checking for intermediate energies in input file complex-0_2.out 394s EXPECTED COMPUTED: 13 394s EXPECTED EXPECTED: 13 394s 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] 394s 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'] 394s COMPUTED RESULT 97.76035707281 394s COMPUTED RESULT 101.7611498797 394s COMPUTED RESULT 208.4282010393 394s COMPUTED RESULT 0.0 394s COMPUTED RESULT 0.0 394s COMPUTED RESULT 0.0 394s COMPUTED RESULT 97.7604 394s COMPUTED RESULT 101.761 394s COMPUTED RESULT 208.428 394s COMPUTED RESULT 96.5336 394s COMPUTED RESULT 100.656 394s COMPUTED RESULT 203.83 394s COMPUTED RESULT 8.906694086751 394s BINARY: /usr/bin/apbs 394s INPUT: complex-0_3.in 394s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 394s 394s ---------------------------------------------------------------------- 394s APBS -- Adaptive Poisson-Boltzmann Solver 394s Version APBS 3.4.1 394s 394s Nathan A. Baker (nathan.baker@pnnl.gov) 394s Pacific Northwest National Laboratory 394s 394s Additional contributing authors listed in the code documentation. 394s 394s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 394s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 394s Northwest Division for the U.S. Department of Energy. 394s 394s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 394s Portions Copyright (c) 2002-2020, Nathan A. Baker. 394s Portions Copyright (c) 1999-2002, The Regents of the University of California. 394s Portions Copyright (c) 1995, Michael Holst. 394s All rights reserved. 394s 394s Redistribution and use in source and binary forms, with or without 394s modification, are permitted provided that the following conditions are met: 394s 394s * Redistributions of source code must retain the above copyright notice, this 394s list of conditions and the following disclaimer. 394s 394s * Redistributions in binary form must reproduce the above copyright notice, 394s this list of conditions and the following disclaimer in the documentation 394s and/or other materials provided with the distribution. 394s 394s * Neither the name of the developer nor the names of its contributors may be 394s used to endorse or promote products derived from this software without 394s specific prior written permission. 394s 394s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 394s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 394s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 394s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 394s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 394s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 394s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 394s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 394s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 394s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 394s ---------------------------------------------------------------------- 394s APBS uses FETK (the Finite Element ToolKit) to solve the 394s Poisson-Boltzmann equation numerically. FETK is a portable collection 394s of finite element modeling class libraries developed by the Michael Holst 394s research group and written in an object-oriented form of C. FEtk is 394s designed to solve general coupled systems of nonlinear partial differential 394s equations using adaptive finite element methods, inexact Newton methods, 394s and algebraic multilevel methods. More information about FEtk may be found 394s at . 394s ---------------------------------------------------------------------- 394s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 394s Aqua is a modified form of the Holst group PMG library 394s which has been modified by Patrice Koehl 394s for improved efficiency and 394s memory usage when solving the Poisson-Boltzmann equation. 394s ---------------------------------------------------------------------- 394s Please cite your use of APBS as: 394s 394s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 394s nanosystems: application to microtubules and the ribosome. Proc. 394s Natl. Acad. Sci. USA 98, 10037-10041 2001. 394s 394s 394s This executable compiled on Jan 3 2025 at 11:01:42 394s 394s Parsing input file complex-0_3.in... 394s rank 0 size 1... 394s Parsed input file. 394s Got paths for 3 molecules 394s Reading PQR-format atom data from mol0.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 1 atoms 394s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 394s Net charge 1.00e+00 e 394s Reading PQR-format atom data from mol3.pqr. 394s asc_getToken: Error occurred (bailing out). 394s Vio_scanf: Format problem with input. 394s 1 atoms 394s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 394s Net charge 1.00e+00 e 394s Reading PQR-format atom data from complex-0_3.pqr. 394s 2 atoms 394s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 394s Net charge 2.00e+00 e 394s Preparing to run 3 PBE calculations. 