0s autopkgtest [16:09:18]: starting date and time: 2025-10-18 16:09:18+0000 0s autopkgtest [16:09:18]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:09:18]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.om3ljj18/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade apbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-1.secgroup --name adt-resolute-s390x-apbs-20251018-160918-juju-7f2275-prod-proposed-migration-environment-15-ec5d5cce-faf8-49ce-be92-8bfbe658354e --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-apbs-20251018-160918-juju-7f2275-prod-proposed-migration-environment-15-ec5d5cce-faf8-49ce-be92-8bfbe658354e from image adt/ubuntu-resolute-s390x-server-20251018.img (UUID c47ab411-f9be-46ce-b861-20d934d06dba)... 46s autopkgtest [16:10:04]: testbed dpkg architecture: s390x 46s autopkgtest [16:10:04]: testbed apt version: 3.1.6ubuntu2 47s autopkgtest [16:10:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s autopkgtest [16:10:05]: testbed release detected to be: None 48s autopkgtest [16:10:06]: updating testbed package index (apt update) 48s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 48s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 49s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 49s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 49s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 49s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [74.0 kB] 49s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 49s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [226 kB] 49s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [3812 B] 49s Fetched 781 kB in 1s (771 kB/s) 49s Reading package lists... 50s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 50s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 50s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 50s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 51s Reading package lists... 51s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s Calculating upgrade... 51s The following packages will be upgraded: 51s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 51s libpython3-stdlib lto-disabled-list python3 python3-minimal 51s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 2763 kB of archives. 51s After this operation, 14.3 kB of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.13.7-2 [27.8 kB] 51s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.13.7-2 [23.9 kB] 51s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.13.7-2 [10.6 kB] 51s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libapt-pkg7.0 s390x 3.1.8ubuntu1 [1144 kB] 52s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x apt s390x 3.1.8ubuntu1 [1432 kB] 52s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libgirepository-1.0-1 s390x 1.86.0-6 [86.9 kB] 52s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x gir1.2-girepository-2.0 s390x 1.86.0-6 [25.1 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x lto-disabled-list all 71 [12.5 kB] 53s dpkg-preconfigure: unable to re-open stdin: No such file or directory 53s Fetched 2763 kB in 1s (1923 kB/s) 53s (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 ... 56852 files and directories currently installed.) 53s Preparing to unpack .../python3-minimal_3.13.7-2_s390x.deb ... 53s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 53s Setting up python3-minimal (3.13.7-2) ... 53s (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 ... 56852 files and directories currently installed.) 53s Preparing to unpack .../0-python3_3.13.7-2_s390x.deb ... 53s running python pre-rtupdate hooks for python3.13... 53s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 53s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_s390x.deb ... 53s Unpacking libpython3-stdlib:s390x (3.13.7-2) over (3.13.7-1) ... 53s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_s390x.deb ... 53s Unpacking libapt-pkg7.0:s390x (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 53s Preparing to unpack .../3-apt_3.1.8ubuntu1_s390x.deb ... 53s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 53s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_s390x.deb ... 53s Unpacking libgirepository-1.0-1:s390x (1.86.0-6) over (1.84.0-1) ... 53s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_s390x.deb ... 53s Unpacking gir1.2-girepository-2.0:s390x (1.86.0-6) over (1.84.0-1) ... 53s Preparing to unpack .../6-lto-disabled-list_71_all.deb ... 53s Unpacking lto-disabled-list (71) over (69) ... 53s Setting up lto-disabled-list (71) ... 53s Setting up libgirepository-1.0-1:s390x (1.86.0-6) ... 53s Setting up libapt-pkg7.0:s390x (3.1.8ubuntu1) ... 53s Setting up libpython3-stdlib:s390x (3.13.7-2) ... 53s Setting up apt (3.1.8ubuntu1) ... 54s Setting up python3 (3.13.7-2) ... 54s running python rtupdate hooks for python3.13... 54s running python post-rtupdate hooks for python3.13... 54s Setting up gir1.2-girepository-2.0:s390x (1.86.0-6) ... 54s Processing triggers for man-db (2.13.1-1) ... 55s Processing triggers for libc-bin (2.42-0ubuntu3) ... 55s autopkgtest [16:10:13]: upgrading testbed (apt dist-upgrade and autopurge) 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Solving dependencies... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s autopkgtest [16:10:15]: rebooting testbed after setup commands that affected boot 70s autopkgtest [16:10:28]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 72s autopkgtest [16:10:30]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 82s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 82s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 82s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 82s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 82s gpgv: Can't check signature: No public key 82s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 84s autopkgtest [16:10:42]: testing package apbs version 3.4.1-6build2 92s autopkgtest [16:10:50]: build not needed 103s autopkgtest [16:11:01]: test test-apbs: preparing testbed 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s Solving dependencies... 103s The following NEW packages will be installed: 103s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax libamd3 103s libapbs-dev libapbs3t64 libarpack2t64 libblas3 libcamd3 libccolamd3 103s libcholmod5 libcolamd3 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 103s libfabric1 libfetk-dev libfetk1.9t64 libgfortran5 libgomp1 libhwloc-plugins 103s libhwloc15 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore 103s liblapack3 libmaloc-dev libmaloc1 libopenmpi40 libpciaccess0 librdmacm1t64 103s libspqr4 libsuitesparseconfig7 libsuperlu7 libumfpack6 libxnvctrl0 103s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 103s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 32.7 MB of archives. 103s After this operation, 127 MB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1 [2781 kB] 105s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x apbs-data all 3.4.1-6build2 [1769 kB] 106s Get:3 http://ftpmaster.internal/ubuntu resolute/universe s390x libmaloc1 s390x 1.5-2 [102 kB] 106s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 106s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x libsuperlu7 s390x 7.0.1+dfsg1-2 [233 kB] 106s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-5ubuntu1 [154 kB] 106s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libsuitesparseconfig7 s390x 1:7.10.1+dfsg-1 [21.3 kB] 106s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x libamd3 s390x 1:7.10.1+dfsg-1 [43.3 kB] 106s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x libcamd3 s390x 1:7.10.1+dfsg-1 [37.8 kB] 106s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x libccolamd3 s390x 1:7.10.1+dfsg-1 [40.8 kB] 106s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libcolamd3 s390x 1:7.10.1+dfsg-1 [31.2 kB] 106s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 106s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 106s Get:14 http://ftpmaster.internal/ubuntu resolute/universe s390x libcholmod5 s390x 1:7.10.1+dfsg-1 [927 kB] 107s Get:15 http://ftpmaster.internal/ubuntu resolute/universe s390x libumfpack6 s390x 1:7.10.1+dfsg-1 [378 kB] 107s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x libfetk1.9t64 s390x 3.4.1-6build2 [666 kB] 107s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x libapbs3t64 s390x 3.4.1-6build2 [292 kB] 107s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 107s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 108s Get:20 http://ftpmaster.internal/ubuntu resolute/universe s390x libarpack2t64 s390x 3.9.1-6 [110 kB] 108s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libevent-core-2.1-7t64 s390x 2.1.12-stable-10build1 [93.1 kB] 108s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10build1 [8060 B] 108s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x librdmacm1t64 s390x 56.1-1ubuntu1 [73.6 kB] 108s Get:24 http://ftpmaster.internal/ubuntu resolute/universe s390x libfabric1 s390x 2.1.0-1.1 [640 kB] 108s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x libhwloc15 s390x 2.12.2-1 [175 kB] 108s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x libpciaccess0 s390x 0.18.1-1ubuntu2 [19.1 kB] 108s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 108s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x ocl-icd-libopencl1 s390x 2.3.3-1 [44.9 kB] 108s Get:29 http://ftpmaster.internal/ubuntu resolute/universe s390x libhwloc-plugins s390x 2.12.2-1 [15.9 kB] 108s Get:30 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmpi40 s390x 5.0.8-8ubuntu1 [2907 kB] 108s Get:31 http://ftpmaster.internal/ubuntu resolute/universe s390x libspqr4 s390x 1:7.10.1+dfsg-1 [179 kB] 108s Get:32 http://ftpmaster.internal/ubuntu resolute/universe s390x apbs s390x 3.4.1-6build2 [75.2 kB] 108s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 108s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 108s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 108s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 108s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 108s Get:38 http://ftpmaster.internal/ubuntu resolute/universe s390x apbs-doc all 3.4.1-6build2 [5850 kB] 109s Get:39 http://ftpmaster.internal/ubuntu resolute/universe s390x libapbs-dev s390x 3.4.1-6build2 [99.5 kB] 109s Get:40 http://ftpmaster.internal/ubuntu resolute/universe s390x libmaloc-dev s390x 1.5-2 [903 kB] 109s Get:41 http://ftpmaster.internal/ubuntu resolute/universe s390x libfetk-dev s390x 3.4.1-6build2 [144 kB] 109s Get:42 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-apbslib s390x 3.4.1-6build2 [213 kB] 109s Fetched 32.7 MB in 5s (5995 kB/s) 109s Selecting previously unselected package fonts-lato. 109s (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 ... 56852 files and directories currently installed.) 109s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 109s Unpacking fonts-lato (2.015-1) ... 109s Selecting previously unselected package apbs-data. 109s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 109s Unpacking apbs-data (3.4.1-6build2) ... 109s Selecting previously unselected package libmaloc1:s390x. 109s Preparing to unpack .../02-libmaloc1_1.5-2_s390x.deb ... 109s Unpacking libmaloc1:s390x (1.5-2) ... 109s Selecting previously unselected package libblas3:s390x. 109s Preparing to unpack .../03-libblas3_3.12.1-6build1_s390x.deb ... 109s Unpacking libblas3:s390x (3.12.1-6build1) ... 109s Selecting previously unselected package libsuperlu7:s390x. 109s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_s390x.deb ... 109s Unpacking libsuperlu7:s390x (7.0.1+dfsg1-2) ... 109s Selecting previously unselected package libgomp1:s390x. 109s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_s390x.deb ... 109s Unpacking libgomp1:s390x (15.2.0-5ubuntu1) ... 109s Selecting previously unselected package libsuitesparseconfig7:s390x. 109s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_s390x.deb ... 109s Unpacking libsuitesparseconfig7:s390x (1:7.10.1+dfsg-1) ... 109s Selecting previously unselected package libamd3:s390x. 109s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 109s Unpacking libamd3:s390x (1:7.10.1+dfsg-1) ... 109s Selecting previously unselected package libcamd3:s390x. 109s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 109s Unpacking libcamd3:s390x (1:7.10.1+dfsg-1) ... 109s Selecting previously unselected package libccolamd3:s390x. 109s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 109s Unpacking libccolamd3:s390x (1:7.10.1+dfsg-1) ... 109s Selecting previously unselected package libcolamd3:s390x. 109s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_s390x.deb ... 109s Unpacking libcolamd3:s390x (1:7.10.1+dfsg-1) ... 109s Selecting previously unselected package libgfortran5:s390x. 109s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 109s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 109s Selecting previously unselected package liblapack3:s390x. 109s Preparing to unpack .../12-liblapack3_3.12.1-6build1_s390x.deb ... 109s Unpacking liblapack3:s390x (3.12.1-6build1) ... 109s Selecting previously unselected package libcholmod5:s390x. 109s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_s390x.deb ... 109s Unpacking libcholmod5:s390x (1:7.10.1+dfsg-1) ... 109s Selecting previously unselected package libumfpack6:s390x. 109s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_s390x.deb ... 109s Unpacking libumfpack6:s390x (1:7.10.1+dfsg-1) ... 109s Selecting previously unselected package libfetk1.9t64:s390x. 109s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_s390x.deb ... 109s Unpacking libfetk1.9t64:s390x (3.4.1-6build2) ... 109s Selecting previously unselected package libapbs3t64:s390x. 109s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_s390x.deb ... 109s Unpacking libapbs3t64:s390x (3.4.1-6build2) ... 109s Selecting previously unselected package fonts-mathjax. 109s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 109s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 110s Selecting previously unselected package libjs-mathjax. 110s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 110s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 110s Selecting previously unselected package libarpack2t64:s390x. 110s Preparing to unpack .../19-libarpack2t64_3.9.1-6_s390x.deb ... 110s Unpacking libarpack2t64:s390x (3.9.1-6) ... 110s Selecting previously unselected package libevent-core-2.1-7t64:s390x. 110s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_s390x.deb ... 110s Unpacking libevent-core-2.1-7t64:s390x (2.1.12-stable-10build1) ... 110s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 110s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_s390x.deb ... 110s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10build1) ... 110s Selecting previously unselected package librdmacm1t64:s390x. 110s Preparing to unpack .../22-librdmacm1t64_56.1-1ubuntu1_s390x.deb ... 110s Unpacking librdmacm1t64:s390x (56.1-1ubuntu1) ... 110s Selecting previously unselected package libfabric1:s390x. 110s Preparing to unpack .../23-libfabric1_2.1.0-1.1_s390x.deb ... 110s Unpacking libfabric1:s390x (2.1.0-1.1) ... 110s Selecting previously unselected package libhwloc15:s390x. 110s Preparing to unpack .../24-libhwloc15_2.12.2-1_s390x.deb ... 110s Unpacking libhwloc15:s390x (2.12.2-1) ... 110s Selecting previously unselected package libpciaccess0:s390x. 110s Preparing to unpack .../25-libpciaccess0_0.18.1-1ubuntu2_s390x.deb ... 110s Unpacking libpciaccess0:s390x (0.18.1-1ubuntu2) ... 110s Selecting previously unselected package libxnvctrl0:s390x. 110s Preparing to unpack .../26-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 110s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 110s Selecting previously unselected package ocl-icd-libopencl1:s390x. 110s Preparing to unpack .../27-ocl-icd-libopencl1_2.3.3-1_s390x.deb ... 110s Unpacking ocl-icd-libopencl1:s390x (2.3.3-1) ... 110s Selecting previously unselected package libhwloc-plugins:s390x. 110s Preparing to unpack .../28-libhwloc-plugins_2.12.2-1_s390x.deb ... 110s Unpacking libhwloc-plugins:s390x (2.12.2-1) ... 110s Selecting previously unselected package libopenmpi40:s390x. 110s Preparing to unpack .../29-libopenmpi40_5.0.8-8ubuntu1_s390x.deb ... 110s Unpacking libopenmpi40:s390x (5.0.8-8ubuntu1) ... 110s Selecting previously unselected package libspqr4:s390x. 110s Preparing to unpack .../30-libspqr4_1%3a7.10.1+dfsg-1_s390x.deb ... 110s Unpacking libspqr4:s390x (1:7.10.1+dfsg-1) ... 110s Selecting previously unselected package apbs. 110s Preparing to unpack .../31-apbs_3.4.1-6build2_s390x.deb ... 110s Unpacking apbs (3.4.1-6build2) ... 110s Selecting previously unselected package libjs-jquery. 110s Preparing to unpack .../32-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 110s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 110s Selecting previously unselected package libjs-underscore. 110s Preparing to unpack .../33-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 110s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 110s Selecting previously unselected package libjs-sphinxdoc. 110s Preparing to unpack .../34-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 110s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 110s Selecting previously unselected package fonts-font-awesome. 110s Preparing to unpack .../35-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 110s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 110s Selecting previously unselected package sphinx-rtd-theme-common. 110s Preparing to unpack .../36-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 110s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 110s Selecting previously unselected package apbs-doc. 110s Preparing to unpack .../37-apbs-doc_3.4.1-6build2_all.deb ... 110s Unpacking apbs-doc (3.4.1-6build2) ... 110s Selecting previously unselected package libapbs-dev:s390x. 110s Preparing to unpack .../38-libapbs-dev_3.4.1-6build2_s390x.deb ... 110s Unpacking libapbs-dev:s390x (3.4.1-6build2) ... 110s Selecting previously unselected package libmaloc-dev. 110s Preparing to unpack .../39-libmaloc-dev_1.5-2_s390x.deb ... 110s Unpacking libmaloc-dev (1.5-2) ... 110s Selecting previously unselected package libfetk-dev:s390x. 110s Preparing to unpack .../40-libfetk-dev_3.4.1-6build2_s390x.deb ... 110s Unpacking libfetk-dev:s390x (3.4.1-6build2) ... 110s Selecting previously unselected package python3-apbslib. 110s Preparing to unpack .../41-python3-apbslib_3.4.1-6build2_s390x.deb ... 110s Unpacking python3-apbslib (3.4.1-6build2) ... 110s Setting up libmaloc1:s390x (1.5-2) ... 110s Setting up libpciaccess0:s390x (0.18.1-1ubuntu2) ... 110s Setting up fonts-lato (2.015-1) ... 110s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 110s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 110s Setting up apbs-data (3.4.1-6build2) ... 110s Setting up libgomp1:s390x (15.2.0-5ubuntu1) ... 110s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 110s Setting up libblas3:s390x (3.12.1-6build1) ... 110s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 110s Setting up libhwloc15:s390x (2.12.2-1) ... 110s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 110s Setting up ocl-icd-libopencl1:s390x (2.3.3-1) ... 110s Setting up libsuitesparseconfig7:s390x (1:7.10.1+dfsg-1) ... 110s Setting up librdmacm1t64:s390x (56.1-1ubuntu1) ... 110s Setting up libevent-core-2.1-7t64:s390x (2.1.12-stable-10build1) ... 110s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 110s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 110s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 110s Setting up libmaloc-dev (1.5-2) ... 110s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 110s Setting up libfabric1:s390x (2.1.0-1.1) ... 110s Setting up liblapack3:s390x (3.12.1-6build1) ... 110s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 110s Setting up libarpack2t64:s390x (3.9.1-6) ... 110s Setting up libamd3:s390x (1:7.10.1+dfsg-1) ... 110s Setting up libcolamd3:s390x (1:7.10.1+dfsg-1) ... 110s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10build1) ... 110s Setting up libhwloc-plugins:s390x (2.12.2-1) ... 110s Setting up libcamd3:s390x (1:7.10.1+dfsg-1) ... 110s Setting up libsuperlu7:s390x (7.0.1+dfsg1-2) ... 110s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 110s Setting up libccolamd3:s390x (1:7.10.1+dfsg-1) ... 110s Setting up libopenmpi40:s390x (5.0.8-8ubuntu1) ... 110s Setting up libcholmod5:s390x (1:7.10.1+dfsg-1) ... 110s Setting up libspqr4:s390x (1:7.10.1+dfsg-1) ... 110s Setting up apbs-doc (3.4.1-6build2) ... 110s Setting up libumfpack6:s390x (1:7.10.1+dfsg-1) ... 110s Setting up libfetk1.9t64:s390x (3.4.1-6build2) ... 110s Setting up libapbs3t64:s390x (3.4.1-6build2) ... 110s Setting up libfetk-dev:s390x (3.4.1-6build2) ... 110s Setting up libapbs-dev:s390x (3.4.1-6build2) ... 110s Setting up apbs (3.4.1-6build2) ... 110s Setting up python3-apbslib (3.4.1-6build2) ... 110s Processing triggers for man-db (2.13.1-1) ... 111s Processing triggers for libc-bin (2.42-0ubuntu3) ... 113s autopkgtest [16:11:11]: test test-apbs: [----------------------- 113s TESTING WITH BINARY_NAME:apbs 113s START_DIR:/tmp/autopkgtest.v8loXO/autopkgtest_tmp/build 113s -------------------------------------------------------------------------------- 113s Testing forces from apbs-forces.in 113s 113s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000548 seconds 113s -------------------------------------------------------------------------------- 113s -------------------------------------------------------------------------------- 113s Testing input file apbs-mol-auto.in 113s 114s CHECKING:/usr/local/sbin/apbs 114s CHECKING:/usr/local/bin/apbs 114s CHECKING:/usr/sbin/apbs 114s CHECKING:/usr/bin/apbs 114s NOTE: Using apbs binary:/usr/bin/apbs 114s Testing all sections 114s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 114s ================================================================================ 114s Running tests for born section 114s BINARY: /usr/bin/apbs 114s INPUT: apbs-mol-auto.in 114s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 114s asc_getToken: Error occurred (bailing out). 114s Vio_scanf: Format problem with input. 114s 114s 114s ---------------------------------------------------------------------- 114s APBS -- Adaptive Poisson-Boltzmann Solver 114s Version APBS 3.4.1 114s 114s Nathan A. Baker (nathan.baker@pnnl.gov) 114s Pacific Northwest National Laboratory 114s 114s Additional contributing authors listed in the code documentation. 114s 114s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 114s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 114s Northwest Division for the U.S. Department of Energy. 114s 114s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 114s Portions Copyright (c) 2002-2020, Nathan A. Baker. 114s Portions Copyright (c) 1999-2002, The Regents of the University of California. 114s Portions Copyright (c) 1995, Michael Holst. 114s All rights reserved. 114s 114s Redistribution and use in source and binary forms, with or without 114s modification, are permitted provided that the following conditions are met: 114s 114s * Redistributions of source code must retain the above copyright notice, this 114s list of conditions and the following disclaimer. 114s 114s * Redistributions in binary form must reproduce the above copyright notice, 114s this list of conditions and the following disclaimer in the documentation 114s and/or other materials provided with the distribution. 114s 114s * Neither the name of the developer nor the names of its contributors may be 114s used to endorse or promote products derived from this software without 114s specific prior written permission. 114s 114s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 114s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 114s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 114s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 114s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 114s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 114s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 114s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 114s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 114s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 114s ---------------------------------------------------------------------- 114s APBS uses FETK (the Finite Element ToolKit) to solve the 114s Poisson-Boltzmann equation numerically. FETK is a portable collection 114s of finite element modeling class libraries developed by the Michael Holst 114s research group and written in an object-oriented form of C. FEtk is 114s designed to solve general coupled systems of nonlinear partial differential 114s equations using adaptive finite element methods, inexact Newton methods, 114s and algebraic multilevel methods. More information about FEtk may be found 114s at . 114s ---------------------------------------------------------------------- 114s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 114s Aqua is a modified form of the Holst group PMG library 114s which has been modified by Patrice Koehl 114s for improved efficiency and 114s memory usage when solving the Poisson-Boltzmann equation. 114s ---------------------------------------------------------------------- 114s Please cite your use of APBS as: 114s 114s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 114s nanosystems: application to microtubules and the ribosome. Proc. 114s Natl. Acad. Sci. USA 98, 10037-10041 2001. 114s 114s 114s This executable compiled on Jan 3 2025 at 11:01:42 114s 114s Parsing input file apbs-mol-auto.in... 114s rank 0 size 1... 114s Parsed input file. 114s Got paths for 1 molecules 114s Reading PQR-format atom data from ion.pqr. 114s 1 atoms 114s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 114s Net charge 1.00e+00 e 114s Preparing to run 6 PBE calculations. 114s ---------------------------------------- 114s CALCULATION #1 (solvated): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.280 MB total, 61.280 MB high water 114s Using cubic spline charge discretization. 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.781 x 0.781 x 0.781 114s Grid lengths: 50.000 x 50.000 x 50.000 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Multiple Debye-Huckel sphere boundary conditions 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 78.540 114s Using "molecular" surface definition; no smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 9.607073836227E+02 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s CALCULATION #2 (solvated): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.280 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.383 x 0.383 x 0.383 114s Grid lengths: 24.495 x 24.495 x 24.495 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 78.540 114s Using "molecular" surface definition; no smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 2.200266567971E+03 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s CALCULATION #3 (solvated): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.280 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.188 x 0.188 x 0.188 114s Grid lengths: 12.000 x 12.000 x 12.000 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 78.540 114s Using "molecular" surface definition; no smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Potential to be written to potential.dx.gz 114s Total electrostatic energy = 4.732245131587E+03 kJ/mol 114s Calculating forces... 114s Writing potential to potential-PE0.dx.gz 114s ---------------------------------------- 114s CALCULATION #4 (reference): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.207 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.781 x 0.781 x 0.781 114s Grid lengths: 50.000 x 50.000 x 50.000 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Multiple Debye-Huckel sphere boundary conditions 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 1.000 114s Using "molecular" surface definition; no smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 1.190871482831E+03 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s CALCULATION #5 (reference): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.207 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.383 x 0.383 x 0.383 114s Grid lengths: 24.495 x 24.495 x 24.495 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 1.000 114s Using "molecular" surface definition; no smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 2.430874049735E+03 kJ/mol 114s Calculating forces... 114s [focusFillBound()]: WARNING: 114s Unusually large potential values 114s detected on the focusing boundary! 114s Convergence not guaranteed for NPBE/NRPBE calculations! 114s 114s ---------------------------------------- 114s CALCULATION #6 (reference): MULTIGRID 114s Setting up problem... 114s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 114s Debye length: 0 A 114s Current memory usage: 61.207 MB total, 122.102 MB high water 114s Using cubic spline charge discretization. 114s Grid dimensions: 65 x 65 x 65 114s Grid spacings: 0.188 x 0.188 x 0.188 114s Grid lengths: 12.000 x 12.000 x 12.000 114s Grid center: (0.000, 0.000, 0.000) 114s Multigrid levels: 5 114s Molecule ID: 1 114s Linearized traditional PBE 114s Boundary conditions from focusing 114s 0 ion species (0.000 M ionic strength): 114s Solute dielectric: 1.000 114s Solvent dielectric: 1.000 114s Using "molecular" surface definition; no smoothing 114s Solvent probe radius: 1.400 A 114s Temperature: 298.150 K 114s Electrostatic energies will be calculated 114s Total electrostatic energy = 4.962018684215E+03 kJ/mol 114s Calculating forces... 114s ---------------------------------------- 114s PRINT STATEMENTS 114s 114s print energy 1 (solvated) - 2 (reference) end 114s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 114s Global net ELEC energy = -2.297735526282E+02 kJ/mol 114s ---------------------------------------- 114s CLEANING UP AND SHUTTING DOWN... 114s Destroying force arrays. 114s No energy arrays to destroy. 114s Destroying multigrid structures. 114s Destroying finite element structures. 114s Destroying 1 molecules 114s Final memory usage: 0.001 MB total, 122.102 MB high water 114s 114s 114s Thanks for using APBS! 114s 114s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 114s *** PASSED *** 114s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 114s *** PASSED *** 114s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 114s *** PASSED *** 114s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 114s *** PASSED *** 114s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 114s *** PASSED *** 114s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 114s *** PASSED *** 114s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 114s *** PASSED *** 114s Elapsed time: 0.959608 seconds 114s -------------------------------------------------------------------------------- 114s -------------------------------------------------------------------------------- 114s Testing input file apbs-smol-auto.in 114s 115s Checking for intermediate energies in input file apbs-mol-auto.out 115s EXPECTED COMPUTED: 7 115s EXPECTED EXPECTED: 7 115s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 115s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 115s COMPUTED RESULT 960.7073836227 115s COMPUTED RESULT 2200.266567971 115s COMPUTED RESULT 4732.245131587 115s COMPUTED RESULT 1190.871482831 115s COMPUTED RESULT 2430.874049735 115s COMPUTED RESULT 4962.018684215 115s COMPUTED RESULT -229.7735526282 115s BINARY: /usr/bin/apbs 115s INPUT: apbs-smol-auto.in 115s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 115s asc_getToken: Error occurred (bailing out). 115s Vio_scanf: Format problem with input. 115s 115s 115s ---------------------------------------------------------------------- 115s APBS -- Adaptive Poisson-Boltzmann Solver 115s Version APBS 3.4.1 115s 115s Nathan A. Baker (nathan.baker@pnnl.gov) 115s Pacific Northwest National Laboratory 115s 115s Additional contributing authors listed in the code documentation. 115s 115s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 115s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 115s Northwest Division for the U.S. Department of Energy. 115s 115s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 115s Portions Copyright (c) 2002-2020, Nathan A. Baker. 115s Portions Copyright (c) 1999-2002, The Regents of the University of California. 115s Portions Copyright (c) 1995, Michael Holst. 115s All rights reserved. 115s 115s Redistribution and use in source and binary forms, with or without 115s modification, are permitted provided that the following conditions are met: 115s 115s * Redistributions of source code must retain the above copyright notice, this 115s list of conditions and the following disclaimer. 115s 115s * Redistributions in binary form must reproduce the above copyright notice, 115s this list of conditions and the following disclaimer in the documentation 115s and/or other materials provided with the distribution. 115s 115s * Neither the name of the developer nor the names of its contributors may be 115s used to endorse or promote products derived from this software without 115s specific prior written permission. 115s 115s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 115s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 115s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 115s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 115s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 115s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 115s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 115s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 115s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 115s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 115s ---------------------------------------------------------------------- 115s APBS uses FETK (the Finite Element ToolKit) to solve the 115s Poisson-Boltzmann equation numerically. FETK is a portable collection 115s of finite element modeling class libraries developed by the Michael Holst 115s research group and written in an object-oriented form of C. FEtk is 115s designed to solve general coupled systems of nonlinear partial differential 115s equations using adaptive finite element methods, inexact Newton methods, 115s and algebraic multilevel methods. More information about FEtk may be found 115s at . 115s ---------------------------------------------------------------------- 115s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 115s Aqua is a modified form of the Holst group PMG library 115s which has been modified by Patrice Koehl 115s for improved efficiency and 115s memory usage when solving the Poisson-Boltzmann equation. 115s ---------------------------------------------------------------------- 115s Please cite your use of APBS as: 115s 115s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 115s nanosystems: application to microtubules and the ribosome. Proc. 115s Natl. Acad. Sci. USA 98, 10037-10041 2001. 115s 115s 115s This executable compiled on Jan 3 2025 at 11:01:42 115s 115s Parsing input file apbs-smol-auto.in... 115s rank 0 size 1... 115s Parsed input file. 115s Got paths for 1 molecules 115s Reading PQR-format atom data from ion.pqr. 115s 1 atoms 115s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 115s Net charge 1.00e+00 e 115s Preparing to run 6 PBE calculations. 115s ---------------------------------------- 115s CALCULATION #1 (solvated): MULTIGRID 115s Setting up problem... 115s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 115s Debye length: 0 A 115s Current memory usage: 61.280 MB total, 61.280 MB high water 115s Using cubic spline charge discretization. 115s Grid dimensions: 65 x 65 x 65 115s Grid spacings: 0.781 x 0.781 x 0.781 115s Grid lengths: 50.000 x 50.000 x 50.000 115s Grid center: (0.000, 0.000, 0.000) 115s Multigrid levels: 5 115s Molecule ID: 1 115s Linearized traditional PBE 115s Multiple Debye-Huckel sphere boundary conditions 115s 0 ion species (0.000 M ionic strength): 115s Solute dielectric: 1.000 115s Solvent dielectric: 78.540 115s Using "molecular" surface definition;harmonic average smoothing 115s Solvent probe radius: 1.400 A 115s Temperature: 298.150 K 115s Electrostatic energies will be calculated 115s Total electrostatic energy = 9.532928767450E+02 kJ/mol 115s Calculating forces... 115s ---------------------------------------- 115s CALCULATION #2 (solvated): MULTIGRID 115s Setting up problem... 115s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 115s Debye length: 0 A 115s Current memory usage: 61.280 MB total, 122.102 MB high water 115s Using cubic spline charge discretization. 115s Grid dimensions: 65 x 65 x 65 115s Grid spacings: 0.383 x 0.383 x 0.383 115s Grid lengths: 24.495 x 24.495 x 24.495 115s Grid center: (0.000, 0.000, 0.000) 115s Multigrid levels: 5 115s Molecule ID: 1 115s Linearized traditional PBE 115s Boundary conditions from focusing 115s 0 ion species (0.000 M ionic strength): 115s Solute dielectric: 1.000 115s Solvent dielectric: 78.540 115s Using "molecular" surface definition;harmonic average smoothing 115s Solvent probe radius: 1.400 A 115s Temperature: 298.150 K 115s Electrostatic energies will be calculated 115s Total electrostatic energy = 2.201243880085E+03 kJ/mol 115s Calculating forces... 115s ---------------------------------------- 115s CALCULATION #3 (solvated): MULTIGRID 115s Setting up problem... 115s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 115s Debye length: 0 A 115s Current memory usage: 61.280 MB total, 122.102 MB high water 115s Using cubic spline charge discretization. 115s Grid dimensions: 65 x 65 x 65 115s Grid spacings: 0.188 x 0.188 x 0.188 115s Grid lengths: 12.000 x 12.000 x 12.000 115s Grid center: (0.000, 0.000, 0.000) 115s Multigrid levels: 5 115s Molecule ID: 1 115s Linearized traditional PBE 115s Boundary conditions from focusing 115s 0 ion species (0.000 M ionic strength): 115s Solute dielectric: 1.000 115s Solvent dielectric: 78.540 115s Using "molecular" surface definition;harmonic average smoothing 115s Solvent probe radius: 1.400 A 115s Temperature: 298.150 K 115s Electrostatic energies will be calculated 115s Total electrostatic energy = 4.733006258977E+03 kJ/mol 115s Calculating forces... 115s ---------------------------------------- 115s CALCULATION #4 (reference): MULTIGRID 115s Setting up problem... 115s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 115s Debye length: 0 A 115s Current memory usage: 61.207 MB total, 122.102 MB high water 115s Using cubic spline charge discretization. 115s Grid dimensions: 65 x 65 x 65 115s Grid spacings: 0.781 x 0.781 x 0.781 115s Grid lengths: 50.000 x 50.000 x 50.000 115s Grid center: (0.000, 0.000, 0.000) 115s Multigrid levels: 5 115s Molecule ID: 1 115s Linearized traditional PBE 115s Multiple Debye-Huckel sphere boundary conditions 115s 0 ion species (0.000 M ionic strength): 115s Solute dielectric: 1.000 115s Solvent dielectric: 1.000 115s Using "molecular" surface definition;harmonic average smoothing 115s Solvent probe radius: 1.400 A 115s Temperature: 298.150 K 115s Electrostatic energies will be calculated 115s Total electrostatic energy = 1.190871482831E+03 kJ/mol 115s Calculating forces... 115s ---------------------------------------- 115s CALCULATION #5 (reference): MULTIGRID 115s Setting up problem... 115s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 115s Debye length: 0 A 115s Current memory usage: 61.207 MB total, 122.102 MB high water 115s Using cubic spline charge discretization. 115s Grid dimensions: 65 x 65 x 65 115s Grid spacings: 0.383 x 0.383 x 0.383 115s Grid lengths: 24.495 x 24.495 x 24.495 115s Grid center: (0.000, 0.000, 0.000) 115s Multigrid levels: 5 115s Molecule ID: 1 115s Linearized traditional PBE 115s Boundary conditions from focusing 115s 0 ion species (0.000 M ionic strength): 115s Solute dielectric: 1.000 115s Solvent dielectric: 1.000 115s Using "molecular" surface definition;harmonic average smoothing 115s Solvent probe radius: 1.400 A 115s Temperature: 298.150 K 115s Electrostatic energies will be calculated 115s Total electrostatic energy = 2.430874049735E+03 kJ/mol 115s Calculating forces... 115s [focusFillBound()]: WARNING: 115s Unusually large potential values 115s detected on the focusing boundary! 115s Convergence not guaranteed for NPBE/NRPBE calculations! 115s 115s ---------------------------------------- 115s CALCULATION #6 (reference): MULTIGRID 115s Setting up problem... 115s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 115s Debye length: 0 A 115s Current memory usage: 61.207 MB total, 122.102 MB high water 115s Using cubic spline charge discretization. 115s Grid dimensions: 65 x 65 x 65 115s Grid spacings: 0.188 x 0.188 x 0.188 115s Grid lengths: 12.000 x 12.000 x 12.000 115s Grid center: (0.000, 0.000, 0.000) 115s Multigrid levels: 5 115s Molecule ID: 1 115s Linearized traditional PBE 115s Boundary conditions from focusing 115s 0 ion species (0.000 M ionic strength): 115s Solute dielectric: 1.000 115s Solvent dielectric: 1.000 115s Using "molecular" surface definition;harmonic average smoothing 115s Solvent probe radius: 1.400 A 115s Temperature: 298.150 K 115s Electrostatic energies will be calculated 115s Total electrostatic energy = 4.962018684215E+03 kJ/mol 115s Calculating forces... 115s ---------------------------------------- 115s PRINT STATEMENTS 115s 115s print energy 1 (solvated) - 2 (reference) end 115s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 115s Global net ELEC energy = -2.290124252387E+02 kJ/mol 115s ---------------------------------------- 115s CLEANING UP AND SHUTTING DOWN... 115s Destroying force arrays. 115s No energy arrays to destroy. 115s Destroying multigrid structures. 115s Destroying finite element structures. 115s Destroying 1 molecules 115s Final memory usage: 0.001 MB total, 122.102 MB high water 115s 115s 115s Thanks for using APBS! 115s 115s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 115s *** PASSED *** 115s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 115s *** PASSED *** 115s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 115s *** PASSED *** 115s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 115s *** PASSED *** 115s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 115s *** PASSED *** 115s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 115s *** PASSED *** 115s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 115s *** PASSED *** 115s Elapsed time: 0.875958 seconds 115s -------------------------------------------------------------------------------- 115s -------------------------------------------------------------------------------- 115s Testing input file apbs-mol-parallel.in 115s 115s Splitting the input file into 4 separate files using the inputgen utility 115s 116s Checking for intermediate energies in input file apbs-smol-auto.out 116s EXPECTED COMPUTED: 7 116s EXPECTED EXPECTED: 7 116s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 116s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 116s COMPUTED RESULT 953.292876745 116s COMPUTED RESULT 2201.243880085 116s COMPUTED RESULT 4733.006258977 116s COMPUTED RESULT 1190.871482831 116s COMPUTED RESULT 2430.874049735 116s COMPUTED RESULT 4962.018684215 116s COMPUTED RESULT -229.0124252387 116s BINARY: /usr/bin/apbs 116s INPUT: apbs-mol-parallel-PE0.in 116s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 116s asc_getToken: Error occurred (bailing out). 116s Vio_scanf: Format problem with input. 116s 116s 116s ---------------------------------------------------------------------- 116s APBS -- Adaptive Poisson-Boltzmann Solver 116s Version APBS 3.4.1 116s 116s Nathan A. Baker (nathan.baker@pnnl.gov) 116s Pacific Northwest National Laboratory 116s 116s Additional contributing authors listed in the code documentation. 116s 116s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 116s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 116s Northwest Division for the U.S. Department of Energy. 116s 116s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 116s Portions Copyright (c) 2002-2020, Nathan A. Baker. 116s Portions Copyright (c) 1999-2002, The Regents of the University of California. 116s Portions Copyright (c) 1995, Michael Holst. 116s All rights reserved. 116s 116s Redistribution and use in source and binary forms, with or without 116s modification, are permitted provided that the following conditions are met: 116s 116s * Redistributions of source code must retain the above copyright notice, this 116s list of conditions and the following disclaimer. 116s 116s * Redistributions in binary form must reproduce the above copyright notice, 116s this list of conditions and the following disclaimer in the documentation 116s and/or other materials provided with the distribution. 116s 116s * Neither the name of the developer nor the names of its contributors may be 116s used to endorse or promote products derived from this software without 116s specific prior written permission. 116s 116s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 116s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 116s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 116s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 116s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 116s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 116s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 116s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 116s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 116s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 116s ---------------------------------------------------------------------- 116s APBS uses FETK (the Finite Element ToolKit) to solve the 116s Poisson-Boltzmann equation numerically. FETK is a portable collection 116s of finite element modeling class libraries developed by the Michael Holst 116s research group and written in an object-oriented form of C. FEtk is 116s designed to solve general coupled systems of nonlinear partial differential 116s equations using adaptive finite element methods, inexact Newton methods, 116s and algebraic multilevel methods. More information about FEtk may be found 116s at . 116s ---------------------------------------------------------------------- 116s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 116s Aqua is a modified form of the Holst group PMG library 116s which has been modified by Patrice Koehl 116s for improved efficiency and 116s memory usage when solving the Poisson-Boltzmann equation. 116s ---------------------------------------------------------------------- 116s Please cite your use of APBS as: 116s 116s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 116s nanosystems: application to microtubules and the ribosome. Proc. 116s Natl. Acad. Sci. USA 98, 10037-10041 2001. 116s 116s 116s This executable compiled on Jan 3 2025 at 11:01:42 116s 116s Parsing input file apbs-mol-parallel-PE0.in... 116s rank 0 size 1... 116s Parsed input file. 116s Got paths for 1 molecules 116s Reading PQR-format atom data from ion.pqr. 116s 1 atoms 116s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 116s Net charge 1.00e+00 e 116s Preparing to run 6 PBE calculations. 116s ---------------------------------------- 116s CALCULATION #1 (solvated): MULTIGRID 116s Setting up problem... 116s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 116s Debye length: 0 A 116s Current memory usage: 61.280 MB total, 61.280 MB high water 116s Using cubic spline charge discretization. 116s Partition overlap fraction = 0.1 116s Processor array = 2 x 2 x 1 116s Grid dimensions: 65 x 65 x 65 116s Grid spacings: 0.781 x 0.781 x 0.781 116s Grid lengths: 50.000 x 50.000 x 50.000 116s Grid center: (0.000, 0.000, 0.000) 116s Multigrid levels: 5 116s Molecule ID: 1 116s Linearized traditional PBE 116s Multiple Debye-Huckel sphere boundary conditions 116s 0 ion species (0.000 M ionic strength): 116s Solute dielectric: 1.000 116s Solvent dielectric: 78.540 116s Using "molecular" surface definition; no smoothing 116s Solvent probe radius: 1.400 A 116s Temperature: 298.150 K 116s Electrostatic energies will be calculated 116s Total electrostatic energy = 2.401768459022E+02 kJ/mol 116s Calculating forces... 116s ---------------------------------------- 116s CALCULATION #2 (solvated): MULTIGRID 116s Setting up problem... 116s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 116s Debye length: 0 A 116s Current memory usage: 61.280 MB total, 122.102 MB high water 116s Using cubic spline charge discretization. 116s Partition overlap fraction = 0.1 116s Processor array = 2 x 2 x 1 116s Grid dimensions: 65 x 65 x 65 116s Grid spacings: 0.296 x 0.296 x 0.383 116s Grid lengths: 18.944 x 18.944 x 24.495 116s Grid center: (-2.411, -2.411, 0.000) 116s Multigrid levels: 5 116s Molecule ID: 1 116s Linearized traditional PBE 116s Boundary conditions from focusing 116s 0 ion species (0.000 M ionic strength): 116s Solute dielectric: 1.000 116s Solvent dielectric: 78.540 116s Using "molecular" surface definition; no smoothing 116s Solvent probe radius: 1.400 A 116s Temperature: 298.150 K 116s Electrostatic energies will be calculated 116s Total electrostatic energy = 8.142935592471E+02 kJ/mol 116s Calculating forces... 116s [focusFillBound()]: WARNING: 116s Unusually large potential values 116s detected on the focusing boundary! 116s Convergence not guaranteed for NPBE/NRPBE calculations! 116s 116s ---------------------------------------- 116s CALCULATION #3 (solvated): MULTIGRID 116s Setting up problem... 116s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 116s Debye length: 0 A 116s Current memory usage: 61.280 MB total, 122.102 MB high water 116s Using cubic spline charge discretization. 116s Partition overlap fraction = 0.1 116s Processor array = 2 x 2 x 1 116s Grid dimensions: 65 x 65 x 65 116s Grid spacings: 0.112 x 0.112 x 0.188 116s Grid lengths: 7.178 x 7.178 x 12.000 116s Grid center: (-2.411, -2.411, 0.000) 116s Multigrid levels: 5 116s Molecule ID: 1 116s Linearized traditional PBE 116s Boundary conditions from focusing 116s 0 ion species (0.000 M ionic strength): 116s Solute dielectric: 1.000 116s Solvent dielectric: 78.540 116s Using "molecular" surface definition; no smoothing 116s Solvent probe radius: 1.400 A 116s Temperature: 298.150 K 116s Electrostatic energies will be calculated 116s Total electrostatic energy = 1.485255308186E+03 kJ/mol 116s Calculating forces... 116s ---------------------------------------- 116s CALCULATION #4 (reference): MULTIGRID 116s Setting up problem... 116s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 116s Debye length: 0 A 116s Current memory usage: 61.207 MB total, 122.102 MB high water 116s Using cubic spline charge discretization. 116s Partition overlap fraction = 0.1 116s Processor array = 2 x 2 x 1 116s Grid dimensions: 65 x 65 x 65 116s Grid spacings: 0.781 x 0.781 x 0.781 116s Grid lengths: 50.000 x 50.000 x 50.000 116s Grid center: (0.000, 0.000, 0.000) 116s Multigrid levels: 5 116s Molecule ID: 1 116s Linearized traditional PBE 116s Multiple Debye-Huckel sphere boundary conditions 116s 0 ion species (0.000 M ionic strength): 116s Solute dielectric: 1.000 116s Solvent dielectric: 1.000 116s Using "molecular" surface definition; no smoothing 116s Solvent probe radius: 1.400 A 116s Temperature: 298.150 K 116s Electrostatic energies will be calculated 116s Total electrostatic energy = 2.977178707009E+02 kJ/mol 116s Calculating forces... 