394s ---------------------------------------- 394s CALCULATION #1 (point1): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.060 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 1 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 9.776035707281E+01 kJ/mol 394s Fixed charge energy = 97.7604 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 96.5336 kJ/mol 394s Per-atom energies: 394s Atom 0: 9.776035707281E+01 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #2 (point2): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.067 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 2 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 1.337661883222E+02 kJ/mol 394s Fixed charge energy = 133.766 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 132.672 kJ/mol 394s Per-atom energies: 394s Atom 0: 1.337661883222E+02 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s CALCULATION #3 (complex): MULTIGRID 394s Setting up problem... 394s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 394s Debye length: 0 A 394s Current memory usage: 61.060 MB total, 61.068 MB high water 394s Using linear spline charge discretization. 394s Grid dimensions: 65 x 65 x 65 394s Grid spacings: 0.210 x 0.210 x 0.210 394s Grid lengths: 13.440 x 13.440 x 13.440 394s Grid center: (0.000, 0.000, 0.000) 394s Multigrid levels: 5 394s Molecule ID: 3 394s Linearized traditional PBE 394s Multiple Debye-Huckel sphere boundary conditions 394s 0 ion species (0.000 M ionic strength): 394s Solute dielectric: 78.540 394s Solvent dielectric: 78.540 394s Using spline-based surface definition;window = 0.300 394s Temperature: 298.150 K 394s Electrostatic energies will be calculated 394s Total electrostatic energy = 2.374361452120E+02 kJ/mol 394s Fixed charge energy = 237.436 kJ/mol 394s Mobile charge energy = 0 kJ/mol 394s Dielectric energy = 232.924 kJ/mol 394s Per-atom energies: 394s Atom 0: 1.007151570480E+02 kJ/mol 394s Atom 1: 1.367209881640E+02 kJ/mol 394s Calculating forces... 394s ---------------------------------------- 394s PRINT STATEMENTS 394s 394s print energy 3 (complex) - 1 (point1) - 2 (point2) end 394s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 394s Global net ELEC energy = 5.909599816984E+00 kJ/mol 394s ---------------------------------------- 394s CLEANING UP AND SHUTTING DOWN... 394s Destroying force arrays. 394s No energy arrays to destroy. 394s Destroying multigrid structures. 394s Destroying finite element structures. 394s Destroying 3 molecules 394s Final memory usage: 0.001 MB total, 61.068 MB high water 394s 394s 394s Thanks for using APBS! 394s 394s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 394s *** PASSED *** 394s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 394s *** PASSED *** 394s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 394s *** PASSED *** 394s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 394s *** PASSED *** 394s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 394s *** PASSED *** 394s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 394s *** PASSED *** 394s Elapsed time: 0.401615 seconds 394s -------------------------------------------------------------------------------- 394s -------------------------------------------------------------------------------- 394s Testing input file complex-0_4.in 394s 395s Checking for intermediate energies in input file complex-0_3.out 395s EXPECTED COMPUTED: 13 395s EXPECTED EXPECTED: 13 395s 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] 395s 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'] 395s COMPUTED RESULT 97.76035707281 395s COMPUTED RESULT 133.7661883222 395s COMPUTED RESULT 237.436145212 395s COMPUTED RESULT 0.0 395s COMPUTED RESULT 0.0 395s COMPUTED RESULT 0.0 395s COMPUTED RESULT 97.7604 395s COMPUTED RESULT 133.766 395s COMPUTED RESULT 237.436 395s COMPUTED RESULT 96.5336 395s COMPUTED RESULT 132.672 395s COMPUTED RESULT 232.924 395s COMPUTED RESULT 5.909599816984 395s BINARY: /usr/bin/apbs 395s INPUT: complex-0_4.in 395s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 395s asc_getToken: Error occurred (bailing out). 395s Vio_scanf: Format problem with input. 395s 395s 395s ---------------------------------------------------------------------- 395s APBS -- Adaptive Poisson-Boltzmann Solver 395s Version APBS 3.4.1 395s 395s Nathan A. Baker (nathan.baker@pnnl.gov) 395s Pacific Northwest National Laboratory 395s 395s Additional contributing authors listed in the code documentation. 395s 395s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 395s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 395s Northwest Division for the U.S. Department of Energy. 395s 395s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 395s Portions Copyright (c) 2002-2020, Nathan A. Baker. 395s Portions Copyright (c) 1999-2002, The Regents of the University of California. 395s Portions Copyright (c) 1995, Michael Holst. 395s All rights reserved. 395s 395s Redistribution and use in source and binary forms, with or without 395s modification, are permitted provided that the following conditions are met: 395s 395s * Redistributions of source code must retain the above copyright notice, this 395s list of conditions and the following disclaimer. 395s 395s * Redistributions in binary form must reproduce the above copyright notice, 395s this list of conditions and the following disclaimer in the documentation 395s and/or other materials provided with the distribution. 395s 395s * Neither the name of the developer nor the names of its contributors may be 395s used to endorse or promote products derived from this software without 395s specific prior written permission. 395s 395s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 395s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 395s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 395s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 395s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 395s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 395s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 395s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 395s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 395s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 395s ---------------------------------------------------------------------- 395s APBS uses FETK (the Finite Element ToolKit) to solve the 395s Poisson-Boltzmann equation numerically. FETK is a portable collection 395s of finite element modeling class libraries developed by the Michael Holst 395s research group and written in an object-oriented form of C. FEtk is 395s designed to solve general coupled systems of nonlinear partial differential 395s equations using adaptive finite element methods, inexact Newton methods, 395s and algebraic multilevel methods. More information about FEtk may be found 395s at . 395s ---------------------------------------------------------------------- 395s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 395s Aqua is a modified form of the Holst group PMG library 395s which has been modified by Patrice Koehl 395s for improved efficiency and 395s memory usage when solving the Poisson-Boltzmann equation. 395s ---------------------------------------------------------------------- 395s Please cite your use of APBS as: 395s 395s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 395s nanosystems: application to microtubules and the ribosome. Proc. 395s Natl. Acad. Sci. USA 98, 10037-10041 2001. 395s 395s 395s This executable compiled on Jan 3 2025 at 11:01:42 395s 395s Parsing input file complex-0_4.in... 395s rank 0 size 1... 395s Parsed input file. 395s Got paths for 3 molecules 395s Reading PQR-format atom data from mol0.pqr. 395s asc_getToken: Error occurred (bailing out). 395s Vio_scanf: Format problem with input. 395s 1 atoms 395s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 395s Net charge 1.00e+00 e 395s Reading PQR-format atom data from mol4.pqr. 395s asc_getToken: Error occurred (bailing out). 395s Vio_scanf: Format problem with input. 395s 1 atoms 395s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 395s Net charge 1.00e+00 e 395s Reading PQR-format atom data from complex-0_4.pqr. 395s 2 atoms 395s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 395s Net charge 2.00e+00 e 395s Preparing to run 3 PBE calculations. 395s ---------------------------------------- 395s CALCULATION #1 (point1): MULTIGRID 395s Setting up problem... 395s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 395s Debye length: 0 A 395s Current memory usage: 61.060 MB total, 61.060 MB high water 395s Using linear spline charge discretization. 395s Grid dimensions: 65 x 65 x 65 395s Grid spacings: 0.210 x 0.210 x 0.210 395s Grid lengths: 13.440 x 13.440 x 13.440 395s Grid center: (0.000, 0.000, 0.000) 395s Multigrid levels: 5 395s Molecule ID: 1 395s Linearized traditional PBE 395s Multiple Debye-Huckel sphere boundary conditions 395s 0 ion species (0.000 M ionic strength): 395s Solute dielectric: 78.540 395s Solvent dielectric: 78.540 395s Using spline-based surface definition;window = 0.300 395s Temperature: 298.150 K 395s Electrostatic energies will be calculated 395s Total electrostatic energy = 9.776035707281E+01 kJ/mol 395s Fixed charge energy = 97.7604 kJ/mol 395s Mobile charge energy = 0 kJ/mol 395s Dielectric energy = 96.5336 kJ/mol 395s Per-atom energies: 395s Atom 0: 9.776035707281E+01 kJ/mol 395s Calculating forces... 395s ---------------------------------------- 395s CALCULATION #2 (point2): MULTIGRID 395s Setting up problem... 395s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 395s Debye length: 0 A 395s Current memory usage: 61.060 MB total, 61.067 MB high water 395s Using linear spline charge discretization. 395s Grid dimensions: 65 x 65 x 65 395s Grid spacings: 0.210 x 0.210 x 0.210 395s Grid lengths: 13.440 x 13.440 x 13.440 395s Grid center: (0.000, 0.000, 0.000) 395s Multigrid levels: 5 395s Molecule ID: 2 395s Linearized traditional PBE 395s Multiple Debye-Huckel sphere boundary conditions 395s 0 ion species (0.000 M ionic strength): 395s Solute dielectric: 78.540 395s Solvent dielectric: 78.540 395s Using spline-based surface definition;window = 0.300 395s Temperature: 298.150 K 395s Electrostatic energies will be calculated 395s Total electrostatic energy = 1.017611498797E+02 kJ/mol 395s Fixed charge energy = 101.761 kJ/mol 395s Mobile charge energy = 0 kJ/mol 395s Dielectric energy = 100.654 kJ/mol 395s Per-atom energies: 395s Atom 0: 1.017611498797E+02 kJ/mol 395s Calculating forces... 395s ---------------------------------------- 395s CALCULATION #3 (complex): MULTIGRID 395s Setting up problem... 