116s ---------------------------------------- 116s CALCULATION #5 (reference): MULTIGRID 116s Setting up problem... 116s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 116s Debye length: 0 A 116s Current memory usage: 61.207 MB total, 122.102 MB high water 116s Using cubic spline charge discretization. 116s Partition overlap fraction = 0.1 116s Processor array = 2 x 2 x 1 116s Grid dimensions: 65 x 65 x 65 116s Grid spacings: 0.296 x 0.296 x 0.383 116s Grid lengths: 18.944 x 18.944 x 24.495 116s Grid center: (-2.411, -2.411, 0.000) 116s Multigrid levels: 5 116s Molecule ID: 1 116s Linearized traditional PBE 116s Boundary conditions from focusing 116s 0 ion species (0.000 M ionic strength): 116s Solute dielectric: 1.000 116s Solvent dielectric: 1.000 116s Using "molecular" surface definition; no smoothing 116s Solvent probe radius: 1.400 A 116s Temperature: 298.150 K 116s Electrostatic energies will be calculated 116s Total electrostatic energy = 8.799304557588E+02 kJ/mol 116s Calculating forces... 116s [focusFillBound()]: WARNING: 116s Unusually large potential values 116s detected on the focusing boundary! 116s Convergence not guaranteed for NPBE/NRPBE calculations! 116s 116s ---------------------------------------- 116s CALCULATION #6 (reference): MULTIGRID 116s Setting up problem... 116s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 116s Debye length: 0 A 116s Current memory usage: 61.207 MB total, 122.102 MB high water 116s Using cubic spline charge discretization. 116s Partition overlap fraction = 0.1 116s Processor array = 2 x 2 x 1 116s Grid dimensions: 65 x 65 x 65 116s Grid spacings: 0.112 x 0.112 x 0.188 116s Grid lengths: 7.178 x 7.178 x 12.000 116s Grid center: (-2.411, -2.411, 0.000) 116s Multigrid levels: 5 116s Molecule ID: 1 116s Linearized traditional PBE 116s Boundary conditions from focusing 116s 0 ion species (0.000 M ionic strength): 116s Solute dielectric: 1.000 116s Solvent dielectric: 1.000 116s Using "molecular" surface definition; no smoothing 116s Solvent probe radius: 1.400 A 116s Temperature: 298.150 K 116s Electrostatic energies will be calculated 116s Total electrostatic energy = 1.542873949131E+03 kJ/mol 116s Calculating forces... 116s ---------------------------------------- 116s PRINT STATEMENTS 116s 116s print energy 1 (solvated) - 2 (reference) end 116s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 116s Global net ELEC energy = -5.761864094552E+01 kJ/mol 116s ---------------------------------------- 116s CLEANING UP AND SHUTTING DOWN... 116s Destroying force arrays. 116s No energy arrays to destroy. 116s Destroying multigrid structures. 116s Destroying finite element structures. 116s Destroying 1 molecules 116s Final memory usage: 0.001 MB total, 122.102 MB high water 116s 116s 116s Thanks for using APBS! 116s 116s Processor 0 results: 116s 2.401768459022e+02 116s 8.142935592471e+02 116s 1.485255308186e+03 116s 2.977178707009e+02 116s 8.799304557588e+02 116s 1.542873949131e+03 116s -5.761864094552e+01 116s 117s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 117s BINARY: /usr/bin/apbs 117s INPUT: apbs-mol-parallel-PE1.in 117s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 117s asc_getToken: Error occurred (bailing out). 117s Vio_scanf: Format problem with input. 117s 117s 117s ---------------------------------------------------------------------- 117s APBS -- Adaptive Poisson-Boltzmann Solver 117s Version APBS 3.4.1 117s 117s Nathan A. Baker (nathan.baker@pnnl.gov) 117s Pacific Northwest National Laboratory 117s 117s Additional contributing authors listed in the code documentation. 117s 117s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 117s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 117s Northwest Division for the U.S. Department of Energy. 117s 117s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 117s Portions Copyright (c) 2002-2020, Nathan A. Baker. 117s Portions Copyright (c) 1999-2002, The Regents of the University of California. 117s Portions Copyright (c) 1995, Michael Holst. 117s All rights reserved. 117s 117s Redistribution and use in source and binary forms, with or without 117s modification, are permitted provided that the following conditions are met: 117s 117s * Redistributions of source code must retain the above copyright notice, this 117s list of conditions and the following disclaimer. 117s 117s * Redistributions in binary form must reproduce the above copyright notice, 117s this list of conditions and the following disclaimer in the documentation 117s and/or other materials provided with the distribution. 117s 117s * Neither the name of the developer nor the names of its contributors may be 117s used to endorse or promote products derived from this software without 117s specific prior written permission. 117s 117s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 117s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 117s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 117s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 117s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 117s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 117s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 117s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 117s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 117s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 117s ---------------------------------------------------------------------- 117s APBS uses FETK (the Finite Element ToolKit) to solve the 117s Poisson-Boltzmann equation numerically. FETK is a portable collection 117s of finite element modeling class libraries developed by the Michael Holst 117s research group and written in an object-oriented form of C. FEtk is 117s designed to solve general coupled systems of nonlinear partial differential 117s equations using adaptive finite element methods, inexact Newton methods, 117s and algebraic multilevel methods. More information about FEtk may be found 117s at . 117s ---------------------------------------------------------------------- 117s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 117s Aqua is a modified form of the Holst group PMG library 117s which has been modified by Patrice Koehl 117s for improved efficiency and 117s memory usage when solving the Poisson-Boltzmann equation. 117s ---------------------------------------------------------------------- 117s Please cite your use of APBS as: 117s 117s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 117s nanosystems: application to microtubules and the ribosome. Proc. 117s Natl. Acad. Sci. USA 98, 10037-10041 2001. 117s 117s 117s This executable compiled on Jan 3 2025 at 11:01:42 117s 117s Parsing input file apbs-mol-parallel-PE1.in... 117s rank 0 size 1... 117s Parsed input file. 117s Got paths for 1 molecules 117s Reading PQR-format atom data from ion.pqr. 117s 1 atoms 117s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 117s Net charge 1.00e+00 e 117s Preparing to run 6 PBE calculations. 117s ---------------------------------------- 117s CALCULATION #1 (solvated): MULTIGRID 117s Setting up problem... 117s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 117s Debye length: 0 A 117s Current memory usage: 61.280 MB total, 61.280 MB high water 117s Using cubic spline charge discretization. 117s Partition overlap fraction = 0.1 117s Processor array = 2 x 2 x 1 117s Grid dimensions: 65 x 65 x 65 117s Grid spacings: 0.781 x 0.781 x 0.781 117s Grid lengths: 50.000 x 50.000 x 50.000 117s Grid center: (0.000, 0.000, 0.000) 117s Multigrid levels: 5 117s Molecule ID: 1 117s Linearized traditional PBE 117s Multiple Debye-Huckel sphere boundary conditions 117s 0 ion species (0.000 M ionic strength): 117s Solute dielectric: 1.000 117s Solvent dielectric: 78.540 117s Using "molecular" surface definition; no smoothing 117s Solvent probe radius: 1.400 A 117s Temperature: 298.150 K 117s Electrostatic energies will be calculated 117s Total electrostatic energy = 2.401768459022E+02 kJ/mol 117s Calculating forces... 117s ---------------------------------------- 117s CALCULATION #2 (solvated): MULTIGRID 117s Setting up problem... 117s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 117s Debye length: 0 A 117s Current memory usage: 61.280 MB total, 122.102 MB high water 117s Using cubic spline charge discretization. 117s Partition overlap fraction = 0.1 117s Processor array = 2 x 2 x 1 117s Grid dimensions: 65 x 65 x 65 117s Grid spacings: 0.296 x 0.296 x 0.383 117s Grid lengths: 18.944 x 18.944 x 24.495 117s Grid center: (2.411, -2.411, 0.000) 117s Multigrid levels: 5 117s Molecule ID: 1 117s Linearized traditional PBE 117s Boundary conditions from focusing 117s 0 ion species (0.000 M ionic strength): 117s Solute dielectric: 1.000 117s Solvent dielectric: 78.540 117s Using "molecular" surface definition; no smoothing 117s Solvent probe radius: 1.400 A 117s Temperature: 298.150 K 117s Electrostatic energies will be calculated 117s Total electrostatic energy = 8.142778312125E+02 kJ/mol 117s Calculating forces... 117s [focusFillBound()]: WARNING: 117s Unusually large potential values 117s detected on the focusing boundary! 117s Convergence not guaranteed for NPBE/NRPBE calculations! 117s 117s ---------------------------------------- 117s CALCULATION #3 (solvated): MULTIGRID 117s Setting up problem... 117s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 117s Debye length: 0 A 117s Current memory usage: 61.280 MB total, 122.102 MB high water 117s Using cubic spline charge discretization. 117s Partition overlap fraction = 0.1 117s Processor array = 2 x 2 x 1 117s Grid dimensions: 65 x 65 x 65 117s Grid spacings: 0.112 x 0.112 x 0.188 117s Grid lengths: 7.178 x 7.178 x 12.000 117s Grid center: (2.411, -2.411, 0.000) 117s Multigrid levels: 5 117s Molecule ID: 1 117s Linearized traditional PBE 117s Boundary conditions from focusing 117s 0 ion species (0.000 M ionic strength): 117s Solute dielectric: 1.000 117s Solvent dielectric: 78.540 117s Using "molecular" surface definition; no smoothing 117s Solvent probe radius: 1.400 A 117s Temperature: 298.150 K 117s Electrostatic energies will be calculated 117s Total electrostatic energy = 1.485246667424E+03 kJ/mol 117s Calculating forces... 117s ---------------------------------------- 117s CALCULATION #4 (reference): MULTIGRID 117s Setting up problem... 117s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 117s Debye length: 0 A 117s Current memory usage: 61.207 MB total, 122.102 MB high water 117s Using cubic spline charge discretization. 117s Partition overlap fraction = 0.1 117s Processor array = 2 x 2 x 1 117s Grid dimensions: 65 x 65 x 65 117s Grid spacings: 0.781 x 0.781 x 0.781 117s Grid lengths: 50.000 x 50.000 x 50.000 117s Grid center: (0.000, 0.000, 0.000) 117s Multigrid levels: 5 117s Molecule ID: 1 117s Linearized traditional PBE 117s Multiple Debye-Huckel sphere boundary conditions 117s 0 ion species (0.000 M ionic strength): 117s Solute dielectric: 1.000 117s Solvent dielectric: 1.000 117s Using "molecular" surface definition; no smoothing 117s Solvent probe radius: 1.400 A 117s Temperature: 298.150 K 117s Electrostatic energies will be calculated 117s Total electrostatic energy = 2.977178707009E+02 kJ/mol 117s Calculating forces... 117s ---------------------------------------- 117s CALCULATION #5 (reference): MULTIGRID 117s Setting up problem... 117s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 117s Debye length: 0 A 117s Current memory usage: 61.207 MB total, 122.102 MB high water 117s Using cubic spline charge discretization. 117s Partition overlap fraction = 0.1 117s Processor array = 2 x 2 x 1 117s Grid dimensions: 65 x 65 x 65 117s Grid spacings: 0.296 x 0.296 x 0.383 117s Grid lengths: 18.944 x 18.944 x 24.495 117s Grid center: (2.411, -2.411, 0.000) 117s Multigrid levels: 5 117s Molecule ID: 1 117s Linearized traditional PBE 117s Boundary conditions from focusing 117s 0 ion species (0.000 M ionic strength): 117s Solute dielectric: 1.000 117s Solvent dielectric: 1.000 117s Using "molecular" surface definition; no smoothing 117s Solvent probe radius: 1.400 A 117s Temperature: 298.150 K 117s Electrostatic energies will be calculated 117s Total electrostatic energy = 8.799304557588E+02 kJ/mol 117s Calculating forces... 117s [focusFillBound()]: WARNING: 117s Unusually large potential values 117s detected on the focusing boundary! 117s Convergence not guaranteed for NPBE/NRPBE calculations! 117s 117s ---------------------------------------- 117s CALCULATION #6 (reference): MULTIGRID 117s Setting up problem... 117s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 117s Debye length: 0 A 117s Current memory usage: 61.207 MB total, 122.102 MB high water 117s Using cubic spline charge discretization. 117s Partition overlap fraction = 0.1 117s Processor array = 2 x 2 x 1 117s Grid dimensions: 65 x 65 x 65 117s Grid spacings: 0.112 x 0.112 x 0.188 117s Grid lengths: 7.178 x 7.178 x 12.000 117s Grid center: (2.411, -2.411, 0.000) 117s Multigrid levels: 5 117s Molecule ID: 1 117s Linearized traditional PBE 117s Boundary conditions from focusing 117s 0 ion species (0.000 M ionic strength): 117s Solute dielectric: 1.000 117s Solvent dielectric: 1.000 117s Using "molecular" surface definition; no smoothing 117s Solvent probe radius: 1.400 A 117s Temperature: 298.150 K 117s Electrostatic energies will be calculated 117s Total electrostatic energy = 1.542873949131E+03 kJ/mol 117s Calculating forces... 117s ---------------------------------------- 117s PRINT STATEMENTS 117s 117s print energy 1 (solvated) - 2 (reference) end 117s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 117s Global net ELEC energy = -5.762728170718E+01 kJ/mol 117s ---------------------------------------- 117s CLEANING UP AND SHUTTING DOWN... 117s Destroying force arrays. 117s No energy arrays to destroy. 117s Destroying multigrid structures. 117s Destroying finite element structures. 117s Destroying 1 molecules 117s Final memory usage: 0.001 MB total, 122.102 MB high water 117s 117s 117s Thanks for using APBS! 117s 117s Processor 1 results: 117s 2.401768459022e+02 117s 8.142778312125e+02 117s 1.485246667424e+03 117s 2.977178707009e+02 117s 8.799304557588e+02 117s 1.542873949131e+03 117s -5.762728170718e+01 117s 118s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 118s BINARY: /usr/bin/apbs 118s INPUT: apbs-mol-parallel-PE2.in 118s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 118s asc_getToken: Error occurred (bailing out). 118s Vio_scanf: Format problem with input. 118s 118s 118s ---------------------------------------------------------------------- 118s APBS -- Adaptive Poisson-Boltzmann Solver 118s Version APBS 3.4.1 118s 118s Nathan A. Baker (nathan.baker@pnnl.gov) 118s Pacific Northwest National Laboratory 118s 118s Additional contributing authors listed in the code documentation. 118s 118s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 118s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 118s Northwest Division for the U.S. Department of Energy. 118s 118s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 118s Portions Copyright (c) 2002-2020, Nathan A. Baker. 118s Portions Copyright (c) 1999-2002, The Regents of the University of California. 118s Portions Copyright (c) 1995, Michael Holst. 118s All rights reserved. 118s 118s Redistribution and use in source and binary forms, with or without 118s modification, are permitted provided that the following conditions are met: 118s 118s * Redistributions of source code must retain the above copyright notice, this 118s list of conditions and the following disclaimer. 118s 118s * Redistributions in binary form must reproduce the above copyright notice, 118s this list of conditions and the following disclaimer in the documentation 118s and/or other materials provided with the distribution. 118s 118s * Neither the name of the developer nor the names of its contributors may be 118s used to endorse or promote products derived from this software without 118s specific prior written permission. 118s 118s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 118s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 118s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 118s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 118s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 118s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 118s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 118s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 118s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 118s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 118s ---------------------------------------------------------------------- 118s APBS uses FETK (the Finite Element ToolKit) to solve the 118s Poisson-Boltzmann equation numerically. FETK is a portable collection 118s of finite element modeling class libraries developed by the Michael Holst 118s research group and written in an object-oriented form of C. FEtk is 118s designed to solve general coupled systems of nonlinear partial differential 118s equations using adaptive finite element methods, inexact Newton methods, 118s and algebraic multilevel methods. More information about FEtk may be found 118s at . 118s ---------------------------------------------------------------------- 118s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 118s Aqua is a modified form of the Holst group PMG library 118s which has been modified by Patrice Koehl 118s for improved efficiency and 118s memory usage when solving the Poisson-Boltzmann equation. 118s ---------------------------------------------------------------------- 118s Please cite your use of APBS as: 118s 118s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 118s nanosystems: application to microtubules and the ribosome. Proc. 118s Natl. Acad. Sci. USA 98, 10037-10041 2001. 118s 118s 118s This executable compiled on Jan 3 2025 at 11:01:42 118s 118s Parsing input file apbs-mol-parallel-PE2.in... 118s rank 0 size 1... 118s Parsed input file. 118s Got paths for 1 molecules 118s Reading PQR-format atom data from ion.pqr. 118s 1 atoms 118s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 118s Net charge 1.00e+00 e 118s Preparing to run 6 PBE calculations. 118s ---------------------------------------- 118s CALCULATION #1 (solvated): MULTIGRID 118s Setting up problem... 118s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 118s Debye length: 0 A 118s Current memory usage: 61.280 MB total, 61.280 MB high water 118s Using cubic spline charge discretization. 118s Partition overlap fraction = 0.1 118s Processor array = 2 x 2 x 1 118s Grid dimensions: 65 x 65 x 65 118s Grid spacings: 0.781 x 0.781 x 0.781 118s Grid lengths: 50.000 x 50.000 x 50.000 118s Grid center: (0.000, 0.000, 0.000) 118s Multigrid levels: 5 118s Molecule ID: 1 118s Linearized traditional PBE 118s Multiple Debye-Huckel sphere boundary conditions 118s 0 ion species (0.000 M ionic strength): 118s Solute dielectric: 1.000 118s Solvent dielectric: 78.540 118s Using "molecular" surface definition; no smoothing 118s Solvent probe radius: 1.400 A 118s Temperature: 298.150 K 118s Electrostatic energies will be calculated 118s Total electrostatic energy = 2.401768459091E+02 kJ/mol 118s Calculating forces... 118s ---------------------------------------- 118s CALCULATION #2 (solvated): MULTIGRID 118s Setting up problem... 118s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 118s Debye length: 0 A 118s Current memory usage: 61.280 MB total, 122.102 MB high water 118s Using cubic spline charge discretization. 118s Partition overlap fraction = 0.1 118s Processor array = 2 x 2 x 1 118s Grid dimensions: 65 x 65 x 65 118s Grid spacings: 0.296 x 0.296 x 0.383 118s Grid lengths: 18.944 x 18.944 x 24.495 118s Grid center: (-2.411, 2.411, 0.000) 118s Multigrid levels: 5 118s Molecule ID: 1 118s Linearized traditional PBE 118s Boundary conditions from focusing 118s 0 ion species (0.000 M ionic strength): 118s Solute dielectric: 1.000 118s Solvent dielectric: 78.540 118s Using "molecular" surface definition; no smoothing 118s Solvent probe radius: 1.400 A 118s Temperature: 298.150 K 118s Electrostatic energies will be calculated 118s Total electrostatic energy = 8.142935605695E+02 kJ/mol 118s Calculating forces... 118s [focusFillBound()]: WARNING: 118s Unusually large potential values 118s detected on the focusing boundary! 118s Convergence not guaranteed for NPBE/NRPBE calculations! 118s 118s ---------------------------------------- 118s CALCULATION #3 (solvated): MULTIGRID 118s Setting up problem... 118s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 118s Debye length: 0 A 118s Current memory usage: 61.280 MB total, 122.102 MB high water 118s Using cubic spline charge discretization. 118s Partition overlap fraction = 0.1 118s Processor array = 2 x 2 x 1 118s Grid dimensions: 65 x 65 x 65 118s Grid spacings: 0.112 x 0.112 x 0.188 118s Grid lengths: 7.178 x 7.178 x 12.000 118s Grid center: (-2.411, 2.411, 0.000) 118s Multigrid levels: 5 118s Molecule ID: 1 118s Linearized traditional PBE 118s Boundary conditions from focusing 118s 0 ion species (0.000 M ionic strength): 118s Solute dielectric: 1.000 118s Solvent dielectric: 78.540 118s Using "molecular" surface definition; no smoothing 118s Solvent probe radius: 1.400 A 118s Temperature: 298.150 K 118s Electrostatic energies will be calculated 118s Total electrostatic energy = 1.485255306569E+03 kJ/mol 118s Calculating forces... 118s ---------------------------------------- 118s CALCULATION #4 (reference): MULTIGRID 118s Setting up problem... 118s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 118s Debye length: 0 A 118s Current memory usage: 61.207 MB total, 122.102 MB high water 118s Using cubic spline charge discretization. 118s Partition overlap fraction = 0.1 118s Processor array = 2 x 2 x 1 118s Grid dimensions: 65 x 65 x 65 118s Grid spacings: 0.781 x 0.781 x 0.781 118s Grid lengths: 50.000 x 50.000 x 50.000 118s Grid center: (0.000, 0.000, 0.000) 118s Multigrid levels: 5 118s Molecule ID: 1 118s Linearized traditional PBE 118s Multiple Debye-Huckel sphere boundary conditions 118s 0 ion species (0.000 M ionic strength): 118s Solute dielectric: 1.000 118s Solvent dielectric: 1.000 118s Using "molecular" surface definition; no smoothing 118s Solvent probe radius: 1.400 A 118s Temperature: 298.150 K 118s Electrostatic energies will be calculated 118s Total electrostatic energy = 2.977178707146E+02 kJ/mol 118s Calculating forces... 118s ---------------------------------------- 118s CALCULATION #5 (reference): MULTIGRID 118s Setting up problem... 118s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 118s Debye length: 0 A 118s Current memory usage: 61.207 MB total, 122.102 MB high water 118s Using cubic spline charge discretization. 118s Partition overlap fraction = 0.1 118s Processor array = 2 x 2 x 1 118s Grid dimensions: 65 x 65 x 65 118s Grid spacings: 0.296 x 0.296 x 0.383 118s Grid lengths: 18.944 x 18.944 x 24.495 118s Grid center: (-2.411, 2.411, 0.000) 118s Multigrid levels: 5 118s Molecule ID: 1 118s Linearized traditional PBE 118s Boundary conditions from focusing 118s 0 ion species (0.000 M ionic strength): 118s Solute dielectric: 1.000 118s Solvent dielectric: 1.000 118s Using "molecular" surface definition; no smoothing 118s Solvent probe radius: 1.400 A 118s Temperature: 298.150 K 118s Electrostatic energies will be calculated 118s Total electrostatic energy = 8.799304557596E+02 kJ/mol 118s Calculating forces... 118s [focusFillBound()]: WARNING: 118s Unusually large potential values 118s detected on the focusing boundary! 118s Convergence not guaranteed for NPBE/NRPBE calculations! 118s 118s ---------------------------------------- 118s CALCULATION #6 (reference): MULTIGRID 118s Setting up problem... 118s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 118s Debye length: 0 A 118s Current memory usage: 61.207 MB total, 122.102 MB high water 118s Using cubic spline charge discretization. 118s Partition overlap fraction = 0.1 118s Processor array = 2 x 2 x 1 118s Grid dimensions: 65 x 65 x 65 118s Grid spacings: 0.112 x 0.112 x 0.188 118s Grid lengths: 7.178 x 7.178 x 12.000 118s Grid center: (-2.411, 2.411, 0.000) 118s Multigrid levels: 5 118s Molecule ID: 1 118s Linearized traditional PBE 118s Boundary conditions from focusing 118s 0 ion species (0.000 M ionic strength): 118s Solute dielectric: 1.000 118s Solvent dielectric: 1.000 118s Using "molecular" surface definition; no smoothing 118s Solvent probe radius: 1.400 A 118s Temperature: 298.150 K 118s Electrostatic energies will be calculated 118s Total electrostatic energy = 1.542873949141E+03 kJ/mol 118s Calculating forces... 118s ---------------------------------------- 118s PRINT STATEMENTS 118s 118s print energy 1 (solvated) - 2 (reference) end 118s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 118s Global net ELEC energy = -5.761864257239E+01 kJ/mol 118s ---------------------------------------- 118s CLEANING UP AND SHUTTING DOWN... 118s Destroying force arrays. 118s No energy arrays to destroy. 118s Destroying multigrid structures. 118s Destroying finite element structures. 118s Destroying 1 molecules 118s Final memory usage: 0.001 MB total, 122.102 MB high water 118s 118s 118s Thanks for using APBS! 118s 118s Processor 2 results: 118s 2.401768459091e+02 118s 8.142935605695e+02 118s 1.485255306569e+03 118s 2.977178707146e+02 118s 8.799304557596e+02 118s 1.542873949141e+03 118s -5.761864257239e+01 118s 119s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 119s BINARY: /usr/bin/apbs 119s INPUT: apbs-mol-parallel-PE3.in 119s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 119s asc_getToken: Error occurred (bailing out). 119s Vio_scanf: Format problem with input. 119s 119s 119s ---------------------------------------------------------------------- 119s APBS -- Adaptive Poisson-Boltzmann Solver 119s Version APBS 3.4.1 119s 119s Nathan A. Baker (nathan.baker@pnnl.gov) 119s Pacific Northwest National Laboratory 119s 119s Additional contributing authors listed in the code documentation. 119s 119s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 119s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 119s Northwest Division for the U.S. Department of Energy. 119s 119s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 119s Portions Copyright (c) 2002-2020, Nathan A. Baker. 119s Portions Copyright (c) 1999-2002, The Regents of the University of California. 119s Portions Copyright (c) 1995, Michael Holst. 119s All rights reserved. 119s 119s Redistribution and use in source and binary forms, with or without 119s modification, are permitted provided that the following conditions are met: 119s 119s * Redistributions of source code must retain the above copyright notice, this 119s list of conditions and the following disclaimer. 119s 119s * Redistributions in binary form must reproduce the above copyright notice, 119s this list of conditions and the following disclaimer in the documentation 119s and/or other materials provided with the distribution. 119s 119s * Neither the name of the developer nor the names of its contributors may be 119s used to endorse or promote products derived from this software without 119s specific prior written permission. 119s 119s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 119s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 119s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 119s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 119s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 119s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 119s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 119s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 119s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 119s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 119s ---------------------------------------------------------------------- 119s APBS uses FETK (the Finite Element ToolKit) to solve the 119s Poisson-Boltzmann equation numerically. FETK is a portable collection 119s of finite element modeling class libraries developed by the Michael Holst 119s research group and written in an object-oriented form of C. FEtk is 119s designed to solve general coupled systems of nonlinear partial differential 119s equations using adaptive finite element methods, inexact Newton methods, 119s and algebraic multilevel methods. More information about FEtk may be found 119s at . 119s ---------------------------------------------------------------------- 119s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 119s Aqua is a modified form of the Holst group PMG library 119s which has been modified by Patrice Koehl 119s for improved efficiency and 119s memory usage when solving the Poisson-Boltzmann equation. 119s ---------------------------------------------------------------------- 119s Please cite your use of APBS as: 119s 119s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 119s nanosystems: application to microtubules and the ribosome. Proc. 119s Natl. Acad. Sci. USA 98, 10037-10041 2001. 119s 119s 119s This executable compiled on Jan 3 2025 at 11:01:42 119s 119s Parsing input file apbs-mol-parallel-PE3.in... 119s rank 0 size 1... 119s Parsed input file. 119s Got paths for 1 molecules 119s Reading PQR-format atom data from ion.pqr. 119s 1 atoms 119s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 119s Net charge 1.00e+00 e 119s Preparing to run 6 PBE calculations. 119s ---------------------------------------- 119s CALCULATION #1 (solvated): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 119s Debye length: 0 A 119s Current memory usage: 61.280 MB total, 61.280 MB high water 119s Using cubic spline charge discretization. 119s Partition overlap fraction = 0.1 119s Processor array = 2 x 2 x 1 119s Grid dimensions: 65 x 65 x 65 119s Grid spacings: 0.781 x 0.781 x 0.781 119s Grid lengths: 50.000 x 50.000 x 50.000 119s Grid center: (0.000, 0.000, 0.000) 119s Multigrid levels: 5 119s Molecule ID: 1 119s Linearized traditional PBE 119s Multiple Debye-Huckel sphere boundary conditions 119s 0 ion species (0.000 M ionic strength): 119s Solute dielectric: 1.000 119s Solvent dielectric: 78.540 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 2.401768459091E+02 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #2 (solvated): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 119s Debye length: 0 A 119s Current memory usage: 61.280 MB total, 122.102 MB high water 119s Using cubic spline charge discretization. 119s Partition overlap fraction = 0.1 119s Processor array = 2 x 2 x 1 119s Grid dimensions: 65 x 65 x 65 119s Grid spacings: 0.296 x 0.296 x 0.383 119s Grid lengths: 18.944 x 18.944 x 24.495 119s Grid center: (2.411, 2.411, 0.000) 119s Multigrid levels: 5 119s Molecule ID: 1 119s Linearized traditional PBE 119s Boundary conditions from focusing 119s 0 ion species (0.000 M ionic strength): 119s Solute dielectric: 1.000 119s Solvent dielectric: 78.540 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 8.142778325440E+02 kJ/mol 119s Calculating forces... 119s [focusFillBound()]: WARNING: 119s Unusually large potential values 119s detected on the focusing boundary! 119s Convergence not guaranteed for NPBE/NRPBE calculations! 119s 119s ---------------------------------------- 119s CALCULATION #3 (solvated): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 119s Debye length: 0 A 119s Current memory usage: 61.280 MB total, 122.102 MB high water 119s Using cubic spline charge discretization. 119s Partition overlap fraction = 0.1 119s Processor array = 2 x 2 x 1 119s Grid dimensions: 65 x 65 x 65 119s Grid spacings: 0.112 x 0.112 x 0.188 119s Grid lengths: 7.178 x 7.178 x 12.000 119s Grid center: (2.411, 2.411, 0.000) 119s Multigrid levels: 5 119s Molecule ID: 1 119s Linearized traditional PBE 119s Boundary conditions from focusing 119s 0 ion species (0.000 M ionic strength): 119s Solute dielectric: 1.000 119s Solvent dielectric: 78.540 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 1.485246665692E+03 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #4 (reference): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 119s Debye length: 0 A 119s Current memory usage: 61.207 MB total, 122.102 MB high water 119s Using cubic spline charge discretization. 119s Partition overlap fraction = 0.1 119s Processor array = 2 x 2 x 1 119s Grid dimensions: 65 x 65 x 65 119s Grid spacings: 0.781 x 0.781 x 0.781 119s Grid lengths: 50.000 x 50.000 x 50.000 119s Grid center: (0.000, 0.000, 0.000) 119s Multigrid levels: 5 119s Molecule ID: 1 119s Linearized traditional PBE 119s Multiple Debye-Huckel sphere boundary conditions 119s 0 ion species (0.000 M ionic strength): 119s Solute dielectric: 1.000 119s Solvent dielectric: 1.000 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 2.977178707146E+02 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s CALCULATION #5 (reference): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 119s Debye length: 0 A 119s Current memory usage: 61.207 MB total, 122.102 MB high water 119s Using cubic spline charge discretization. 119s Partition overlap fraction = 0.1 119s Processor array = 2 x 2 x 1 119s Grid dimensions: 65 x 65 x 65 119s Grid spacings: 0.296 x 0.296 x 0.383 119s Grid lengths: 18.944 x 18.944 x 24.495 119s Grid center: (2.411, 2.411, 0.000) 119s Multigrid levels: 5 119s Molecule ID: 1 119s Linearized traditional PBE 119s Boundary conditions from focusing 119s 0 ion species (0.000 M ionic strength): 119s Solute dielectric: 1.000 119s Solvent dielectric: 1.000 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 8.799304557596E+02 kJ/mol 119s Calculating forces... 119s [focusFillBound()]: WARNING: 119s Unusually large potential values 119s detected on the focusing boundary! 119s Convergence not guaranteed for NPBE/NRPBE calculations! 119s 119s ---------------------------------------- 119s CALCULATION #6 (reference): MULTIGRID 119s Setting up problem... 119s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 119s Debye length: 0 A 119s Current memory usage: 61.207 MB total, 122.102 MB high water 119s Using cubic spline charge discretization. 119s Partition overlap fraction = 0.1 119s Processor array = 2 x 2 x 1 119s Grid dimensions: 65 x 65 x 65 119s Grid spacings: 0.112 x 0.112 x 0.188 119s Grid lengths: 7.178 x 7.178 x 12.000 119s Grid center: (2.411, 2.411, 0.000) 119s Multigrid levels: 5 119s Molecule ID: 1 119s Linearized traditional PBE 119s Boundary conditions from focusing 119s 0 ion species (0.000 M ionic strength): 119s Solute dielectric: 1.000 119s Solvent dielectric: 1.000 119s Using "molecular" surface definition; no smoothing 119s Solvent probe radius: 1.400 A 119s Temperature: 298.150 K 119s Electrostatic energies will be calculated 119s Total electrostatic energy = 1.542873949141E+03 kJ/mol 119s Calculating forces... 119s ---------------------------------------- 119s PRINT STATEMENTS 119s 119s print energy 1 (solvated) - 2 (reference) end 119s Local net energy (PE 0) = -5.762728344953E+01 kJ/mol 119s Global net ELEC energy = -5.762728344953E+01 kJ/mol 119s ---------------------------------------- 119s CLEANING UP AND SHUTTING DOWN... 119s Destroying force arrays. 119s No energy arrays to destroy. 119s Destroying multigrid structures. 119s Destroying finite element structures. 119s Destroying 1 molecules 119s Final memory usage: 0.001 MB total, 122.102 MB high water 119s 119s 119s Thanks for using APBS! 119s 119s Processor 3 results: 119s 2.401768459091e+02 119s 8.142778325440e+02 119s 1.485246665692e+03 119s 2.977178707146e+02 119s 8.799304557596e+02 119s 1.542873949141e+03 119s -5.762728344953e+01 119s 119s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 119s *** PASSED *** 119s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 119s *** PASSED *** 119s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 119s *** PASSED *** 119s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 119s *** PASSED *** 119s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 119s *** PASSED *** 119s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 119s *** PASSED *** 119s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 119s *** PASSED *** 119s Elapsed time: 4.069549 seconds 119s -------------------------------------------------------------------------------- 119s -------------------------------------------------------------------------------- 119s Testing input file apbs-smol-parallel.in 119s 119s Splitting the input file into 4 separate files using the inputgen utility 119s 120s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 120s EXPECTED COMPUTED: 7 120s EXPECTED EXPECTED: 7 120s COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 120s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 120s COMPUTED RESULT 960.7073836226 120s COMPUTED RESULT 3257.1427835730997 120s COMPUTED RESULT 5941.0039478710005 120s COMPUTED RESULT 1190.8714828309999 120s COMPUTED RESULT 3519.7218230368003 120s COMPUTED RESULT 6171.495796544 120s COMPUTED RESULT -230.49184867462003 120s BINARY: /usr/bin/apbs 120s INPUT: apbs-smol-parallel-PE0.in 120s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 120s asc_getToken: Error occurred (bailing out). 120s Vio_scanf: Format problem with input. 120s 120s 120s ---------------------------------------------------------------------- 120s APBS -- Adaptive Poisson-Boltzmann Solver 120s Version APBS 3.4.1 120s 120s Nathan A. Baker (nathan.baker@pnnl.gov) 120s Pacific Northwest National Laboratory 120s 120s Additional contributing authors listed in the code documentation. 120s 120s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 120s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 120s Northwest Division for the U.S. Department of Energy. 120s 120s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 120s Portions Copyright (c) 2002-2020, Nathan A. Baker. 120s Portions Copyright (c) 1999-2002, The Regents of the University of California. 120s Portions Copyright (c) 1995, Michael Holst. 120s All rights reserved. 120s 120s Redistribution and use in source and binary forms, with or without 120s modification, are permitted provided that the following conditions are met: 120s 120s * Redistributions of source code must retain the above copyright notice, this 120s list of conditions and the following disclaimer. 120s 120s * Redistributions in binary form must reproduce the above copyright notice, 120s this list of conditions and the following disclaimer in the documentation 120s and/or other materials provided with the distribution. 120s 120s * Neither the name of the developer nor the names of its contributors may be 120s used to endorse or promote products derived from this software without 120s specific prior written permission. 120s 120s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 120s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 120s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 120s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 120s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 120s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 120s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 120s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 120s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 120s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 120s ---------------------------------------------------------------------- 120s APBS uses FETK (the Finite Element ToolKit) to solve the 120s Poisson-Boltzmann equation numerically. FETK is a portable collection 120s of finite element modeling class libraries developed by the Michael Holst 120s research group and written in an object-oriented form of C. FEtk is 120s designed to solve general coupled systems of nonlinear partial differential 120s equations using adaptive finite element methods, inexact Newton methods, 120s and algebraic multilevel methods. More information about FEtk may be found 120s at . 120s ---------------------------------------------------------------------- 120s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 120s Aqua is a modified form of the Holst group PMG library 120s which has been modified by Patrice Koehl 120s for improved efficiency and 120s memory usage when solving the Poisson-Boltzmann equation. 120s ---------------------------------------------------------------------- 120s Please cite your use of APBS as: 120s 120s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 120s nanosystems: application to microtubules and the ribosome. Proc. 120s Natl. Acad. Sci. USA 98, 10037-10041 2001. 120s 120s 120s This executable compiled on Jan 3 2025 at 11:01:42 120s 120s Parsing input file apbs-smol-parallel-PE0.in... 120s rank 0 size 1... 120s Parsed input file. 120s Got paths for 1 molecules 120s Reading PQR-format atom data from ion.pqr. 120s 1 atoms 120s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 120s Net charge 1.00e+00 e 120s Preparing to run 6 PBE calculations. 120s ---------------------------------------- 120s CALCULATION #1 (solvated): MULTIGRID 120s Setting up problem... 120s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 120s Debye length: 0 A 120s Current memory usage: 61.280 MB total, 61.280 MB high water 120s Using cubic spline charge discretization. 120s Partition overlap fraction = 0.1 120s Processor array = 2 x 2 x 1 120s Grid dimensions: 65 x 65 x 65 120s Grid spacings: 0.781 x 0.781 x 0.781 120s Grid lengths: 50.000 x 50.000 x 50.000 120s Grid center: (0.000, 0.000, 0.000) 120s Multigrid levels: 5 120s Molecule ID: 1 120s Linearized traditional PBE 120s Multiple Debye-Huckel sphere boundary conditions 120s 0 ion species (0.000 M ionic strength): 120s Solute dielectric: 1.000 120s Solvent dielectric: 78.540 120s Using "molecular" surface definition;harmonic average smoothing 120s Solvent probe radius: 1.400 A 120s Temperature: 298.150 K 120s Electrostatic energies will be calculated 120s Total electrostatic energy = 2.383232191816E+02 kJ/mol 120s Calculating forces... 120s ---------------------------------------- 120s CALCULATION #2 (solvated): MULTIGRID 120s Setting up problem... 120s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 120s Debye length: 0 A 120s Current memory usage: 61.280 MB total, 122.102 MB high water 120s Using cubic spline charge discretization. 120s Partition overlap fraction = 0.1 120s Processor array = 2 x 2 x 1 120s Grid dimensions: 65 x 65 x 65 120s Grid spacings: 0.296 x 0.296 x 0.383 120s Grid lengths: 18.944 x 18.944 x 24.495 120s Grid center: (-2.411, -2.411, 0.000) 120s Multigrid levels: 5 120s Molecule ID: 1 120s Linearized traditional PBE 120s Boundary conditions from focusing 120s 0 ion species (0.000 M ionic strength): 120s Solute dielectric: 1.000 120s Solvent dielectric: 78.540 120s Using "molecular" surface definition;harmonic average smoothing 120s Solvent probe radius: 1.400 A 120s Temperature: 298.150 K 120s Electrostatic energies will be calculated 120s Total electrostatic energy = 8.145369591602E+02 kJ/mol 120s Calculating forces... 120s [focusFillBound()]: WARNING: 120s Unusually large potential values 120s detected on the focusing boundary! 120s Convergence not guaranteed for NPBE/NRPBE calculations! 120s 120s ---------------------------------------- 120s CALCULATION #3 (solvated): MULTIGRID 120s Setting up problem... 120s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 120s Debye length: 0 A 120s Current memory usage: 61.280 MB total, 122.102 MB high water 120s Using cubic spline charge discretization. 120s Partition overlap fraction = 0.1 120s Processor array = 2 x 2 x 1 120s Grid dimensions: 65 x 65 x 65 120s Grid spacings: 0.112 x 0.112 x 0.188 120s Grid lengths: 7.178 x 7.178 x 12.000 120s Grid center: (-2.411, -2.411, 0.000) 120s Multigrid levels: 5 120s Molecule ID: 1 120s Linearized traditional PBE 120s Boundary conditions from focusing 120s 0 ion species (0.000 M ionic strength): 120s Solute dielectric: 1.000 120s Solvent dielectric: 78.540 120s Using "molecular" surface definition;harmonic average smoothing 120s Solvent probe radius: 1.400 A 120s Temperature: 298.150 K 120s Electrostatic energies will be calculated 120s Total electrostatic energy = 1.485524998001E+03 kJ/mol 120s Calculating forces... 120s ---------------------------------------- 120s CALCULATION #4 (reference): MULTIGRID 120s Setting up problem... 120s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 120s Debye length: 0 A 120s Current memory usage: 61.207 MB total, 122.102 MB high water 120s Using cubic spline charge discretization. 120s Partition overlap fraction = 0.1 120s Processor array = 2 x 2 x 1 120s Grid dimensions: 65 x 65 x 65 120s Grid spacings: 0.781 x 0.781 x 0.781 120s Grid lengths: 50.000 x 50.000 x 50.000 120s Grid center: (0.000, 0.000, 0.000) 120s Multigrid levels: 5 120s Molecule ID: 1 120s Linearized traditional PBE 120s Multiple Debye-Huckel sphere boundary conditions 120s 0 ion species (0.000 M ionic strength): 120s Solute dielectric: 1.000 120s Solvent dielectric: 1.000 120s Using "molecular" surface definition;harmonic average smoothing 120s Solvent probe radius: 1.400 A 120s Temperature: 298.150 K 120s Electrostatic energies will be calculated 120s Total electrostatic energy = 2.977178707009E+02 kJ/mol 120s Calculating forces... 120s ---------------------------------------- 120s CALCULATION #5 (reference): MULTIGRID 120s Setting up problem... 120s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 120s Debye length: 0 A 120s Current memory usage: 61.207 MB total, 122.102 MB high water 120s Using cubic spline charge discretization. 120s Partition overlap fraction = 0.1 120s Processor array = 2 x 2 x 1 120s Grid dimensions: 65 x 65 x 65 120s Grid spacings: 0.296 x 0.296 x 0.383 120s Grid lengths: 18.944 x 18.944 x 24.495 120s Grid center: (-2.411, -2.411, 0.000) 120s Multigrid levels: 5 120s Molecule ID: 1 120s Linearized traditional PBE 120s Boundary conditions from focusing 120s 0 ion species (0.000 M ionic strength): 120s Solute dielectric: 1.000 120s Solvent dielectric: 1.000 120s Using "molecular" surface definition;harmonic average smoothing 120s Solvent probe radius: 1.400 A 120s Temperature: 298.150 K 120s Electrostatic energies will be calculated 120s Total electrostatic energy = 8.799304557588E+02 kJ/mol 120s Calculating forces... 120s [focusFillBound()]: WARNING: 120s Unusually large potential values 120s detected on the focusing boundary! 120s Convergence not guaranteed for NPBE/NRPBE calculations! 120s 120s ---------------------------------------- 120s CALCULATION #6 (reference): MULTIGRID 120s Setting up problem... 120s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 120s Debye length: 0 A 120s Current memory usage: 61.207 MB total, 122.102 MB high water 120s Using cubic spline charge discretization. 120s Partition overlap fraction = 0.1 120s Processor array = 2 x 2 x 1 120s Grid dimensions: 65 x 65 x 65 120s Grid spacings: 0.112 x 0.112 x 0.188 120s Grid lengths: 7.178 x 7.178 x 12.000 120s Grid center: (-2.411, -2.411, 0.000) 120s Multigrid levels: 5 120s Molecule ID: 1 120s Linearized traditional PBE 120s Boundary conditions from focusing 120s 0 ion species (0.000 M ionic strength): 120s Solute dielectric: 1.000 120s Solvent dielectric: 1.000 120s Using "molecular" surface definition;harmonic average smoothing 120s Solvent probe radius: 1.400 A 120s Temperature: 298.150 K 120s Electrostatic energies will be calculated 120s Total electrostatic energy = 1.542873949131E+03 kJ/mol 120s Calculating forces... 120s ---------------------------------------- 120s PRINT STATEMENTS 120s 120s print energy 1 (solvated) - 2 (reference) end 120s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 120s Global net ELEC energy = -5.734895113069E+01 kJ/mol 120s ---------------------------------------- 120s CLEANING UP AND SHUTTING DOWN... 120s Destroying force arrays. 120s No energy arrays to destroy. 120s Destroying multigrid structures. 120s Destroying finite element structures. 120s Destroying 1 molecules 120s Final memory usage: 0.001 MB total, 122.102 MB high water 120s 120s 120s Thanks for using APBS! 120s 120s Processor 0 results: 120s 2.383232191816e+02 120s 8.145369591602e+02 120s 1.485524998001e+03 120s 2.977178707009e+02 120s 8.799304557588e+02 120s 1.542873949131e+03 120s -5.734895113069e+01 120s 121s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 121s BINARY: /usr/bin/apbs 121s INPUT: apbs-smol-parallel-PE1.in 121s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 121s asc_getToken: Error occurred (bailing out). 121s Vio_scanf: Format problem with input. 121s 121s 121s ---------------------------------------------------------------------- 121s APBS -- Adaptive Poisson-Boltzmann Solver 121s Version APBS 3.4.1 121s 121s Nathan A. Baker (nathan.baker@pnnl.gov) 121s Pacific Northwest National Laboratory 121s 121s Additional contributing authors listed in the code documentation. 121s 121s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 121s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 121s Northwest Division for the U.S. Department of Energy. 121s 121s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 121s Portions Copyright (c) 2002-2020, Nathan A. Baker. 121s Portions Copyright (c) 1999-2002, The Regents of the University of California. 121s Portions Copyright (c) 1995, Michael Holst. 121s All rights reserved. 121s 121s Redistribution and use in source and binary forms, with or without 121s modification, are permitted provided that the following conditions are met: 121s 121s * Redistributions of source code must retain the above copyright notice, this 121s list of conditions and the following disclaimer. 121s 121s * Redistributions in binary form must reproduce the above copyright notice, 121s this list of conditions and the following disclaimer in the documentation 121s and/or other materials provided with the distribution. 121s 121s * Neither the name of the developer nor the names of its contributors may be 121s used to endorse or promote products derived from this software without 121s specific prior written permission. 121s 121s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 121s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 121s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 121s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 121s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 121s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 121s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 121s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 121s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 121s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 121s ---------------------------------------------------------------------- 121s APBS uses FETK (the Finite Element ToolKit) to solve the 121s Poisson-Boltzmann equation numerically. FETK is a portable collection 121s of finite element modeling class libraries developed by the Michael Holst 121s research group and written in an object-oriented form of C. FEtk is 121s designed to solve general coupled systems of nonlinear partial differential 121s equations using adaptive finite element methods, inexact Newton methods, 121s and algebraic multilevel methods. More information about FEtk may be found 121s at . 121s ---------------------------------------------------------------------- 121s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 121s Aqua is a modified form of the Holst group PMG library 121s which has been modified by Patrice Koehl 121s for improved efficiency and 121s memory usage when solving the Poisson-Boltzmann equation. 