395s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 395s Debye length: 0 A 395s Current memory usage: 61.061 MB total, 61.068 MB high water 395s Using linear spline charge discretization. 395s Grid dimensions: 65 x 65 x 65 395s Grid spacings: 0.210 x 0.210 x 0.210 395s Grid lengths: 13.440 x 13.440 x 13.440 395s Grid center: (0.000, 0.000, 0.000) 395s Multigrid levels: 5 395s Molecule ID: 3 395s Linearized traditional PBE 395s Multiple Debye-Huckel sphere boundary conditions 395s 0 ion species (0.000 M ionic strength): 395s Solute dielectric: 78.540 395s Solvent dielectric: 78.540 395s Using spline-based surface definition;window = 0.300 395s Temperature: 298.150 K 395s Electrostatic energies will be calculated 395s Total electrostatic energy = 2.039516519000E+02 kJ/mol 395s Fixed charge energy = 203.952 kJ/mol 395s Mobile charge energy = 0 kJ/mol 395s Dielectric energy = 199.493 kJ/mol 395s Per-atom energies: 395s Atom 0: 9.997541697022E+01 kJ/mol 395s Atom 1: 1.039762349297E+02 kJ/mol 395s Calculating forces... 395s ---------------------------------------- 395s PRINT STATEMENTS 395s 395s print energy 3 (complex) - 1 (point1) - 2 (point2) end 395s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 395s Global net ELEC energy = 4.430144947418E+00 kJ/mol 395s ---------------------------------------- 395s CLEANING UP AND SHUTTING DOWN... 395s Destroying force arrays. 395s No energy arrays to destroy. 395s Destroying multigrid structures. 395s Destroying finite element structures. 395s Destroying 3 molecules 395s Final memory usage: 0.001 MB total, 61.068 MB high water 395s 395s 395s Thanks for using APBS! 395s 395s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 395s *** PASSED *** 395s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 395s *** PASSED *** 395s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 395s *** PASSED *** 395s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 395s *** PASSED *** 395s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 395s *** PASSED *** 395s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 395s *** PASSED *** 395s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 395s *** PASSED *** 395s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 395s *** PASSED *** 395s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 395s *** PASSED *** 395s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 395s *** PASSED *** 395s Elapsed time: 0.481993 seconds 395s -------------------------------------------------------------------------------- 395s Total elapsed time: 1.665713 seconds 395s Test results have been logged 395s -------------------------------------------------------------------------------- 395s -------------------------------------------------------------------------------- 395s Testing input file apbs-mol.in 395s 396s Checking for intermediate energies in input file complex-0_4.out 396s EXPECTED COMPUTED: 13 396s EXPECTED EXPECTED: 13 396s 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] 396s 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'] 396s COMPUTED RESULT 97.76035707281 396s COMPUTED RESULT 101.7611498797 396s COMPUTED RESULT 203.9516519 396s COMPUTED RESULT 0.0 396s COMPUTED RESULT 0.0 396s COMPUTED RESULT 0.0 396s COMPUTED RESULT 97.7604 396s COMPUTED RESULT 101.761 396s COMPUTED RESULT 203.952 396s COMPUTED RESULT 96.5336 396s COMPUTED RESULT 100.654 396s COMPUTED RESULT 199.493 396s COMPUTED RESULT 4.430144947418 396s Running tests for solv section 396s BINARY: /usr/bin/apbs 396s INPUT: apbs-mol.in 396s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 396s asc_getToken: Error occurred (bailing out). 396s Vio_scanf: Format problem with input. 396s 396s 396s ---------------------------------------------------------------------- 396s APBS -- Adaptive Poisson-Boltzmann Solver 396s Version APBS 3.4.1 396s 396s Nathan A. Baker (nathan.baker@pnnl.gov) 396s Pacific Northwest National Laboratory 396s 396s Additional contributing authors listed in the code documentation. 396s 396s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 396s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 396s Northwest Division for the U.S. Department of Energy. 396s 396s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 396s Portions Copyright (c) 2002-2020, Nathan A. Baker. 396s Portions Copyright (c) 1999-2002, The Regents of the University of California. 396s Portions Copyright (c) 1995, Michael Holst. 396s All rights reserved. 396s 396s Redistribution and use in source and binary forms, with or without 396s modification, are permitted provided that the following conditions are met: 396s 396s * Redistributions of source code must retain the above copyright notice, this 396s list of conditions and the following disclaimer. 396s 396s * Redistributions in binary form must reproduce the above copyright notice, 396s this list of conditions and the following disclaimer in the documentation 396s and/or other materials provided with the distribution. 396s 396s * Neither the name of the developer nor the names of its contributors may be 396s used to endorse or promote products derived from this software without 396s specific prior written permission. 