121s ---------------------------------------------------------------------- 121s Please cite your use of APBS as: 121s 121s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 121s nanosystems: application to microtubules and the ribosome. Proc. 121s Natl. Acad. Sci. USA 98, 10037-10041 2001. 121s 121s 121s This executable compiled on Jan 3 2025 at 11:01:42 121s 121s Parsing input file apbs-smol-parallel-PE1.in... 121s rank 0 size 1... 121s Parsed input file. 121s Got paths for 1 molecules 121s Reading PQR-format atom data from ion.pqr. 121s 1 atoms 121s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 121s Net charge 1.00e+00 e 121s Preparing to run 6 PBE calculations. 121s ---------------------------------------- 121s CALCULATION #1 (solvated): MULTIGRID 121s Setting up problem... 121s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 121s Debye length: 0 A 121s Current memory usage: 61.280 MB total, 61.280 MB high water 121s Using cubic spline charge discretization. 121s Partition overlap fraction = 0.1 121s Processor array = 2 x 2 x 1 121s Grid dimensions: 65 x 65 x 65 121s Grid spacings: 0.781 x 0.781 x 0.781 121s Grid lengths: 50.000 x 50.000 x 50.000 121s Grid center: (0.000, 0.000, 0.000) 121s Multigrid levels: 5 121s Molecule ID: 1 121s Linearized traditional PBE 121s Multiple Debye-Huckel sphere boundary conditions 121s 0 ion species (0.000 M ionic strength): 121s Solute dielectric: 1.000 121s Solvent dielectric: 78.540 121s Using "molecular" surface definition;harmonic average smoothing 121s Solvent probe radius: 1.400 A 121s Temperature: 298.150 K 121s Electrostatic energies will be calculated 121s Total electrostatic energy = 2.383232191816E+02 kJ/mol 121s Calculating forces... 121s ---------------------------------------- 121s CALCULATION #2 (solvated): MULTIGRID 121s Setting up problem... 121s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 121s Debye length: 0 A 121s Current memory usage: 61.280 MB total, 122.102 MB high water 121s Using cubic spline charge discretization. 121s Partition overlap fraction = 0.1 121s Processor array = 2 x 2 x 1 121s Grid dimensions: 65 x 65 x 65 121s Grid spacings: 0.296 x 0.296 x 0.383 121s Grid lengths: 18.944 x 18.944 x 24.495 121s Grid center: (2.411, -2.411, 0.000) 121s Multigrid levels: 5 121s Molecule ID: 1 121s Linearized traditional PBE 121s Boundary conditions from focusing 121s 0 ion species (0.000 M ionic strength): 121s Solute dielectric: 1.000 121s Solvent dielectric: 78.540 121s Using "molecular" surface definition;harmonic average smoothing 121s Solvent probe radius: 1.400 A 121s Temperature: 298.150 K 121s Electrostatic energies will be calculated 121s Total electrostatic energy = 8.145419898332E+02 kJ/mol 121s Calculating forces... 121s [focusFillBound()]: WARNING: 121s Unusually large potential values 121s detected on the focusing boundary! 121s Convergence not guaranteed for NPBE/NRPBE calculations! 121s 121s ---------------------------------------- 121s CALCULATION #3 (solvated): MULTIGRID 121s Setting up problem... 121s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 121s Debye length: 0 A 121s Current memory usage: 61.280 MB total, 122.102 MB high water 121s Using cubic spline charge discretization. 121s Partition overlap fraction = 0.1 121s Processor array = 2 x 2 x 1 121s Grid dimensions: 65 x 65 x 65 121s Grid spacings: 0.112 x 0.112 x 0.188 121s Grid lengths: 7.178 x 7.178 x 12.000 121s Grid center: (2.411, -2.411, 0.000) 121s Multigrid levels: 5 121s Molecule ID: 1 121s Linearized traditional PBE 121s Boundary conditions from focusing 121s 0 ion species (0.000 M ionic strength): 121s Solute dielectric: 1.000 121s Solvent dielectric: 78.540 121s Using "molecular" surface definition;harmonic average smoothing 121s Solvent probe radius: 1.400 A 121s Temperature: 298.150 K 121s Electrostatic energies will be calculated 121s Total electrostatic energy = 1.485529328612E+03 kJ/mol 121s Calculating forces... 121s ---------------------------------------- 121s CALCULATION #4 (reference): MULTIGRID 121s Setting up problem... 121s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 121s Debye length: 0 A 121s Current memory usage: 61.207 MB total, 122.102 MB high water 121s Using cubic spline charge discretization. 121s Partition overlap fraction = 0.1 121s Processor array = 2 x 2 x 1 121s Grid dimensions: 65 x 65 x 65 121s Grid spacings: 0.781 x 0.781 x 0.781 121s Grid lengths: 50.000 x 50.000 x 50.000 121s Grid center: (0.000, 0.000, 0.000) 121s Multigrid levels: 5 121s Molecule ID: 1 121s Linearized traditional PBE 121s Multiple Debye-Huckel sphere boundary conditions 121s 0 ion species (0.000 M ionic strength): 121s Solute dielectric: 1.000 121s Solvent dielectric: 1.000 121s Using "molecular" surface definition;harmonic average smoothing 121s Solvent probe radius: 1.400 A 121s Temperature: 298.150 K 121s Electrostatic energies will be calculated 121s Total electrostatic energy = 2.977178707009E+02 kJ/mol 121s Calculating forces... 121s ---------------------------------------- 121s CALCULATION #5 (reference): MULTIGRID 121s Setting up problem... 121s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 121s Debye length: 0 A 121s Current memory usage: 61.207 MB total, 122.102 MB high water 121s Using cubic spline charge discretization. 121s Partition overlap fraction = 0.1 121s Processor array = 2 x 2 x 1 121s Grid dimensions: 65 x 65 x 65 121s Grid spacings: 0.296 x 0.296 x 0.383 121s Grid lengths: 18.944 x 18.944 x 24.495 121s Grid center: (2.411, -2.411, 0.000) 121s Multigrid levels: 5 121s Molecule ID: 1 121s Linearized traditional PBE 121s Boundary conditions from focusing 121s 0 ion species (0.000 M ionic strength): 121s Solute dielectric: 1.000 121s Solvent dielectric: 1.000 121s Using "molecular" surface definition;harmonic average smoothing 121s Solvent probe radius: 1.400 A 121s Temperature: 298.150 K 121s Electrostatic energies will be calculated 121s Total electrostatic energy = 8.799304557588E+02 kJ/mol 121s Calculating forces... 121s [focusFillBound()]: WARNING: 121s Unusually large potential values 121s detected on the focusing boundary! 121s Convergence not guaranteed for NPBE/NRPBE calculations! 121s 121s ---------------------------------------- 121s CALCULATION #6 (reference): MULTIGRID 121s Setting up problem... 121s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 121s Debye length: 0 A 121s Current memory usage: 61.207 MB total, 122.102 MB high water 121s Using cubic spline charge discretization. 121s Partition overlap fraction = 0.1 121s Processor array = 2 x 2 x 1 121s Grid dimensions: 65 x 65 x 65 121s Grid spacings: 0.112 x 0.112 x 0.188 121s Grid lengths: 7.178 x 7.178 x 12.000 121s Grid center: (2.411, -2.411, 0.000) 121s Multigrid levels: 5 121s Molecule ID: 1 121s Linearized traditional PBE 121s Boundary conditions from focusing 121s 0 ion species (0.000 M ionic strength): 121s Solute dielectric: 1.000 121s Solvent dielectric: 1.000 121s Using "molecular" surface definition;harmonic average smoothing 121s Solvent probe radius: 1.400 A 121s Temperature: 298.150 K 121s Electrostatic energies will be calculated 121s Total electrostatic energy = 1.542873949131E+03 kJ/mol 121s Calculating forces... 121s ---------------------------------------- 121s PRINT STATEMENTS 121s 121s print energy 1 (solvated) - 2 (reference) end 121s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 121s Global net ELEC energy = -5.734462051928E+01 kJ/mol 121s ---------------------------------------- 121s CLEANING UP AND SHUTTING DOWN... 121s Destroying force arrays. 121s No energy arrays to destroy. 121s Destroying multigrid structures. 121s Destroying finite element structures. 121s Destroying 1 molecules 121s Final memory usage: 0.001 MB total, 122.102 MB high water 121s 121s 121s Thanks for using APBS! 121s 121s Processor 1 results: 121s 2.383232191816e+02 121s 8.145419898332e+02 121s 1.485529328612e+03 121s 2.977178707009e+02 121s 8.799304557588e+02 121s 1.542873949131e+03 121s -5.734462051928e+01 121s 122s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 122s BINARY: /usr/bin/apbs 122s INPUT: apbs-smol-parallel-PE2.in 122s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 122s asc_getToken: Error occurred (bailing out). 122s Vio_scanf: Format problem with input. 122s 122s 122s ---------------------------------------------------------------------- 122s APBS -- Adaptive Poisson-Boltzmann Solver 122s Version APBS 3.4.1 122s 122s Nathan A. Baker (nathan.baker@pnnl.gov) 122s Pacific Northwest National Laboratory 122s 122s Additional contributing authors listed in the code documentation. 122s 122s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 122s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 122s Northwest Division for the U.S. Department of Energy. 122s 122s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 122s Portions Copyright (c) 2002-2020, Nathan A. Baker. 122s Portions Copyright (c) 1999-2002, The Regents of the University of California. 122s Portions Copyright (c) 1995, Michael Holst. 122s All rights reserved. 122s 122s Redistribution and use in source and binary forms, with or without 122s modification, are permitted provided that the following conditions are met: 122s 122s * Redistributions of source code must retain the above copyright notice, this 122s list of conditions and the following disclaimer. 122s 122s * Redistributions in binary form must reproduce the above copyright notice, 122s this list of conditions and the following disclaimer in the documentation 122s and/or other materials provided with the distribution. 122s 122s * Neither the name of the developer nor the names of its contributors may be 122s used to endorse or promote products derived from this software without 122s specific prior written permission. 122s 122s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 122s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 122s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 122s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 122s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 122s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 122s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 122s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 122s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 122s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 122s ---------------------------------------------------------------------- 122s APBS uses FETK (the Finite Element ToolKit) to solve the 122s Poisson-Boltzmann equation numerically. FETK is a portable collection 122s of finite element modeling class libraries developed by the Michael Holst 122s research group and written in an object-oriented form of C. FEtk is 122s designed to solve general coupled systems of nonlinear partial differential 122s equations using adaptive finite element methods, inexact Newton methods, 122s and algebraic multilevel methods. More information about FEtk may be found 122s at . 122s ---------------------------------------------------------------------- 122s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 122s Aqua is a modified form of the Holst group PMG library 122s which has been modified by Patrice Koehl 122s for improved efficiency and 122s memory usage when solving the Poisson-Boltzmann equation. 122s ---------------------------------------------------------------------- 122s Please cite your use of APBS as: 122s 122s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 122s nanosystems: application to microtubules and the ribosome. Proc. 122s Natl. Acad. Sci. USA 98, 10037-10041 2001. 122s 122s 122s This executable compiled on Jan 3 2025 at 11:01:42 122s 122s Parsing input file apbs-smol-parallel-PE2.in... 122s rank 0 size 1... 122s Parsed input file. 122s Got paths for 1 molecules 122s Reading PQR-format atom data from ion.pqr. 122s 1 atoms 122s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 122s Net charge 1.00e+00 e 122s Preparing to run 6 PBE calculations. 122s ---------------------------------------- 122s CALCULATION #1 (solvated): MULTIGRID 122s Setting up problem... 122s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 122s Debye length: 0 A 122s Current memory usage: 61.280 MB total, 61.280 MB high water 122s Using cubic spline charge discretization. 122s Partition overlap fraction = 0.1 122s Processor array = 2 x 2 x 1 122s Grid dimensions: 65 x 65 x 65 122s Grid spacings: 0.781 x 0.781 x 0.781 122s Grid lengths: 50.000 x 50.000 x 50.000 122s Grid center: (0.000, 0.000, 0.000) 122s Multigrid levels: 5 122s Molecule ID: 1 122s Linearized traditional PBE 122s Multiple Debye-Huckel sphere boundary conditions 122s 0 ion species (0.000 M ionic strength): 122s Solute dielectric: 1.000 122s Solvent dielectric: 78.540 122s Using "molecular" surface definition;harmonic average smoothing 122s Solvent probe radius: 1.400 A 122s Temperature: 298.150 K 122s Electrostatic energies will be calculated 122s Total electrostatic energy = 2.383232191909E+02 kJ/mol 122s Calculating forces... 122s ---------------------------------------- 122s CALCULATION #2 (solvated): MULTIGRID 122s Setting up problem... 122s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 122s Debye length: 0 A 122s Current memory usage: 61.280 MB total, 122.102 MB high water 122s Using cubic spline charge discretization. 122s Partition overlap fraction = 0.1 122s Processor array = 2 x 2 x 1 122s Grid dimensions: 65 x 65 x 65 122s Grid spacings: 0.296 x 0.296 x 0.383 122s Grid lengths: 18.944 x 18.944 x 24.495 122s Grid center: (-2.411, 2.411, 0.000) 122s Multigrid levels: 5 122s Molecule ID: 1 122s Linearized traditional PBE 122s Boundary conditions from focusing 122s 0 ion species (0.000 M ionic strength): 122s Solute dielectric: 1.000 122s Solvent dielectric: 78.540 122s Using "molecular" surface definition;harmonic average smoothing 122s Solvent probe radius: 1.400 A 122s Temperature: 298.150 K 122s Electrostatic energies will be calculated 122s Total electrostatic energy = 8.145369593489E+02 kJ/mol 122s Calculating forces... 122s [focusFillBound()]: WARNING: 122s Unusually large potential values 122s detected on the focusing boundary! 122s Convergence not guaranteed for NPBE/NRPBE calculations! 122s 122s ---------------------------------------- 122s CALCULATION #3 (solvated): MULTIGRID 122s Setting up problem... 122s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 122s Debye length: 0 A 122s Current memory usage: 61.280 MB total, 122.102 MB high water 122s Using cubic spline charge discretization. 122s Partition overlap fraction = 0.1 122s Processor array = 2 x 2 x 1 122s Grid dimensions: 65 x 65 x 65 122s Grid spacings: 0.112 x 0.112 x 0.188 122s Grid lengths: 7.178 x 7.178 x 12.000 122s Grid center: (-2.411, 2.411, 0.000) 122s Multigrid levels: 5 122s Molecule ID: 1 122s Linearized traditional PBE 122s Boundary conditions from focusing 122s 0 ion species (0.000 M ionic strength): 122s Solute dielectric: 1.000 122s Solvent dielectric: 78.540 122s Using "molecular" surface definition;harmonic average smoothing 122s Solvent probe radius: 1.400 A 122s Temperature: 298.150 K 122s Electrostatic energies will be calculated 122s Total electrostatic energy = 1.485524997676E+03 kJ/mol 122s Calculating forces... 122s ---------------------------------------- 122s CALCULATION #4 (reference): MULTIGRID 122s Setting up problem... 122s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 122s Debye length: 0 A 122s Current memory usage: 61.207 MB total, 122.102 MB high water 122s Using cubic spline charge discretization. 122s Partition overlap fraction = 0.1 122s Processor array = 2 x 2 x 1 122s Grid dimensions: 65 x 65 x 65 122s Grid spacings: 0.781 x 0.781 x 0.781 122s Grid lengths: 50.000 x 50.000 x 50.000 122s Grid center: (0.000, 0.000, 0.000) 122s Multigrid levels: 5 122s Molecule ID: 1 122s Linearized traditional PBE 122s Multiple Debye-Huckel sphere boundary conditions 122s 0 ion species (0.000 M ionic strength): 122s Solute dielectric: 1.000 122s Solvent dielectric: 1.000 122s Using "molecular" surface definition;harmonic average smoothing 122s Solvent probe radius: 1.400 A 122s Temperature: 298.150 K 122s Electrostatic energies will be calculated 122s Total electrostatic energy = 2.977178707146E+02 kJ/mol 122s Calculating forces... 122s ---------------------------------------- 122s CALCULATION #5 (reference): MULTIGRID 122s Setting up problem... 122s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 122s Debye length: 0 A 122s Current memory usage: 61.207 MB total, 122.102 MB high water 122s Using cubic spline charge discretization. 122s Partition overlap fraction = 0.1 122s Processor array = 2 x 2 x 1 122s Grid dimensions: 65 x 65 x 65 122s Grid spacings: 0.296 x 0.296 x 0.383 122s Grid lengths: 18.944 x 18.944 x 24.495 122s Grid center: (-2.411, 2.411, 0.000) 122s Multigrid levels: 5 122s Molecule ID: 1 122s Linearized traditional PBE 122s Boundary conditions from focusing 122s 0 ion species (0.000 M ionic strength): 122s Solute dielectric: 1.000 122s Solvent dielectric: 1.000 122s Using "molecular" surface definition;harmonic average smoothing 122s Solvent probe radius: 1.400 A 122s Temperature: 298.150 K 122s Electrostatic energies will be calculated 122s Total electrostatic energy = 8.799304557596E+02 kJ/mol 122s Calculating forces... 122s [focusFillBound()]: WARNING: 122s Unusually large potential values 122s detected on the focusing boundary! 122s Convergence not guaranteed for NPBE/NRPBE calculations! 122s 122s ---------------------------------------- 122s CALCULATION #6 (reference): MULTIGRID 122s Setting up problem... 122s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 122s Debye length: 0 A 122s Current memory usage: 61.207 MB total, 122.102 MB high water 122s Using cubic spline charge discretization. 122s Partition overlap fraction = 0.1 122s Processor array = 2 x 2 x 1 122s Grid dimensions: 65 x 65 x 65 122s Grid spacings: 0.112 x 0.112 x 0.188 122s Grid lengths: 7.178 x 7.178 x 12.000 122s Grid center: (-2.411, 2.411, 0.000) 122s Multigrid levels: 5 122s Molecule ID: 1 122s Linearized traditional PBE 122s Boundary conditions from focusing 122s 0 ion species (0.000 M ionic strength): 122s Solute dielectric: 1.000 122s Solvent dielectric: 1.000 122s Using "molecular" surface definition;harmonic average smoothing 122s Solvent probe radius: 1.400 A 122s Temperature: 298.150 K 122s Electrostatic energies will be calculated 122s Total electrostatic energy = 1.542873949141E+03 kJ/mol 122s Calculating forces... 122s ---------------------------------------- 122s PRINT STATEMENTS 122s 122s print energy 1 (solvated) - 2 (reference) end 122s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 122s Global net ELEC energy = -5.734895146550E+01 kJ/mol 122s ---------------------------------------- 122s CLEANING UP AND SHUTTING DOWN... 122s Destroying force arrays. 122s No energy arrays to destroy. 122s Destroying multigrid structures. 122s Destroying finite element structures. 122s Destroying 1 molecules 122s Final memory usage: 0.001 MB total, 122.102 MB high water 122s 122s 122s Thanks for using APBS! 122s 122s Processor 2 results: 122s 2.383232191909e+02 122s 8.145369593489e+02 122s 1.485524997676e+03 122s 2.977178707146e+02 122s 8.799304557596e+02 122s 1.542873949141e+03 122s -5.734895146550e+01 122s 123s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 123s BINARY: /usr/bin/apbs 123s INPUT: apbs-smol-parallel-PE3.in 123s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 123s Processor 3 results: 123s 2.383232191909e+02 123s 8.145419900310e+02 123s 1.485529328301e+03 123s 2.977178707146e+02 123s 8.799304557596e+02 123s 1.542873949141e+03 123s -5.734462084052e+01 123s 123s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 123s *** PASSED *** 123s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 123s *** PASSED *** 123s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 123s *** PASSED *** 123s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 123s *** PASSED *** 123s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 123s *** PASSED *** 123s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 123s *** PASSED *** 123s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 123s *** PASSED *** 123s Elapsed time: 4.083448 seconds 123s -------------------------------------------------------------------------------- 123s Total elapsed time: 9.989111 seconds 123s Test results have been logged 123s -------------------------------------------------------------------------------- 123s -------------------------------------------------------------------------------- 123s Testing input file apbs-mol-auto.in 123s 123s asc_getToken: Error occurred (bailing out). 123s Vio_scanf: Format problem with input. 123s 123s 123s ---------------------------------------------------------------------- 123s APBS -- Adaptive Poisson-Boltzmann Solver 123s Version APBS 3.4.1 123s 123s Nathan A. Baker (nathan.baker@pnnl.gov) 123s Pacific Northwest National Laboratory 123s 123s Additional contributing authors listed in the code documentation. 123s 123s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 123s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 123s Northwest Division for the U.S. Department of Energy. 123s 123s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 123s Portions Copyright (c) 2002-2020, Nathan A. Baker. 123s Portions Copyright (c) 1999-2002, The Regents of the University of California. 123s Portions Copyright (c) 1995, Michael Holst. 123s All rights reserved. 123s 123s Redistribution and use in source and binary forms, with or without 123s modification, are permitted provided that the following conditions are met: 123s 123s * Redistributions of source code must retain the above copyright notice, this 123s list of conditions and the following disclaimer. 123s 123s * Redistributions in binary form must reproduce the above copyright notice, 123s this list of conditions and the following disclaimer in the documentation 123s and/or other materials provided with the distribution. 123s 123s * Neither the name of the developer nor the names of its contributors may be 123s used to endorse or promote products derived from this software without 123s specific prior written permission. 123s 123s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 123s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 123s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 123s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 123s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 123s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 123s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 123s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 123s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 123s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 123s ---------------------------------------------------------------------- 123s APBS uses FETK (the Finite Element ToolKit) to solve the 123s Poisson-Boltzmann equation numerically. FETK is a portable collection 123s of finite element modeling class libraries developed by the Michael Holst 123s research group and written in an object-oriented form of C. FEtk is 123s designed to solve general coupled systems of nonlinear partial differential 123s equations using adaptive finite element methods, inexact Newton methods, 123s and algebraic multilevel methods. More information about FEtk may be found 123s at . 123s ---------------------------------------------------------------------- 123s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 123s Aqua is a modified form of the Holst group PMG library 123s which has been modified by Patrice Koehl 123s for improved efficiency and 123s memory usage when solving the Poisson-Boltzmann equation. 123s ---------------------------------------------------------------------- 123s Please cite your use of APBS as: 123s 123s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 123s nanosystems: application to microtubules and the ribosome. Proc. 123s Natl. Acad. Sci. USA 98, 10037-10041 2001. 123s 123s 123s This executable compiled on Jan 3 2025 at 11:01:42 123s 123s Parsing input file apbs-smol-parallel-PE3.in... 123s rank 0 size 1... 123s Parsed input file. 123s Got paths for 1 molecules 123s Reading PQR-format atom data from ion.pqr. 123s 1 atoms 123s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 123s Net charge 1.00e+00 e 123s Preparing to run 6 PBE calculations. 123s ---------------------------------------- 123s CALCULATION #1 (solvated): MULTIGRID 123s Setting up problem... 123s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 123s Debye length: 0 A 123s Current memory usage: 61.280 MB total, 61.280 MB high water 123s Using cubic spline charge discretization. 123s Partition overlap fraction = 0.1 123s Processor array = 2 x 2 x 1 123s Grid dimensions: 65 x 65 x 65 123s Grid spacings: 0.781 x 0.781 x 0.781 123s Grid lengths: 50.000 x 50.000 x 50.000 123s Grid center: (0.000, 0.000, 0.000) 123s Multigrid levels: 5 123s Molecule ID: 1 123s Linearized traditional PBE 123s Multiple Debye-Huckel sphere boundary conditions 123s 0 ion species (0.000 M ionic strength): 123s Solute dielectric: 1.000 123s Solvent dielectric: 78.540 123s Using "molecular" surface definition;harmonic average smoothing 123s Solvent probe radius: 1.400 A 123s Temperature: 298.150 K 123s Electrostatic energies will be calculated 123s Total electrostatic energy = 2.383232191909E+02 kJ/mol 123s Calculating forces... 123s ---------------------------------------- 123s CALCULATION #2 (solvated): MULTIGRID 123s Setting up problem... 123s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 123s Debye length: 0 A 123s Current memory usage: 61.280 MB total, 122.102 MB high water 123s Using cubic spline charge discretization. 123s Partition overlap fraction = 0.1 123s Processor array = 2 x 2 x 1 123s Grid dimensions: 65 x 65 x 65 123s Grid spacings: 0.296 x 0.296 x 0.383 123s Grid lengths: 18.944 x 18.944 x 24.495 123s Grid center: (2.411, 2.411, 0.000) 123s Multigrid levels: 5 123s Molecule ID: 1 123s Linearized traditional PBE 123s Boundary conditions from focusing 123s 0 ion species (0.000 M ionic strength): 123s Solute dielectric: 1.000 123s Solvent dielectric: 78.540 123s Using "molecular" surface definition;harmonic average smoothing 123s Solvent probe radius: 1.400 A 123s Temperature: 298.150 K 123s Electrostatic energies will be calculated 123s Total electrostatic energy = 8.145419900310E+02 kJ/mol 123s Calculating forces... 123s [focusFillBound()]: WARNING: 123s Unusually large potential values 123s detected on the focusing boundary! 123s Convergence not guaranteed for NPBE/NRPBE calculations! 123s 123s ---------------------------------------- 123s CALCULATION #3 (solvated): MULTIGRID 123s Setting up problem... 123s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 123s Debye length: 0 A 123s Current memory usage: 61.280 MB total, 122.102 MB high water 123s Using cubic spline charge discretization. 123s Partition overlap fraction = 0.1 123s Processor array = 2 x 2 x 1 123s Grid dimensions: 65 x 65 x 65 123s Grid spacings: 0.112 x 0.112 x 0.188 123s Grid lengths: 7.178 x 7.178 x 12.000 123s Grid center: (2.411, 2.411, 0.000) 123s Multigrid levels: 5 123s Molecule ID: 1 123s Linearized traditional PBE 123s Boundary conditions from focusing 123s 0 ion species (0.000 M ionic strength): 123s Solute dielectric: 1.000 123s Solvent dielectric: 78.540 123s Using "molecular" surface definition;harmonic average smoothing 123s Solvent probe radius: 1.400 A 123s Temperature: 298.150 K 123s Electrostatic energies will be calculated 123s Total electrostatic energy = 1.485529328301E+03 kJ/mol 123s Calculating forces... 123s ---------------------------------------- 123s CALCULATION #4 (reference): MULTIGRID 123s Setting up problem... 123s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 123s Debye length: 0 A 123s Current memory usage: 61.207 MB total, 122.102 MB high water 123s Using cubic spline charge discretization. 123s Partition overlap fraction = 0.1 123s Processor array = 2 x 2 x 1 123s Grid dimensions: 65 x 65 x 65 123s Grid spacings: 0.781 x 0.781 x 0.781 123s Grid lengths: 50.000 x 50.000 x 50.000 123s Grid center: (0.000, 0.000, 0.000) 123s Multigrid levels: 5 123s Molecule ID: 1 123s Linearized traditional PBE 123s Multiple Debye-Huckel sphere boundary conditions 123s 0 ion species (0.000 M ionic strength): 123s Solute dielectric: 1.000 123s Solvent dielectric: 1.000 123s Using "molecular" surface definition;harmonic average smoothing 123s Solvent probe radius: 1.400 A 123s Temperature: 298.150 K 123s Electrostatic energies will be calculated 123s Total electrostatic energy = 2.977178707146E+02 kJ/mol 123s Calculating forces... 123s ---------------------------------------- 123s CALCULATION #5 (reference): MULTIGRID 123s Setting up problem... 123s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 123s Debye length: 0 A 123s Current memory usage: 61.207 MB total, 122.102 MB high water 123s Using cubic spline charge discretization. 123s Partition overlap fraction = 0.1 123s Processor array = 2 x 2 x 1 123s Grid dimensions: 65 x 65 x 65 123s Grid spacings: 0.296 x 0.296 x 0.383 123s Grid lengths: 18.944 x 18.944 x 24.495 123s Grid center: (2.411, 2.411, 0.000) 123s Multigrid levels: 5 123s Molecule ID: 1 123s Linearized traditional PBE 123s Boundary conditions from focusing 123s 0 ion species (0.000 M ionic strength): 123s Solute dielectric: 1.000 123s Solvent dielectric: 1.000 123s Using "molecular" surface definition;harmonic average smoothing 123s Solvent probe radius: 1.400 A 123s Temperature: 298.150 K 123s Electrostatic energies will be calculated 123s Total electrostatic energy = 8.799304557596E+02 kJ/mol 123s Calculating forces... 123s [focusFillBound()]: WARNING: 123s Unusually large potential values 123s detected on the focusing boundary! 123s Convergence not guaranteed for NPBE/NRPBE calculations! 123s 123s ---------------------------------------- 123s CALCULATION #6 (reference): MULTIGRID 123s Setting up problem... 123s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 123s Debye length: 0 A 123s Current memory usage: 61.207 MB total, 122.102 MB high water 123s Using cubic spline charge discretization. 123s Partition overlap fraction = 0.1 123s Processor array = 2 x 2 x 1 123s Grid dimensions: 65 x 65 x 65 123s Grid spacings: 0.112 x 0.112 x 0.188 123s Grid lengths: 7.178 x 7.178 x 12.000 123s Grid center: (2.411, 2.411, 0.000) 123s Multigrid levels: 5 123s Molecule ID: 1 123s Linearized traditional PBE 123s Boundary conditions from focusing 123s 0 ion species (0.000 M ionic strength): 123s Solute dielectric: 1.000 123s Solvent dielectric: 1.000 123s Using "molecular" surface definition;harmonic average smoothing 123s Solvent probe radius: 1.400 A 123s Temperature: 298.150 K 123s Electrostatic energies will be calculated 123s Total electrostatic energy = 1.542873949141E+03 kJ/mol 123s Calculating forces... 123s ---------------------------------------- 123s PRINT STATEMENTS 123s 123s print energy 1 (solvated) - 2 (reference) end 123s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 123s Global net ELEC energy = -5.734462084052E+01 kJ/mol 123s ---------------------------------------- 123s CLEANING UP AND SHUTTING DOWN... 123s Destroying force arrays. 123s No energy arrays to destroy. 123s Destroying multigrid structures. 123s Destroying finite element structures. 123s Destroying 1 molecules 123s Final memory usage: 0.001 MB total, 122.102 MB high water 123s 123s 123s Thanks for using APBS! 123s 186s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 186s EXPECTED COMPUTED: 7 186s EXPECTED EXPECTED: 7 186s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 186s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 186s COMPUTED RESULT 953.292876745 186s COMPUTED RESULT 3258.1578983732998 186s COMPUTED RESULT 5942.108652589999 186s COMPUTED RESULT 1190.8714828309999 186s COMPUTED RESULT 3519.7218230368003 186s COMPUTED RESULT 6171.495796544 186s COMPUTED RESULT -229.38714395599 186s Running tests for actin-dimer-auto section 186s BINARY: /usr/bin/apbs 186s INPUT: apbs-mol-auto.in 186s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 186s asc_getToken: Error occurred (bailing out). 186s Vio_scanf: Format problem with input. 186s 186s 186s ---------------------------------------------------------------------- 186s APBS -- Adaptive Poisson-Boltzmann Solver 186s Version APBS 3.4.1 186s 186s Nathan A. Baker (nathan.baker@pnnl.gov) 186s Pacific Northwest National Laboratory 186s 186s Additional contributing authors listed in the code documentation. 186s 186s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 186s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 186s Northwest Division for the U.S. Department of Energy. 186s 186s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 186s Portions Copyright (c) 2002-2020, Nathan A. Baker. 186s Portions Copyright (c) 1999-2002, The Regents of the University of California. 186s Portions Copyright (c) 1995, Michael Holst. 186s All rights reserved. 186s 186s Redistribution and use in source and binary forms, with or without 186s modification, are permitted provided that the following conditions are met: 186s 186s * Redistributions of source code must retain the above copyright notice, this 186s list of conditions and the following disclaimer. 186s 186s * Redistributions in binary form must reproduce the above copyright notice, 186s this list of conditions and the following disclaimer in the documentation 186s and/or other materials provided with the distribution. 186s 186s * Neither the name of the developer nor the names of its contributors may be 186s used to endorse or promote products derived from this software without 186s specific prior written permission. 186s 186s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 186s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 186s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 186s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 186s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 186s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 186s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 186s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 186s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 186s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 186s ---------------------------------------------------------------------- 186s APBS uses FETK (the Finite Element ToolKit) to solve the 186s Poisson-Boltzmann equation numerically. FETK is a portable collection 186s of finite element modeling class libraries developed by the Michael Holst 186s research group and written in an object-oriented form of C. FEtk is 186s designed to solve general coupled systems of nonlinear partial differential 186s equations using adaptive finite element methods, inexact Newton methods, 186s and algebraic multilevel methods. More information about FEtk may be found 186s at . 186s ---------------------------------------------------------------------- 186s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 186s Aqua is a modified form of the Holst group PMG library 186s which has been modified by Patrice Koehl 186s for improved efficiency and 186s memory usage when solving the Poisson-Boltzmann equation. 186s ---------------------------------------------------------------------- 186s Please cite your use of APBS as: 186s 186s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 186s nanosystems: application to microtubules and the ribosome. Proc. 186s Natl. Acad. Sci. USA 98, 10037-10041 2001. 186s 186s 186s This executable compiled on Jan 3 2025 at 11:01:42 186s 186s Parsing input file apbs-mol-auto.in... 186s rank 0 size 1... 186s Parsed input file. 186s Got paths for 3 molecules 186s Reading PQR-format atom data from mol1.pqr. 186s asc_getToken: Error occurred (bailing out). 186s Vio_scanf: Format problem with input. 186s 5877 atoms 186s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 186s Net charge -1.20e+01 e 186s Reading PQR-format atom data from mol2.pqr. 186s asc_getToken: Error occurred (bailing out). 186s Vio_scanf: Format problem with input. 186s 5877 atoms 186s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 186s Net charge -1.20e+01 e 186s Reading PQR-format atom data from complex.pqr. 186s 11754 atoms 186s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 186s Net charge -2.40e+01 e 186s Preparing to run 6 PBE calculations. 186s ---------------------------------------- 186s CALCULATION #1 (mol1): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 186s Debye length: 13.5959 A 186s Current memory usage: 1028.322 MB total, 1028.322 MB high water 186s Using linear spline charge discretization. 186s Grid dimensions: 161 x 161 x 161 186s Grid spacings: 0.975 x 0.756 x 1.012 186s Grid lengths: 156.000 x 121.000 x 162.000 186s Grid center: (2.518, -2.465, 16.742) 186s Multigrid levels: 4 186s Molecule ID: 1 186s Nonlinear traditional PBE 186s Single Debye-Huckel sphere boundary conditions 186s 2 ion species (0.050 M ionic strength): 186s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 186s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 186s Solute dielectric: 2.000 186s Solvent dielectric: 78.400 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 1.527617850342E+05 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #2 (mol1): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 186s Debye length: 13.5959 A 186s Current memory usage: 1028.322 MB total, 2042.113 MB high water 186s Using linear spline charge discretization. 186s Grid dimensions: 161 x 161 x 161 186s Grid spacings: 0.700 x 0.569 x 0.725 186s Grid lengths: 112.000 x 91.000 x 116.000 186s Grid center: (2.518, -2.465, 16.742) 186s Multigrid levels: 4 186s Molecule ID: 1 186s Nonlinear traditional PBE 186s Boundary conditions from focusing 186s 2 ion species (0.050 M ionic strength): 186s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 186s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 186s Solute dielectric: 2.000 186s Solvent dielectric: 78.400 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 2.919510754196E+05 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #3 (mol2): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 186s Debye length: 13.5959 A 186s Current memory usage: 1030.291 MB total, 2042.113 MB high water 186s Using linear spline charge discretization. 186s Grid dimensions: 161 x 161 x 161 186s Grid spacings: 0.975 x 0.756 x 1.012 186s Grid lengths: 156.000 x 121.000 x 162.000 186s Grid center: (2.518, -2.465, 16.742) 186s Multigrid levels: 4 186s Molecule ID: 2 186s Nonlinear traditional PBE 186s Single Debye-Huckel sphere boundary conditions 186s 2 ion species (0.050 M ionic strength): 186s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 186s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 186s Solute dielectric: 2.000 186s Solvent dielectric: 78.400 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 1.527671844880E+05 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #4 (mol2): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 186s Debye length: 13.5959 A 186s Current memory usage: 1030.291 MB total, 2046.048 MB high water 186s Using linear spline charge discretization. 186s Grid dimensions: 161 x 161 x 161 186s Grid spacings: 0.700 x 0.569 x 0.725 186s Grid lengths: 112.000 x 91.000 x 116.000 186s Grid center: (2.518, -2.465, 16.742) 186s Multigrid levels: 4 186s Molecule ID: 2 186s Nonlinear traditional PBE 186s Boundary conditions from focusing 186s 2 ion species (0.050 M ionic strength): 186s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 186s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 186s Solute dielectric: 2.000 186s Solvent dielectric: 78.400 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 2.915468859278E+05 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #5 (complex): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 186s Debye length: 13.5959 A 186s Current memory usage: 1046.446 MB total, 2046.048 MB high water 186s Using linear spline charge discretization. 186s Grid dimensions: 161 x 161 x 161 186s Grid spacings: 0.975 x 0.756 x 1.012 186s Grid lengths: 156.000 x 121.000 x 162.000 186s Grid center: (2.518, -2.465, 16.742) 186s Multigrid levels: 4 186s Molecule ID: 3 186s Nonlinear traditional PBE 186s Single Debye-Huckel sphere boundary conditions 186s 2 ion species (0.050 M ionic strength): 186s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 186s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 186s Solute dielectric: 2.000 186s Solvent dielectric: 78.400 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 3.056317807611E+05 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s CALCULATION #6 (complex): MULTIGRID 186s Setting up problem... 186s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 186s Debye length: 13.5959 A 186s Current memory usage: 1046.446 MB total, 2069.492 MB high water 186s Using linear spline charge discretization. 186s Grid dimensions: 161 x 161 x 161 186s Grid spacings: 0.700 x 0.569 x 0.725 186s Grid lengths: 112.000 x 91.000 x 116.000 186s Grid center: (2.518, -2.465, 16.742) 186s Multigrid levels: 4 186s Molecule ID: 3 186s Nonlinear traditional PBE 186s Boundary conditions from focusing 186s 2 ion species (0.050 M ionic strength): 186s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 186s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 186s Solute dielectric: 2.000 186s Solvent dielectric: 78.400 186s Using "molecular" surface definition; no smoothing 186s Solvent probe radius: 1.400 A 186s Temperature: 298.150 K 186s Electrostatic energies will be calculated 186s Total electrostatic energy = 5.836028296532E+05 kJ/mol 186s Calculating forces... 186s ---------------------------------------- 186s PRINT STATEMENTS 186s 186s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 186s Local net energy (PE 0) = 1.048683058621E+02 kJ/mol 186s Global net ELEC energy = 1.048683058621E+02 kJ/mol 186s ---------------------------------------- 186s CLEANING UP AND SHUTTING DOWN... 186s Destroying force arrays. 186s No energy arrays to destroy. 186s Destroying multigrid structures. 186s Destroying finite element structures. 186s Destroying 3 molecules 186s Final memory usage: 0.001 MB total, 2069.492 MB high water 186s 186s 186s Thanks for using APBS! 186s 186s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 186s *** PASSED *** 186s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 186s *** PASSED *** 186s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 186s *** PASSED *** 186s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 186s *** PASSED *** 186s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 186s *** PASSED *** 186s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 186s *** PASSED *** 186s Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) 186s *** PASSED *** 187s Elapsed time: 63.089054 seconds 187s -------------------------------------------------------------------------------- 187s -------------------------------------------------------------------------------- 187s Testing input file apbs-smol-auto.in 187s 237s Checking for intermediate energies in input file apbs-mol-auto.out 237s EXPECTED COMPUTED: 7 237s EXPECTED EXPECTED: 7 237s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] 237s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 237s COMPUTED RESULT 152761.7850342 237s COMPUTED RESULT 291951.0754196 237s COMPUTED RESULT 152767.184488 237s COMPUTED RESULT 291546.8859278 237s COMPUTED RESULT 305631.7807611 237s COMPUTED RESULT 583602.8296532 237s COMPUTED RESULT 104.8683058621 237s BINARY: /usr/bin/apbs 237s INPUT: apbs-smol-auto.in 237s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 237s asc_getToken: Error occurred (bailing out). 237s Vio_scanf: Format problem with input. 237s 237s 237s ---------------------------------------------------------------------- 237s APBS -- Adaptive Poisson-Boltzmann Solver 237s Version APBS 3.4.1 237s 237s Nathan A. Baker (nathan.baker@pnnl.gov) 237s Pacific Northwest National Laboratory 237s 237s Additional contributing authors listed in the code documentation. 237s 237s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 237s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 237s Northwest Division for the U.S. Department of Energy. 237s 237s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 237s Portions Copyright (c) 2002-2020, Nathan A. Baker. 237s Portions Copyright (c) 1999-2002, The Regents of the University of California. 237s Portions Copyright (c) 1995, Michael Holst. 237s All rights reserved. 237s 237s Redistribution and use in source and binary forms, with or without 237s modification, are permitted provided that the following conditions are met: 237s 237s * Redistributions of source code must retain the above copyright notice, this 237s list of conditions and the following disclaimer. 237s 237s * Redistributions in binary form must reproduce the above copyright notice, 237s this list of conditions and the following disclaimer in the documentation 237s and/or other materials provided with the distribution. 237s 237s * Neither the name of the developer nor the names of its contributors may be 237s used to endorse or promote products derived from this software without 237s specific prior written permission. 237s 237s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 237s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 237s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 237s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 237s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 237s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 237s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 237s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 237s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 237s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 237s ---------------------------------------------------------------------- 237s APBS uses FETK (the Finite Element ToolKit) to solve the 237s Poisson-Boltzmann equation numerically. FETK is a portable collection 237s of finite element modeling class libraries developed by the Michael Holst 237s research group and written in an object-oriented form of C. FEtk is 237s designed to solve general coupled systems of nonlinear partial differential 237s equations using adaptive finite element methods, inexact Newton methods, 237s and algebraic multilevel methods. More information about FEtk may be found 237s at . 237s ---------------------------------------------------------------------- 237s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 237s Aqua is a modified form of the Holst group PMG library 237s which has been modified by Patrice Koehl 237s for improved efficiency and 237s memory usage when solving the Poisson-Boltzmann equation. 237s ---------------------------------------------------------------------- 237s Please cite your use of APBS as: 237s 237s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 237s nanosystems: application to microtubules and the ribosome. Proc. 237s Natl. Acad. Sci. USA 98, 10037-10041 2001. 237s 237s 237s This executable compiled on Jan 3 2025 at 11:01:42 237s 237s Parsing input file apbs-smol-auto.in... 237s rank 0 size 1... 237s Parsed input file. 237s Got paths for 3 molecules 237s Reading PQR-format atom data from mol1.pqr. 237s asc_getToken: Error occurred (bailing out). 237s Vio_scanf: Format problem with input. 237s 5877 atoms 237s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 237s Net charge -1.20e+01 e 237s Reading PQR-format atom data from mol2.pqr. 237s asc_getToken: Error occurred (bailing out). 237s Vio_scanf: Format problem with input. 237s 5877 atoms 237s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 237s Net charge -1.20e+01 e 237s Reading PQR-format atom data from complex.pqr. 237s 11754 atoms 237s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 237s Net charge -2.40e+01 e 237s Preparing to run 6 PBE calculations. 237s ---------------------------------------- 237s CALCULATION #1 (mol1): MULTIGRID 237s Setting up problem... 237s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 237s Debye length: 13.5959 A 237s Current memory usage: 1028.322 MB total, 1028.322 MB high water 237s Using linear spline charge discretization. 237s Grid dimensions: 161 x 161 x 161 237s Grid spacings: 0.975 x 0.756 x 1.012 237s Grid lengths: 156.000 x 121.000 x 162.000 237s Grid center: (2.518, -2.465, 16.742) 237s Multigrid levels: 4 237s Molecule ID: 1 237s Nonlinear traditional PBE 237s Single Debye-Huckel sphere boundary conditions 237s 2 ion species (0.050 M ionic strength): 237s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 237s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 237s Solute dielectric: 2.000 237s Solvent dielectric: 78.400 237s Using "molecular" surface definition;harmonic average smoothing 237s Solvent probe radius: 1.400 A 237s Temperature: 298.150 K 237s Electrostatic energies will be calculated 237s Total electrostatic energy = 1.528632421825E+05 kJ/mol 237s Calculating forces... 237s ---------------------------------------- 237s CALCULATION #2 (mol1): MULTIGRID 237s Setting up problem... 237s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 237s Debye length: 13.5959 A 237s Current memory usage: 1028.322 MB total, 2042.113 MB high water 237s Using linear spline charge discretization. 237s Grid dimensions: 161 x 161 x 161 237s Grid spacings: 0.700 x 0.569 x 0.725 237s Grid lengths: 112.000 x 91.000 x 116.000 237s Grid center: (2.518, -2.465, 16.742) 237s Multigrid levels: 4 237s Molecule ID: 1 237s Nonlinear traditional PBE 237s Boundary conditions from focusing 237s 2 ion species (0.050 M ionic strength): 237s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 237s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 237s Solute dielectric: 2.000 237s Solvent dielectric: 78.400 237s Using "molecular" surface definition;harmonic average smoothing 237s Solvent probe radius: 1.400 A 237s Temperature: 298.150 K 237s Electrostatic energies will be calculated 237s Total electrostatic energy = 2.920618662320E+05 kJ/mol 237s Calculating forces... 237s ---------------------------------------- 237s CALCULATION #3 (mol2): MULTIGRID 237s Setting up problem... 237s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 237s Debye length: 13.5959 A 237s Current memory usage: 1030.291 MB total, 2042.113 MB high water 237s Using linear spline charge discretization. 237s Grid dimensions: 161 x 161 x 161 237s Grid spacings: 0.975 x 0.756 x 1.012 237s Grid lengths: 156.000 x 121.000 x 162.000 237s Grid center: (2.518, -2.465, 16.742) 237s Multigrid levels: 4 237s Molecule ID: 2 237s Nonlinear traditional PBE 237s Single Debye-Huckel sphere boundary conditions 237s 2 ion species (0.050 M ionic strength): 237s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 237s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 237s Solute dielectric: 2.000 237s Solvent dielectric: 78.400 237s Using "molecular" surface definition;harmonic average smoothing 237s Solvent probe radius: 1.400 A 237s Temperature: 298.150 K 237s Electrostatic energies will be calculated 237s Total electrostatic energy = 1.529297900572E+05 kJ/mol 237s Calculating forces... 