396s 396s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 396s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 396s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 396s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 396s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 396s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 396s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 396s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 396s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 396s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 396s ---------------------------------------------------------------------- 396s APBS uses FETK (the Finite Element ToolKit) to solve the 396s Poisson-Boltzmann equation numerically. FETK is a portable collection 396s of finite element modeling class libraries developed by the Michael Holst 396s research group and written in an object-oriented form of C. FEtk is 396s designed to solve general coupled systems of nonlinear partial differential 396s equations using adaptive finite element methods, inexact Newton methods, 396s and algebraic multilevel methods. More information about FEtk may be found 396s at . 396s ---------------------------------------------------------------------- 396s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 396s Aqua is a modified form of the Holst group PMG library 396s which has been modified by Patrice Koehl 396s for improved efficiency and 396s memory usage when solving the Poisson-Boltzmann equation. 396s ---------------------------------------------------------------------- 396s Please cite your use of APBS as: 396s 396s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 396s nanosystems: application to microtubules and the ribosome. Proc. 396s Natl. Acad. Sci. USA 98, 10037-10041 2001. 396s 396s 396s This executable compiled on Jan 3 2025 at 11:01:42 396s 396s Parsing input file apbs-mol.in... 396s rank 0 size 1... 396s Parsed input file. 396s Got paths for 2 molecules 396s Reading PQR-format atom data from methanol.pqr. 396s asc_getToken: Error occurred (bailing out). 396s Vio_scanf: Format problem with input. 396s 3 atoms 396s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 396s Net charge 5.55e-17 e 396s Reading PQR-format atom data from methoxide.pqr. 396s 2 atoms 396s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 396s Net charge -1.00e+00 e 396s Preparing to run 4 PBE calculations. 396s ---------------------------------------- 396s CALCULATION #1 (methanol-solv): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.253 MB total, 61.253 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.309, 0.000, -0.242) 396s Multigrid levels: 5 396s Molecule ID: 1 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 78.000 396s Using "molecular" surface definition; no smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 1.847663548071E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s CALCULATION #2 (methanol-ref): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.253 MB total, 61.328 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.309, 0.000, -0.242) 396s Multigrid levels: 5 396s Molecule ID: 1 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 1.000 396s Using "molecular" surface definition; no smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 1.883912182952E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s CALCULATION #3 (methoxide-solv): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.250 MB total, 61.328 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.000, 0.000, -0.128) 396s Multigrid levels: 5 396s Molecule ID: 2 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 78.000 396s Using "molecular" surface definition; no smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 2.732623683321E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s CALCULATION #4 (methoxide-ref): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.250 MB total, 61.328 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.000, 0.000, -0.128) 396s Multigrid levels: 5 396s Molecule ID: 2 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 1.000 396s Using "molecular" surface definition; no smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 3.123035854133E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s PRINT STATEMENTS 396s 396s print energy 1 (methanol-solv) - 2 (methanol-ref) end 396s Local net energy (PE 0) = -3.624863488075E+01 kJ/mol 396s Global net ELEC energy = -3.624863488075E+01 kJ/mol 396s 396s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 396s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 396s Global net ELEC energy = -3.904121708125E+02 kJ/mol 396s 396s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 396s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 396s Global net ELEC energy = -3.541635359318E+02 kJ/mol 396s ---------------------------------------- 396s CLEANING UP AND SHUTTING DOWN... 396s Destroying force arrays. 396s No energy arrays to destroy. 396s Destroying multigrid structures. 396s Destroying finite element structures. 396s Destroying 2 molecules 396s Final memory usage: 0.001 MB total, 61.328 MB high water 396s 396s 396s Thanks for using APBS! 396s 396s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 396s *** PASSED *** 396s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 396s *** PASSED *** 396s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 396s *** PASSED *** 396s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 396s *** PASSED *** 396s Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) 396s *** PASSED *** 396s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 396s *** PASSED *** 396s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 396s *** PASSED *** 396s Elapsed time: 0.633941 seconds 396s -------------------------------------------------------------------------------- 396s -------------------------------------------------------------------------------- 396s Testing input file apbs-smol.in 396s 396s Checking for intermediate energies in input file apbs-mol.out 396s EXPECTED COMPUTED: 7 396s EXPECTED EXPECTED: 7 396s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] 396s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 396s COMPUTED RESULT 1847.663548071 396s COMPUTED RESULT 1883.912182952 396s COMPUTED RESULT 2732.623683321 396s COMPUTED RESULT 3123.035854133 396s COMPUTED RESULT -36.24863488075 396s COMPUTED RESULT -390.4121708125 396s COMPUTED RESULT -354.1635359318 396s BINARY: /usr/bin/apbs 396s INPUT: apbs-smol.in 396s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 396s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 396s *** PASSED *** 396s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 396s *** PASSED *** 396s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 396s *** PASSED *** 396s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 396s *** PASSED *** 396s Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) 396s *** PASSED *** 396s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 396s *** PASSED *** 396s asc_getToken: Error occurred (bailing out). 396s Vio_scanf: Format problem with input. 396s 396s 396s ---------------------------------------------------------------------- 396s APBS -- Adaptive Poisson-Boltzmann Solver 396s Version APBS 3.4.1 396s 396s Nathan A. Baker (nathan.baker@pnnl.gov) 396s Pacific Northwest National Laboratory 396s 396s Additional contributing authors listed in the code documentation. 396s 396s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 396s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 396s Northwest Division for the U.S. Department of Energy. 396s 396s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 396s Portions Copyright (c) 2002-2020, Nathan A. Baker. 396s Portions Copyright (c) 1999-2002, The Regents of the University of California. 396s Portions Copyright (c) 1995, Michael Holst. 396s All rights reserved. 396s 396s Redistribution and use in source and binary forms, with or without 396s modification, are permitted provided that the following conditions are met: 396s 396s * Redistributions of source code must retain the above copyright notice, this 396s list of conditions and the following disclaimer. 396s 396s * Redistributions in binary form must reproduce the above copyright notice, 396s this list of conditions and the following disclaimer in the documentation 396s and/or other materials provided with the distribution. 396s 396s * Neither the name of the developer nor the names of its contributors may be 396s used to endorse or promote products derived from this software without 396s specific prior written permission. 396s 396s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 396s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 396s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 396s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 396s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 396s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 396s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 396s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 396s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 396s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 396s ---------------------------------------------------------------------- 396s APBS uses FETK (the Finite Element ToolKit) to solve the 396s Poisson-Boltzmann equation numerically. FETK is a portable collection 396s of finite element modeling class libraries developed by the Michael Holst 396s research group and written in an object-oriented form of C. FEtk is 396s designed to solve general coupled systems of nonlinear partial differential 396s equations using adaptive finite element methods, inexact Newton methods, 396s and algebraic multilevel methods. More information about FEtk may be found 396s at . 396s ---------------------------------------------------------------------- 396s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 396s Aqua is a modified form of the Holst group PMG library 396s which has been modified by Patrice Koehl 396s for improved efficiency and 396s memory usage when solving the Poisson-Boltzmann equation. 396s ---------------------------------------------------------------------- 396s Please cite your use of APBS as: 396s 396s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 396s nanosystems: application to microtubules and the ribosome. Proc. 396s Natl. Acad. Sci. USA 98, 10037-10041 2001. 