237s ---------------------------------------- 237s CALCULATION #4 (mol2): MULTIGRID 237s Setting up problem... 237s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 237s Debye length: 13.5959 A 237s Current memory usage: 1030.291 MB total, 2046.048 MB high water 237s Using linear spline charge discretization. 237s Grid dimensions: 161 x 161 x 161 237s Grid spacings: 0.700 x 0.569 x 0.725 237s Grid lengths: 112.000 x 91.000 x 116.000 237s Grid center: (2.518, -2.465, 16.742) 237s Multigrid levels: 4 237s Molecule ID: 2 237s Nonlinear traditional PBE 237s Boundary conditions from focusing 237s 2 ion species (0.050 M ionic strength): 237s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 237s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 237s Solute dielectric: 2.000 237s Solvent dielectric: 78.400 237s Using "molecular" surface definition;harmonic average smoothing 237s Solvent probe radius: 1.400 A 237s Temperature: 298.150 K 237s Electrostatic energies will be calculated 237s Total electrostatic energy = 2.916592202835E+05 kJ/mol 237s Calculating forces... 237s ---------------------------------------- 237s CALCULATION #5 (complex): MULTIGRID 237s Setting up problem... 237s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 237s Debye length: 13.5959 A 237s Current memory usage: 1046.446 MB total, 2046.048 MB high water 237s Using linear spline charge discretization. 237s Grid dimensions: 161 x 161 x 161 237s Grid spacings: 0.975 x 0.756 x 1.012 237s Grid lengths: 156.000 x 121.000 x 162.000 237s Grid center: (2.518, -2.465, 16.742) 237s Multigrid levels: 4 237s Molecule ID: 3 237s Nonlinear traditional PBE 237s Single Debye-Huckel sphere boundary conditions 237s 2 ion species (0.050 M ionic strength): 237s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 237s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 237s Solute dielectric: 2.000 237s Solvent dielectric: 78.400 237s Using "molecular" surface definition;harmonic average smoothing 237s Solvent probe radius: 1.400 A 237s Temperature: 298.150 K 237s Electrostatic energies will be calculated 237s Total electrostatic energy = 3.059244262535E+05 kJ/mol 237s Calculating forces... 237s ---------------------------------------- 237s CALCULATION #6 (complex): MULTIGRID 237s Setting up problem... 237s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 237s Debye length: 13.5959 A 237s Current memory usage: 1046.446 MB total, 2069.492 MB high water 237s Using linear spline charge discretization. 237s Grid dimensions: 161 x 161 x 161 237s Grid spacings: 0.700 x 0.569 x 0.725 237s Grid lengths: 112.000 x 91.000 x 116.000 237s Grid center: (2.518, -2.465, 16.742) 237s Multigrid levels: 4 237s Molecule ID: 3 237s Nonlinear traditional PBE 237s Boundary conditions from focusing 237s 2 ion species (0.050 M ionic strength): 237s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 237s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 237s Solute dielectric: 2.000 237s Solvent dielectric: 78.400 237s Using "molecular" surface definition;harmonic average smoothing 237s Solvent probe radius: 1.400 A 237s Temperature: 298.150 K 237s Electrostatic energies will be calculated 237s Total electrostatic energy = 5.838306706232E+05 kJ/mol 237s Calculating forces... 237s ---------------------------------------- 237s PRINT STATEMENTS 237s 237s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 237s Local net energy (PE 0) = 1.095841077688E+02 kJ/mol 237s Global net ELEC energy = 1.095841077688E+02 kJ/mol 237s ---------------------------------------- 237s CLEANING UP AND SHUTTING DOWN... 237s Destroying force arrays. 237s No energy arrays to destroy. 237s Destroying multigrid structures. 237s Destroying finite element structures. 237s Destroying 3 molecules 237s Final memory usage: 0.001 MB total, 2069.492 MB high water 237s 237s 237s Thanks for using APBS! 237s 237s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 237s *** PASSED *** 237s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 237s *** PASSED *** 237s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 237s *** PASSED *** 237s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 237s *** PASSED *** 237s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 237s *** PASSED *** 237s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 237s *** PASSED *** 237s Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) 237s *** PASSED *** 237s Elapsed time: 50.194543 seconds 237s -------------------------------------------------------------------------------- 237s Total elapsed time: 113.283597 seconds 237s Test results have been logged 237s -------------------------------------------------------------------------------- 237s -------------------------------------------------------------------------------- 237s Testing input file alkanes.in 237s 248s Checking for intermediate energies in input file apbs-smol-auto.out 248s EXPECTED COMPUTED: 7 248s EXPECTED EXPECTED: 7 248s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] 248s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 248s COMPUTED RESULT 152863.2421825 248s COMPUTED RESULT 292061.866232 248s COMPUTED RESULT 152929.7900572 248s COMPUTED RESULT 291659.2202835 248s COMPUTED RESULT 305924.4262535 248s COMPUTED RESULT 583830.6706232 248s COMPUTED RESULT 109.5841077688 248s Running tests for alkanes section 248s BINARY: /usr/bin/apbs 248s INPUT: alkanes.in 248s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 248s 248s ---------------------------------------------------------------------- 248s APBS -- Adaptive Poisson-Boltzmann Solver 248s Version APBS 3.4.1 248s 248s Nathan A. Baker (nathan.baker@pnnl.gov) 248s Pacific Northwest National Laboratory 248s 248s Additional contributing authors listed in the code documentation. 248s 248s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 248s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 248s Northwest Division for the U.S. Department of Energy. 248s 248s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 248s Portions Copyright (c) 2002-2020, Nathan A. Baker. 248s Portions Copyright (c) 1999-2002, The Regents of the University of California. 248s Portions Copyright (c) 1995, Michael Holst. 248s All rights reserved. 248s 248s Redistribution and use in source and binary forms, with or without 248s modification, are permitted provided that the following conditions are met: 248s 248s * Redistributions of source code must retain the above copyright notice, this 248s list of conditions and the following disclaimer. 248s 248s * Redistributions in binary form must reproduce the above copyright notice, 248s this list of conditions and the following disclaimer in the documentation 248s and/or other materials provided with the distribution. 248s 248s * Neither the name of the developer nor the names of its contributors may be 248s used to endorse or promote products derived from this software without 248s specific prior written permission. 248s 248s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 248s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 248s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 248s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 248s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 248s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 248s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 248s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 248s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 248s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 248s ---------------------------------------------------------------------- 248s APBS uses FETK (the Finite Element ToolKit) to solve the 248s Poisson-Boltzmann equation numerically. FETK is a portable collection 248s of finite element modeling class libraries developed by the Michael Holst 248s research group and written in an object-oriented form of C. FEtk is 248s designed to solve general coupled systems of nonlinear partial differential 248s equations using adaptive finite element methods, inexact Newton methods, 248s and algebraic multilevel methods. More information about FEtk may be found 248s at . 248s ---------------------------------------------------------------------- 248s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 248s Aqua is a modified form of the Holst group PMG library 248s which has been modified by Patrice Koehl 248s for improved efficiency and 248s memory usage when solving the Poisson-Boltzmann equation. 248s ---------------------------------------------------------------------- 248s Please cite your use of APBS as: 248s 248s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 248s nanosystems: application to microtubules and the ribosome. Proc. 248s Natl. Acad. Sci. USA 98, 10037-10041 2001. 248s 248s 248s This executable compiled on Jan 3 2025 at 11:01:42 248s 248s Parsing input file alkanes.in... 248s rank 0 size 1... 248s Parsed input file. 248s Reading parameter data from parm.dat. 248s Got paths for 11 molecules 248s Reading PDB-format atom data from 2-methylbutane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 17 atoms 248s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 248s Net charge 4.33e+00 e 248s Reading PDB-format atom data from butane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 14 atoms 248s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 248s Net charge 3.51e+00 e 248s Reading PDB-format atom data from cyclohexane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 18 atoms 248s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 248s Net charge 4.93e+00 e 248s Reading PDB-format atom data from cyclopentane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 13 atoms 248s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 248s Net charge 3.88e+00 e 248s Reading PDB-format atom data from ethane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 8 atoms 248s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 248s Net charge 1.87e+00 e 248s Reading PDB-format atom data from hexane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 20 atoms 248s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 248s Net charge 5.16e+00 e 248s Reading PDB-format atom data from isobutane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 14 atoms 248s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 248s Net charge 3.51e+00 e 248s Reading PDB-format atom data from methane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 5 atoms 248s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 248s Net charge 1.05e+00 e 248s Reading PDB-format atom data from neopentane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 17 atoms 248s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 248s Net charge 4.33e+00 e 248s Reading PDB-format atom data from pentane.pdb. 248s asc_getToken: Error occurred (bailing out). 248s Vio_scanf: Format problem with input. 248s 17 atoms 248s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 248s Net charge 4.33e+00 e 248s Reading PDB-format atom data from propane.pdb. 248s 11 atoms 248s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 248s Net charge 2.69e+00 e 248s Preparing to run 11 PBE calculations. 248s ---------------------------------------- 248s CALCULATION #1 (solvated-2-methylbutane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 3.815624614267E+00 248s SASA for atom 1: 0.000000000000E+00 248s SASA for atom 2: 6.122920124655E-01 248s SASA for atom 3: 3.957497153740E+00 248s SASA for atom 4: 4.308445014544E+00 248s SASA for atom 5: 1.843264951960E+01 248s SASA for atom 6: 1.837011296483E+01 248s SASA for atom 7: 1.666599184724E+01 248s SASA for atom 8: 1.480031796315E+01 248s SASA for atom 9: 1.603020354037E+01 248s SASA for atom 10: 1.473778140838E+01 248s SASA for atom 11: 1.611879699297E+01 248s SASA for atom 12: 1.810954398660E+01 248s SASA for atom 13: 1.420100931324E+01 248s SASA for atom 14: 1.437298483886E+01 248s SASA for atom 15: 1.814081226399E+01 248s SASA for atom 16: 2.152820898091E+01 248s 248s Total solvent accessible surface area: 214.202 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 3.243280922127E-02 248s Surface tension*area energy for atom 1: 0.000000000000E+00 248s Surface tension*area energy for atom 2: 5.204482105957E-03 248s Surface tension*area energy for atom 3: 3.363872580679E-02 248s Surface tension*area energy for atom 4: 3.662178262362E-02 248s Surface tension*area energy for atom 5: 1.566775209166E-01 248s Surface tension*area energy for atom 6: 1.561459602010E-01 248s Surface tension*area energy for atom 7: 1.416609307015E-01 248s Surface tension*area energy for atom 8: 1.258027026868E-01 248s Surface tension*area energy for atom 9: 1.362567300932E-01 248s Surface tension*area energy for atom 10: 1.252711419712E-01 248s Surface tension*area energy for atom 11: 1.370097744402E-01 248s Surface tension*area energy for atom 12: 1.539311238861E-01 248s Surface tension*area energy for atom 13: 1.207085791625E-01 248s Surface tension*area energy for atom 14: 1.221703711303E-01 248s Surface tension*area energy for atom 15: 1.541969042439E-01 248s Surface tension*area energy for atom 16: 1.829897763377E-01 248s 248s Total surface tension energy: 1.82072 kJ/mol 248s 248s Total solvent accessible volume: 253.665 A^3 248s 248s Total pressure*volume energy: 60.7274 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.271287875274E+00 248s WCA energy for atom 1: -5.600872869478E+00 248s WCA energy for atom 2: -5.773775123943E+00 248s WCA energy for atom 3: -6.072801488986E+00 248s WCA energy for atom 4: -6.378470721845E+00 248s WCA energy for atom 5: -1.573474558351E+00 248s WCA energy for atom 6: -1.582338715648E+00 248s WCA energy for atom 7: -1.504044838266E+00 248s WCA energy for atom 8: -1.351002262819E+00 248s WCA energy for atom 9: -1.437367175239E+00 248s WCA energy for atom 10: -1.384626257493E+00 248s WCA energy for atom 11: -1.468867560891E+00 248s WCA energy for atom 12: -1.557005662832E+00 248s WCA energy for atom 13: -1.473759654043E+00 248s WCA energy for atom 14: -1.502261431335E+00 248s WCA energy for atom 15: -1.550940901474E+00 248s WCA energy for atom 16: -1.667828659696E+00 248s 248s Total WCA energy: -48.1507 kJ/mol 248s 248s Total non-polar energy = 1.439739455792E+01 kJ/mol 248s ---------------------------------------- 248s CALCULATION #2 (solvated-butane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 4.405515699447E+00 248s SASA for atom 1: 8.213673337951E-01 248s SASA for atom 2: 8.064333822716E-01 248s SASA for atom 3: 4.375647796400E+00 248s SASA for atom 4: 1.855251124959E+01 248s SASA for atom 5: 2.147609518526E+01 248s SASA for atom 6: 1.852645435176E+01 248s SASA for atom 7: 1.660345529247E+01 248s SASA for atom 8: 1.658782115377E+01 248s SASA for atom 9: 1.658260977421E+01 248s SASA for atom 10: 1.658260977421E+01 248s SASA for atom 11: 2.145003828744E+01 248s SASA for atom 12: 1.852124297220E+01 248s SASA for atom 13: 1.856293400871E+01 248s 248s Total solvent accessible surface area: 193.855 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 3.744688344530E-02 248s Surface tension*area energy for atom 1: 6.981622337259E-03 248s Surface tension*area energy for atom 2: 6.854683749309E-03 248s Surface tension*area energy for atom 3: 3.719300626940E-02 248s Surface tension*area energy for atom 4: 1.576963456215E-01 248s Surface tension*area energy for atom 5: 1.825468090747E-01 248s Surface tension*area energy for atom 6: 1.574748619900E-01 248s Surface tension*area energy for atom 7: 1.411293699860E-01 248s Surface tension*area energy for atom 8: 1.409964798071E-01 248s Surface tension*area energy for atom 9: 1.409521830808E-01 248s Surface tension*area energy for atom 10: 1.409521830808E-01 248s Surface tension*area energy for atom 11: 1.823253254433E-01 248s Surface tension*area energy for atom 12: 1.574305652637E-01 248s Surface tension*area energy for atom 13: 1.577849390741E-01 248s 248s Total surface tension energy: 1.64777 kJ/mol 248s 248s Total solvent accessible volume: 217.863 A^3 248s 248s Total pressure*volume energy: 52.1564 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.728858147814E+00 248s WCA energy for atom 1: -6.204037472587E+00 248s WCA energy for atom 2: -6.202937735018E+00 248s WCA energy for atom 3: -6.728762249931E+00 248s WCA energy for atom 4: -1.623549989062E+00 248s WCA energy for atom 5: -1.709092300778E+00 248s WCA energy for atom 6: -1.625196457114E+00 248s WCA energy for atom 7: -1.484289341167E+00 248s WCA energy for atom 8: -1.485410538626E+00 248s WCA energy for atom 9: -1.485593139015E+00 248s WCA energy for atom 10: -1.484878734279E+00 248s WCA energy for atom 11: -1.708585062695E+00 248s WCA energy for atom 12: -1.625094916482E+00 248s WCA energy for atom 13: -1.624416805392E+00 248s 248s Total WCA energy: -41.7207 kJ/mol 248s 248s Total non-polar energy = 1.208346456826E+01 kJ/mol 248s ---------------------------------------- 248s CALCULATION #3 (solvated-cyclohexane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 7.840324549863E-01 248s SASA for atom 1: 8.064333822716E-01 248s SASA for atom 2: 8.288343095569E-01 248s SASA for atom 3: 7.840324549863E-01 248s SASA for atom 4: 7.989664065098E-01 248s SASA for atom 5: 8.363012853187E-01 248s SASA for atom 6: 2.001169752764E+01 248s SASA for atom 7: 1.616048802948E+01 248s SASA for atom 8: 2.001169752764E+01 248s SASA for atom 9: 1.619175630687E+01 248s SASA for atom 10: 1.616048802948E+01 248s SASA for atom 11: 1.993352683418E+01 248s SASA for atom 12: 2.001169752764E+01 248s SASA for atom 13: 1.618133354774E+01 248s SASA for atom 14: 1.617091078861E+01 248s SASA for atom 15: 2.001690890721E+01 248s SASA for atom 16: 1.993873821374E+01 248s SASA for atom 17: 1.617091078861E+01 248s 248s Total solvent accessible surface area: 221.799 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 6.664275867383E-03 248s Surface tension*area energy for atom 1: 6.854683749309E-03 248s Surface tension*area energy for atom 2: 7.045091631234E-03 248s Surface tension*area energy for atom 3: 6.664275867383E-03 248s Surface tension*area energy for atom 4: 6.791214455333E-03 248s Surface tension*area energy for atom 5: 7.108560925209E-03 248s Surface tension*area energy for atom 6: 1.700994289850E-01 248s Surface tension*area energy for atom 7: 1.373641482506E-01 248s Surface tension*area energy for atom 8: 1.700994289850E-01 248s Surface tension*area energy for atom 9: 1.376299286084E-01 248s Surface tension*area energy for atom 10: 1.373641482506E-01 248s Surface tension*area energy for atom 11: 1.694349780905E-01 248s Surface tension*area energy for atom 12: 1.700994289850E-01 248s Surface tension*area energy for atom 13: 1.375413351558E-01 248s Surface tension*area energy for atom 14: 1.374527417032E-01 248s Surface tension*area energy for atom 15: 1.701437257113E-01 248s Surface tension*area energy for atom 16: 1.694792748168E-01 248s Surface tension*area energy for atom 17: 1.374527417032E-01 248s 248s Total surface tension energy: 1.88529 kJ/mol 248s 248s Total solvent accessible volume: 267.435 A^3 248s 248s Total pressure*volume energy: 64.0239 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -5.793234697241E+00 248s WCA energy for atom 1: -5.784370526583E+00 248s WCA energy for atom 2: -5.791799130412E+00 248s WCA energy for atom 3: -5.788504399087E+00 248s WCA energy for atom 4: -5.797319672490E+00 248s WCA energy for atom 5: -5.787358035342E+00 248s WCA energy for atom 6: -1.523887929614E+00 248s WCA energy for atom 7: -1.413678912317E+00 248s WCA energy for atom 8: -1.521751604392E+00 248s WCA energy for atom 9: -1.414741802525E+00 248s WCA energy for atom 10: -1.413367854344E+00 248s WCA energy for atom 11: -1.523407238081E+00 248s WCA energy for atom 12: -1.523000623583E+00 248s WCA energy for atom 13: -1.413922068538E+00 248s WCA energy for atom 14: -1.416316744211E+00 248s WCA energy for atom 15: -1.524577474659E+00 248s WCA energy for atom 16: -1.523300410052E+00 248s WCA energy for atom 17: -1.414522566061E+00 248s 248s Total WCA energy: -52.3691 kJ/mol 248s 248s Total non-polar energy = 1.354016672221E+01 kJ/mol 248s ---------------------------------------- 248s CALCULATION #4 (solvated-cyclopentane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 9.490526193215E+00 248s SASA for atom 1: 9.512927120500E+00 248s SASA for atom 2: 2.299828534626E+00 248s SASA for atom 3: 1.919012770776E+00 248s SASA for atom 4: 2.307295510388E+00 248s SASA for atom 5: 2.325838699632E+01 248s SASA for atom 6: 2.325838699632E+01 248s SASA for atom 7: 2.045987617019E+01 248s SASA for atom 8: 2.067875411190E+01 248s SASA for atom 9: 2.028790064456E+01 248s SASA for atom 10: 1.897463299431E+01 248s SASA for atom 11: 2.048593306801E+01 248s SASA for atom 12: 2.070481100972E+01 248s 248s Total solvent accessible surface area: 193.638 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 8.066947264233E-02 248s Surface tension*area energy for atom 1: 8.085988052425E-02 248s Surface tension*area energy for atom 2: 1.954854254432E-02 248s Surface tension*area energy for atom 3: 1.631160855160E-02 248s Surface tension*area energy for atom 4: 1.961201183830E-02 248s Surface tension*area energy for atom 5: 1.976962894687E-01 248s Surface tension*area energy for atom 6: 1.976962894687E-01 248s Surface tension*area energy for atom 7: 1.739089474466E-01 248s Surface tension*area energy for atom 8: 1.757694099511E-01 248s Surface tension*area energy for atom 9: 1.724471554788E-01 248s Surface tension*area energy for atom 10: 1.612843804516E-01 248s Surface tension*area energy for atom 11: 1.741304310781E-01 248s Surface tension*area energy for atom 12: 1.759908935826E-01 248s 248s Total surface tension energy: 1.64593 kJ/mol 248s 248s Total solvent accessible volume: 217.998 A^3 248s 248s Total pressure*volume energy: 52.1887 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.343496616804E+00 248s WCA energy for atom 1: -6.327869601807E+00 248s WCA energy for atom 2: -6.334858040579E+00 248s WCA energy for atom 3: -6.296075406417E+00 248s WCA energy for atom 4: -6.345600816761E+00 248s WCA energy for atom 5: -1.663697465126E+00 248s WCA energy for atom 6: -1.662444032853E+00 248s WCA energy for atom 7: -1.572325104493E+00 248s WCA energy for atom 8: -1.604626551065E+00 248s WCA energy for atom 9: -1.586431484963E+00 248s WCA energy for atom 10: -1.554291291374E+00 248s WCA energy for atom 11: -1.574315220751E+00 248s WCA energy for atom 12: -1.604941679892E+00 248s 248s Total WCA energy: -44.471 kJ/mol 248s 248s Total non-polar energy = 9.363673200142E+00 kJ/mol 248s ---------------------------------------- 248s CALCULATION #5 (solvated-ethane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 5.995981536705E+00 248s SASA for atom 1: 5.966113633657E+00 248s SASA for atom 2: 2.121552620704E+01 248s SASA for atom 3: 2.124158310486E+01 248s SASA for atom 4: 2.125200586399E+01 248s SASA for atom 5: 2.123116034573E+01 248s SASA for atom 6: 2.125200586399E+01 248s SASA for atom 7: 2.127285138225E+01 248s 248s Total solvent accessible surface area: 139.427 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 5.096584306199E-02 248s Surface tension*area energy for atom 1: 5.071196588609E-02 248s Surface tension*area energy for atom 2: 1.803319727598E-01 248s Surface tension*area energy for atom 3: 1.805534563913E-01 248s Surface tension*area energy for atom 4: 1.806420498439E-01 248s Surface tension*area energy for atom 5: 1.804648629387E-01 248s Surface tension*area energy for atom 6: 1.806420498439E-01 248s Surface tension*area energy for atom 7: 1.808192367491E-01 248s 248s Total surface tension energy: 1.18513 kJ/mol 248s 248s Total solvent accessible volume: 140.346 A^3 248s 248s Total pressure*volume energy: 33.5988 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -7.360066353115E+00 248s WCA energy for atom 1: -7.355483516201E+00 248s WCA energy for atom 2: -1.776106201066E+00 248s WCA energy for atom 3: -1.773973940651E+00 248s WCA energy for atom 4: -1.775401936843E+00 248s WCA energy for atom 5: -1.773464835521E+00 248s WCA energy for atom 6: -1.774382856097E+00 248s WCA energy for atom 7: -1.772366599434E+00 248s 248s Total WCA energy: -25.3612 kJ/mol 248s 248s Total non-polar energy = 9.422717598546E+00 kJ/mol 248s ---------------------------------------- 248s CALCULATION #6 (solvated-hexane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 4.405515699447E+00 248s SASA for atom 1: 8.213673337951E-01 248s SASA for atom 2: 3.285469335181E-01 248s SASA for atom 3: 2.986790304710E-01 248s SASA for atom 4: 1.855251124959E+01 248s SASA for atom 5: 2.147609518526E+01 248s SASA for atom 6: 1.852645435176E+01 248s SASA for atom 7: 1.655655287639E+01 248s SASA for atom 8: 1.655134149682E+01 248s SASA for atom 9: 1.360170066332E+01 248s SASA for atom 10: 1.357043238593E+01 248s SASA for atom 11: 1.381536722546E+01 248s SASA for atom 12: 1.384142412329E+01 248s SASA for atom 13: 7.765654792245E-01 248s SASA for atom 14: 1.684839013200E+01 248s SASA for atom 15: 1.682233323417E+01 248s SASA for atom 16: 4.166572475070E+00 248s SASA for atom 17: 2.179398933870E+01 248s SASA for atom 18: 1.877660057086E+01 248s SASA for atom 19: 1.876096643216E+01 248s 248s Total solvent accessible surface area: 250.291 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 3.744688344530E-02 248s Surface tension*area energy for atom 1: 6.981622337259E-03 248s Surface tension*area energy for atom 2: 2.792648934903E-03 248s Surface tension*area energy for atom 3: 2.538771759003E-03 248s Surface tension*area energy for atom 4: 1.576963456215E-01 248s Surface tension*area energy for atom 5: 1.825468090747E-01 248s Surface tension*area energy for atom 6: 1.574748619900E-01 248s Surface tension*area energy for atom 7: 1.407306994493E-01 248s Surface tension*area energy for atom 