396s 396s 396s This executable compiled on Jan 3 2025 at 11:01:42 396s 396s Parsing input file apbs-smol.in... 396s rank 0 size 1... 396s Parsed input file. 396s Got paths for 2 molecules 396s Reading PQR-format atom data from methanol.pqr. 396s asc_getToken: Error occurred (bailing out). 396s Vio_scanf: Format problem with input. 396s 3 atoms 396s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 396s Net charge 5.55e-17 e 396s Reading PQR-format atom data from methoxide.pqr. 396s 2 atoms 396s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 396s Net charge -1.00e+00 e 396s Preparing to run 4 PBE calculations. 396s ---------------------------------------- 396s CALCULATION #1 (methanol-solv): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.253 MB total, 61.253 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.309, 0.000, -0.242) 396s Multigrid levels: 5 396s Molecule ID: 1 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 78.000 396s Using "molecular" surface definition;harmonic average smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 1.847860440020E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s CALCULATION #2 (methanol-ref): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.253 MB total, 61.328 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.309, 0.000, -0.242) 396s Multigrid levels: 5 396s Molecule ID: 1 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 1.000 396s Using "molecular" surface definition;harmonic average smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 1.885436377745E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s CALCULATION #3 (methoxide-solv): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.250 MB total, 61.328 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.000, 0.000, -0.128) 396s Multigrid levels: 5 396s Molecule ID: 2 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 78.000 396s Using "molecular" surface definition;harmonic average smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 2.734040568569E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s CALCULATION #4 (methoxide-ref): MULTIGRID 396s Setting up problem... 396s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 396s Debye length: 0 A 396s Current memory usage: 61.250 MB total, 61.328 MB high water 396s Using linear spline charge discretization. 396s Grid dimensions: 65 x 65 x 65 396s Grid spacings: 0.250 x 0.250 x 0.250 396s Grid lengths: 16.000 x 16.000 x 16.000 396s Grid center: (0.000, 0.000, -0.128) 396s Multigrid levels: 5 396s Molecule ID: 2 396s Linearized traditional PBE 396s Multiple Debye-Huckel sphere boundary conditions 396s 2 ion species (0.000 M ionic strength): 396s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 396s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 396s Solute dielectric: 2.000 396s Solvent dielectric: 1.000 396s Using "molecular" surface definition;harmonic average smoothing 396s Solvent probe radius: 0.000 A 396s Temperature: 300.000 K 396s Electrostatic energies will be calculated 396s Total electrostatic energy = 3.125279428954E+03 kJ/mol 396s Calculating forces... 396s ---------------------------------------- 396s PRINT STATEMENTS 396s 396s print energy 1 (methanol-solv) - 2 (methanol-ref) end 396s Local net energy (PE 0) = -3.757593772492E+01 kJ/mol 396s Global net ELEC energy = -3.757593772492E+01 kJ/mol 396s 396s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 396s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 396s Global net ELEC energy = -3.912388603848E+02 kJ/mol 396s 396s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 396s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 396s Global net ELEC energy = -3.536629226599E+02 kJ/mol 396s ---------------------------------------- 396s CLEANING UP AND SHUTTING DOWN... 396s Destroying force arrays. 396s No energy arrays to destroy. 396s Destroying multigrid structures. 396s Destroying finite element structures. 396s Destroying 2 molecules 396s Final memory usage: 0.001 MB total, 61.328 MB high water 396s 396s 396s Thanks for using APBS! 396s 396s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 396s *** PASSED *** 396s Elapsed time: 0.637867 seconds 396s -------------------------------------------------------------------------------- 396s Total elapsed time: 1.271808 seconds 396s Test results have been logged 396s -------------------------------------------------------------------------------- 396s Checking for intermediate energies in input file apbs-smol.out 396s EXPECTED COMPUTED: 7 396s EXPECTED EXPECTED: 7 396s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] 396s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 396s COMPUTED RESULT 1847.86044002 396s COMPUTED RESULT 1885.436377745 396s COMPUTED RESULT 2734.040568569 396s COMPUTED RESULT 3125.279428954 396s COMPUTED RESULT -37.57593772492 396s COMPUTED RESULT -391.2388603848 396s COMPUTED RESULT -353.6629226599 397s autopkgtest [19:57:07]: test test-apbs: -----------------------] 398s test-apbs PASS 398s autopkgtest [19:57:08]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 398s autopkgtest [19:57:08]: @@@@@@@@@@@@@@@@@@@@ summary 398s test-apbs PASS