8: 1.406864027230E-01 248s Surface tension*area energy for atom 9: 1.156144556382E-01 248s Surface tension*area energy for atom 10: 1.153486752804E-01 248s Surface tension*area energy for atom 11: 1.174306214164E-01 248s Surface tension*area energy for atom 12: 1.176521050479E-01 248s Surface tension*area energy for atom 13: 6.600806573408E-03 248s Surface tension*area energy for atom 14: 1.432113161220E-01 248s Surface tension*area energy for atom 15: 1.429898324905E-01 248s Surface tension*area energy for atom 16: 3.541586603809E-02 248s Surface tension*area energy for atom 17: 1.852489093789E-01 248s Surface tension*area energy for atom 18: 1.596011048523E-01 248s Surface tension*area energy for atom 19: 1.594682146734E-01 248s 248s Total surface tension energy: 2.12748 kJ/mol 248s 248s Total solvent accessible volume: 298.053 A^3 248s 248s Total pressure*volume energy: 71.3539 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.635406071935E+00 248s WCA energy for atom 1: -5.957247427848E+00 248s WCA energy for atom 2: -5.524801144538E+00 248s WCA energy for atom 3: -5.522294168859E+00 248s WCA energy for atom 4: -1.605314409440E+00 248s WCA energy for atom 5: -1.701051761776E+00 248s WCA energy for atom 6: -1.606669162773E+00 248s WCA energy for atom 7: -1.442505934938E+00 248s WCA energy for atom 8: -1.443059002759E+00 248s WCA energy for atom 9: -1.328947132810E+00 248s WCA energy for atom 10: -1.328906972440E+00 248s WCA energy for atom 11: -1.331566344214E+00 248s WCA energy for atom 12: -1.328041776815E+00 248s WCA energy for atom 13: -5.937562025661E+00 248s WCA energy for atom 14: -1.442277774427E+00 248s WCA energy for atom 15: -1.442777091510E+00 248s WCA energy for atom 16: -6.602262542378E+00 248s WCA energy for atom 17: -1.698172146664E+00 248s WCA energy for atom 18: -1.600970858835E+00 248s WCA energy for atom 19: -1.600841970217E+00 248s 248s Total WCA energy: -57.0807 kJ/mol 248s 248s Total non-polar energy = 1.640068943201E+01 kJ/mol 248s ---------------------------------------- 248s CALCULATION #7 (solvated-isobutane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 3.464676753463E+00 248s SASA for atom 1: 1.984493338158E+01 248s SASA for atom 2: 1.778643845361E+01 248s SASA for atom 3: 1.671289426332E+01 248s SASA for atom 4: 0.000000000000E+00 248s SASA for atom 5: 3.531879535319E+00 248s SASA for atom 6: 1.673895116114E+01 248s SASA for atom 7: 1.793756846098E+01 248s SASA for atom 8: 1.973549441072E+01 248s SASA for atom 9: 1.710895911022E+01 248s SASA for atom 10: 4.599657069253E+00 248s SASA for atom 11: 1.937069784121E+01 248s SASA for atom 12: 1.654613011726E+01 248s SASA for atom 13: 1.936548646165E+01 248s 248s Total solvent accessible surface area: 192.744 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 2.944975240444E-02 248s Surface tension*area energy for atom 1: 1.686819337434E-01 248s Surface tension*area energy for atom 2: 1.511847268556E-01 248s Surface tension*area energy for atom 3: 1.420596012382E-01 248s Surface tension*area energy for atom 4: 0.000000000000E+00 248s Surface tension*area energy for atom 5: 3.002097605021E-02 248s Surface tension*area energy for atom 6: 1.422810848697E-01 248s Surface tension*area energy for atom 7: 1.524693319183E-01 248s Surface tension*area energy for atom 8: 1.677517024912E-01 248s Surface tension*area energy for atom 9: 1.454261524369E-01 248s Surface tension*area energy for atom 10: 3.909708508865E-02 248s Surface tension*area energy for atom 11: 1.646509316503E-01 248s Surface tension*area energy for atom 12: 1.406421059967E-01 248s Surface tension*area energy for atom 13: 1.646066349240E-01 248s 248s Total surface tension energy: 1.63832 kJ/mol 248s 248s Total solvent accessible volume: 218.943 A^3 248s 248s Total pressure*volume energy: 52.415 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.381016335247E+00 248s WCA energy for atom 1: -1.612317964554E+00 248s WCA energy for atom 2: -1.588013719598E+00 248s WCA energy for atom 3: -1.532162371190E+00 248s WCA energy for atom 4: -5.987950445279E+00 248s WCA energy for atom 5: -6.393089030861E+00 248s WCA energy for atom 6: -1.533454887042E+00 248s WCA energy for atom 7: -1.587650918485E+00 248s WCA energy for atom 8: -1.614083521570E+00 248s WCA energy for atom 9: -1.442402031577E+00 248s WCA energy for atom 10: -6.408813541353E+00 248s WCA energy for atom 11: -1.605830214390E+00 248s WCA energy for atom 12: -1.529385873788E+00 248s WCA energy for atom 13: -1.605662490385E+00 248s 248s Total WCA energy: -40.8218 kJ/mol 248s 248s Total non-polar energy = 1.323144287435E+01 kJ/mol 248s ---------------------------------------- 248s CALCULATION #8 (solvated-methane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 1.231304303117E+01 248s SASA for atom 1: 2.323233009850E+01 248s SASA for atom 2: 2.345641941977E+01 248s SASA for atom 3: 2.377431357320E+01 248s SASA for atom 4: 2.264344420771E+01 248s 248s Total solvent accessible surface area: 105.42 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 1.046608657649E-01 248s Surface tension*area energy for atom 1: 1.974748058372E-01 248s Surface tension*area energy for atom 2: 1.993795650680E-01 248s Surface tension*area energy for atom 3: 2.020816653722E-01 248s Surface tension*area energy for atom 4: 1.924692757655E-01 248s 248s Total surface tension energy: 0.896066 kJ/mol 248s 248s Total solvent accessible volume: 95.985 A^3 248s 248s Total pressure*volume energy: 22.9788 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -8.133807570805E+00 248s WCA energy for atom 1: -1.962181541765E+00 248s WCA energy for atom 2: -1.964078319162E+00 248s WCA energy for atom 3: -1.963015006647E+00 248s WCA energy for atom 4: -1.957425549100E+00 248s 248s Total WCA energy: -15.9805 kJ/mol 248s 248s Total non-polar energy = 7.894367190329E+00 kJ/mol 248s ---------------------------------------- 248s CALCULATION #9 (solvated-neopentane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 2.441701074100E+00 248s SASA for atom 1: 1.663993494942E+01 248s SASA for atom 2: 1.715586152630E+01 248s SASA for atom 3: 1.645753666466E+01 248s SASA for atom 4: 0.000000000000E+00 248s SASA for atom 5: 2.389432243768E+00 248s SASA for atom 6: 1.638457735076E+01 248s SASA for atom 7: 1.667641460637E+01 248s SASA for atom 8: 1.721839808108E+01 248s SASA for atom 9: 2.419300146815E+00 248s SASA for atom 10: 1.640021148945E+01 248s SASA for atom 11: 1.666599184724E+01 248s SASA for atom 12: 1.719234118325E+01 248s SASA for atom 13: 2.449168049862E+00 248s SASA for atom 14: 1.723403221977E+01 248s SASA for atom 15: 1.639500010989E+01 248s SASA for atom 16: 1.663472356985E+01 248s 248s Total solvent accessible surface area: 210.755 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 2.075445912985E-02 248s Surface tension*area energy for atom 1: 1.414394470700E-01 248s Surface tension*area energy for atom 2: 1.458248229736E-01 248s Surface tension*area energy for atom 3: 1.398890616496E-01 248s Surface tension*area energy for atom 4: 0.000000000000E+00 248s Surface tension*area energy for atom 5: 2.031017407203E-02 248s Surface tension*area energy for atom 6: 1.392689074814E-01 248s Surface tension*area energy for atom 7: 1.417495241541E-01 248s Surface tension*area energy for atom 8: 1.463563836891E-01 248s Surface tension*area energy for atom 9: 2.056405124793E-02 248s Surface tension*area energy for atom 10: 1.394017976603E-01 248s Surface tension*area energy for atom 11: 1.416609307015E-01 248s Surface tension*area energy for atom 12: 1.461349000577E-01 248s Surface tension*area energy for atom 13: 2.081792842383E-02 248s Surface tension*area energy for atom 14: 1.464892738680E-01 248s Surface tension*area energy for atom 15: 1.393575009340E-01 248s Surface tension*area energy for atom 16: 1.413951503437E-01 248s 248s Total surface tension energy: 1.79141 kJ/mol 248s 248s Total solvent accessible volume: 251.127 A^3 248s 248s Total pressure*volume energy: 60.1198 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.011082520236E+00 248s WCA energy for atom 1: -1.497367782613E+00 248s WCA energy for atom 2: -1.498546483218E+00 248s WCA energy for atom 3: -1.492562171495E+00 248s WCA energy for atom 4: -5.447325863939E+00 248s WCA energy for atom 5: -6.004516149175E+00 248s WCA energy for atom 6: -1.492776531092E+00 248s WCA energy for atom 7: -1.496078170066E+00 248s WCA energy for atom 8: -1.501529655270E+00 248s WCA energy for atom 9: -5.996267554365E+00 248s WCA energy for atom 10: -1.492194267752E+00 248s WCA energy for atom 11: -1.496027211216E+00 248s WCA energy for atom 12: -1.500561393960E+00 248s WCA energy for atom 13: -6.000218612907E+00 248s WCA energy for atom 14: -1.500859921426E+00 248s WCA energy for atom 15: -1.492908499790E+00 248s WCA energy for atom 16: -1.494057174414E+00 248s 248s Total WCA energy: -47.4149 kJ/mol 248s 248s Total non-polar energy = 1.449633815052E+01 kJ/mol 248s ---------------------------------------- 248s CALCULATION #10 (solvated-pentane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 4.405515699447E+00 248s SASA for atom 1: 8.213673337951E-01 248s SASA for atom 2: 3.285469335181E-01 248s SASA for atom 3: 7.466975761774E-01 248s SASA for atom 4: 1.855251124959E+01 248s SASA for atom 5: 2.147609518526E+01 248s SASA for atom 6: 1.852645435176E+01 248s SASA for atom 7: 1.655655287639E+01 248s SASA for atom 8: 1.655134149682E+01 248s SASA for atom 9: 1.360170066332E+01 248s SASA for atom 10: 1.357043238593E+01 248s SASA for atom 11: 1.685881289113E+01 248s SASA for atom 12: 1.687444702982E+01 248s SASA for atom 13: 4.196440378117E+00 248s SASA for atom 14: 1.881308022781E+01 248s SASA for atom 15: 1.882350298694E+01 248s SASA for atom 16: 2.182004623652E+01 248s 248s Total solvent accessible surface area: 222.524 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 3.744688344530E-02 248s Surface tension*area energy for atom 1: 6.981622337259E-03 248s Surface tension*area energy for atom 2: 2.792648934903E-03 248s Surface tension*area energy for atom 3: 6.346929397508E-03 248s Surface tension*area energy for atom 4: 1.576963456215E-01 248s Surface tension*area energy for atom 5: 1.825468090747E-01 248s Surface tension*area energy for atom 6: 1.574748619900E-01 248s Surface tension*area energy for atom 7: 1.407306994493E-01 248s Surface tension*area energy for atom 8: 1.406864027230E-01 248s Surface tension*area energy for atom 9: 1.156144556382E-01 248s Surface tension*area energy for atom 10: 1.153486752804E-01 248s Surface tension*area energy for atom 11: 1.432999095746E-01 248s Surface tension*area energy for atom 12: 1.434327997535E-01 248s Surface tension*area energy for atom 13: 3.566974321399E-02 248s Surface tension*area energy for atom 14: 1.599111819364E-01 248s Surface tension*area energy for atom 15: 1.599997753890E-01 248s Surface tension*area energy for atom 16: 1.854703930104E-01 248s 248s Total surface tension energy: 1.89145 kJ/mol 248s 248s Total solvent accessible volume: 258.93 A^3 248s 248s Total pressure*volume energy: 61.9878 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.655804319869E+00 248s WCA energy for atom 1: -6.027315962813E+00 248s WCA energy for atom 2: -5.696430965386E+00 248s WCA energy for atom 3: -6.016749084714E+00 248s WCA energy for atom 4: -1.608595384643E+00 248s WCA energy for atom 5: -1.703300955380E+00 248s WCA energy for atom 6: -1.609931495887E+00 248s WCA energy for atom 7: -1.457107525189E+00 248s WCA energy for atom 8: -1.457741620594E+00 248s WCA energy for atom 9: -1.354235498709E+00 248s WCA energy for atom 10: -1.354106470090E+00 248s WCA energy for atom 11: -1.456736412636E+00 248s WCA energy for atom 12: -1.455995435596E+00 248s WCA energy for atom 13: -6.633650611186E+00 248s WCA energy for atom 14: -1.605996088477E+00 248s WCA energy for atom 15: -1.606549890103E+00 248s WCA energy for atom 16: -1.700042300035E+00 248s 248s Total WCA energy: -49.4003 kJ/mol 248s 248s Total non-polar energy = 1.447900211546E+01 kJ/mol 248s ---------------------------------------- 248s CALCULATION #11 (solvated-propane): APOLAR 248s 248s Solvent Accessible Surface Area (SASA) for each atom: 248s SASA for atom 0: 3.173464698754E+00 248s SASA for atom 1: 1.931858404557E+01 248s SASA for atom 2: 2.014198201675E+01 248s SASA for atom 3: 2.149694070352E+01 248s SASA for atom 4: 1.904078819252E+00 248s SASA for atom 5: 2.067354273233E+01 248s SASA for atom 6: 1.937590922077E+01 248s SASA for atom 7: 3.098794941136E+00 248s SASA for atom 8: 1.942802301642E+01 248s SASA for atom 9: 1.973028303116E+01 248s SASA for atom 10: 2.204934693736E+01 248s 248s Total solvent accessible surface area: 170.391 A^2 248s 248s Surface tension*area energies (gamma * SASA) for each atom: 248s Surface tension*area energy for atom 0: 2.697444993941E-02 248s Surface tension*area energy for atom 1: 1.642079643873E-01 248s Surface tension*area energy for atom 2: 1.712068471424E-01 248s Surface tension*area energy for atom 3: 1.827239959799E-01 248s Surface tension*area energy for atom 4: 1.618466996365E-02 248s Surface tension*area energy for atom 5: 1.757251132248E-01 248s Surface tension*area energy for atom 6: 1.646952283766E-01 248s Surface tension*area energy for atom 7: 2.633975699966E-02 248s Surface tension*area energy for atom 8: 1.651381956396E-01 248s Surface tension*area energy for atom 9: 1.677074057649E-01 248s Surface tension*area energy for atom 10: 1.874194489675E-01 248s 248s Total surface tension energy: 1.44832 kJ/mol 248s 248s Total solvent accessible volume: 183.573 A^3 248s 248s Total pressure*volume energy: 43.9474 kJ/mol 248s 248s WCA dispersion Energies for each atom: 248s WCA energy for atom 0: -6.818670105515E+00 248s WCA energy for atom 1: -1.641297645338E+00 248s WCA energy for atom 2: -1.649584120441E+00 248s WCA energy for atom 3: -1.711408141255E+00 248s WCA energy for atom 4: -6.624720142882E+00 248s WCA energy for atom 5: -1.610117050515E+00 248s WCA energy for atom 6: -1.596858009746E+00 248s WCA energy for atom 7: -6.816460624835E+00 248s WCA energy for atom 8: -1.642782751806E+00 248s WCA energy for atom 9: -1.645779566650E+00 248s WCA energy for atom 10: -1.714436154542E+00 248s 248s Total WCA energy: -33.4721 kJ/mol 248s 248s Total non-polar energy = 1.192358496286E+01 kJ/mol 248s ---------------------------------------- 248s PRINT STATEMENTS 248s 248s print APOL energy 1 (solvated-2-methylbutane) end 248s Global net APOL energy = 1.439739455792E+01 kJ/mol 248s 248s print APOL energy 2 (solvated-butane) end 248s Global net APOL energy = 1.208346456826E+01 kJ/mol 248s 248s print APOL energy 3 (solvated-cyclohexane) end 248s Global net APOL energy = 1.354016672221E+01 kJ/mol 248s 248s print APOL energy 4 (solvated-cyclopentane) end 248s Global net APOL energy = 9.363673200142E+00 kJ/mol 248s 248s print APOL energy 5 (solvated-ethane) end 248s Global net APOL energy = 9.422717598546E+00 kJ/mol 248s 248s print APOL energy 6 (solvated-hexane) end 248s Global net APOL energy = 1.640068943201E+01 kJ/mol 248s 248s print APOL energy 7 (solvated-isobutane) end 248s Global net APOL energy = 1.323144287435E+01 kJ/mol 248s 248s print APOL energy 8 (solvated-methane) end 248s Global net APOL energy = 7.894367190329E+00 kJ/mol 248s 248s print APOL energy 9 (solvated-neopentane) end 248s Global net APOL energy = 1.449633815052E+01 kJ/mol 248s 248s print APOL energy 10 (solvated-pentane) end 248s Global net APOL energy = 1.447900211546E+01 kJ/mol 248s 248s print APOL energy 11 (solvated-propane) end 248s Global net APOL energy = 1.192358496286E+01 kJ/mol 248s ---------------------------------------- 248s CLEANING UP AND SHUTTING DOWN... 248s Destroying force arrays. 248s No energy arrays to destroy. 248s Destroying multigrid structures. 248s Destroying finite element structures. 248s Destroying 11 molecules 248s Final memory usage: 0.001 MB total, 2.267 MB high water 248s 248s 248s Thanks for using APBS! 248s 248s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 248s *** PASSED *** 248s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 248s *** PASSED *** 248s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 248s *** PASSED *** 248s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 248s *** PASSED *** 248s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 248s *** PASSED *** 248s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 248s *** PASSED *** 248s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 248s *** PASSED *** 248s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 248s *** PASSED *** 248s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 248s *** PASSED *** 248s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 248s *** PASSED *** 248s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 248s *** PASSED *** 248s Elapsed time: 11.506724 seconds 248s -------------------------------------------------------------------------------- 248s Total elapsed time: 11.506724 seconds 248s Test results have been logged 248s -------------------------------------------------------------------------------- 248s -------------------------------------------------------------------------------- 248s Testing input file 1d7h-dmso-mol.in 248s 256s Checking for intermediate energies in input file alkanes.out 256s EXPECTED COMPUTED: 11 256s EXPECTED EXPECTED: 11 256s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 256s 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'] 256s COMPUTED RESULT 14.39739455792 256s COMPUTED RESULT 12.08346456826 256s COMPUTED RESULT 13.54016672221 256s COMPUTED RESULT 9.363673200142 256s COMPUTED RESULT 9.422717598546 256s COMPUTED RESULT 16.40068943201 256s COMPUTED RESULT 13.23144287435 256s COMPUTED RESULT 7.894367190329 256s COMPUTED RESULT 14.49633815052 256s COMPUTED RESULT 14.47900211546 256s COMPUTED RESULT 11.92358496286 256s Running tests for FKBP section 256s BINARY: /usr/bin/apbs 256s INPUT: 1d7h-dmso-mol.in 256s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 256s asc_getToken: Error occurred (bailing out). 256s Vio_scanf: Format problem with input. 256s 256s 256s ---------------------------------------------------------------------- 256s APBS -- Adaptive Poisson-Boltzmann Solver 256s Version APBS 3.4.1 256s 256s Nathan A. Baker (nathan.baker@pnnl.gov) 256s Pacific Northwest National Laboratory 256s 256s Additional contributing authors listed in the code documentation. 256s 256s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 256s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 256s Northwest Division for the U.S. Department of Energy. 256s 256s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 256s Portions Copyright (c) 2002-2020, Nathan A. Baker. 256s Portions Copyright (c) 1999-2002, The Regents of the University of California. 256s Portions Copyright (c) 1995, Michael Holst. 256s All rights reserved. 256s 256s Redistribution and use in source and binary forms, with or without 256s modification, are permitted provided that the following conditions are met: 256s 256s * Redistributions of source code must retain the above copyright notice, this 256s list of conditions and the following disclaimer. 256s 256s * Redistributions in binary form must reproduce the above copyright notice, 256s this list of conditions and the following disclaimer in the documentation 256s and/or other materials provided with the distribution. 256s 256s * Neither the name of the developer nor the names of its contributors may be 256s used to endorse or promote products derived from this software without 256s specific prior written permission. 256s 256s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 256s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 256s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 256s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 256s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 256s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 256s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 256s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 256s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 256s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 256s ---------------------------------------------------------------------- 256s APBS uses FETK (the Finite Element ToolKit) to solve the 256s Poisson-Boltzmann equation numerically. FETK is a portable collection 256s of finite element modeling class libraries developed by the Michael Holst 256s research group and written in an object-oriented form of C. FEtk is 256s designed to solve general coupled systems of nonlinear partial differential 256s equations using adaptive finite element methods, inexact Newton methods, 256s and algebraic multilevel methods. More information about FEtk may be found 256s at . 256s ---------------------------------------------------------------------- 256s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 256s Aqua is a modified form of the Holst group PMG library 256s which has been modified by Patrice Koehl 256s for improved efficiency and 256s memory usage when solving the Poisson-Boltzmann equation. 256s ---------------------------------------------------------------------- 256s Please cite your use of APBS as: 256s 256s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 256s nanosystems: application to microtubules and the ribosome. Proc. 256s Natl. Acad. Sci. USA 98, 10037-10041 2001. 256s 256s 256s This executable compiled on Jan 3 2025 at 11:01:42 256s 256s Parsing input file 1d7h-dmso-mol.in... 256s rank 0 size 1... 256s Parsed input file. 256s Got paths for 3 molecules 256s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 256s asc_getToken: Error occurred (bailing out). 256s Vio_scanf: Format problem with input. 256s 1673 atoms 256s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 256s Net charge 9.91e-01 e 256s Reading PQR-format atom data from dmso-min.pqr. 256s asc_getToken: Error occurred (bailing out). 256s Vio_scanf: Format problem with input. 256s 10 atoms 256s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 256s Net charge 2.78e-17 e 256s Reading PQR-format atom data from 1d7h-min.pqr. 256s 1663 atoms 256s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 256s Net charge 9.91e-01 e 256s Preparing to run 12 PBE calculations. 256s ---------------------------------------- 256s CALCULATION #1 (complex-solv-coarse): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 30.4176 A 256s Current memory usage: 122.059 MB total, 122.059 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 1.500 x 1.500 x 1.500 256s Grid lengths: 96.000 x 96.000 x 96.000 256s Grid center: (25.875, 18.349, 19.112) 256s Multigrid levels: 5 256s Molecule ID: 1 256s Linearized traditional PBE 256s Multiple Debye-Huckel sphere boundary conditions 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 78.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 1.060899690259E+04 kJ/mol 256s Calculating forces... 256s [focusFillBound()]: WARNING: 256s Unusually large potential values 256s detected on the focusing boundary! 256s Convergence not guaranteed for NPBE/NRPBE calculations! 256s 256s ---------------------------------------- 256s CALCULATION #2 (complex-solv-fine): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 30.4176 A 256s Current memory usage: 122.059 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 0.225 x 0.225 x 0.225 256s Grid lengths: 14.400 x 14.400 x 14.400 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 1 256s Linearized traditional PBE 256s Boundary conditions from focusing 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 78.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 4.276523673491E+04 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s CALCULATION #3 (complex-ref-coarse): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 4.87072 A 256s Current memory usage: 122.059 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 1.500 x 1.500 x 1.500 256s Grid lengths: 96.000 x 96.000 x 96.000 256s Grid center: (25.875, 18.349, 19.112) 256s Multigrid levels: 5 256s Molecule ID: 1 256s Linearized traditional PBE 256s Multiple Debye-Huckel sphere boundary conditions 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 2.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 1.399234956777E+04 kJ/mol 256s Calculating forces... 256s [focusFillBound()]: WARNING: 256s Unusually large potential values 256s detected on the focusing boundary! 256s Convergence not guaranteed for NPBE/NRPBE calculations! 256s 256s ---------------------------------------- 256s CALCULATION #4 (complex-ref-fine): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 4.87072 A 256s Current memory usage: 122.059 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 0.225 x 0.225 x 0.225 256s Grid lengths: 14.400 x 14.400 x 14.400 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 1 256s Linearized traditional PBE 256s Boundary conditions from focusing 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 2.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 4.610066575192E+04 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 30.4176 A 256s Current memory usage: 62.428 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 1.500 x 1.500 x 1.500 256s Grid lengths: 96.000 x 96.000 x 96.000 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 2 256s Linearized traditional PBE 256s Multiple Debye-Huckel sphere boundary conditions 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 78.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 3.961107503213E+01 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s CALCULATION #6 (dmso-solv-fine): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 30.4176 A 256s Current memory usage: 62.428 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 0.225 x 0.225 x 0.225 256s Grid lengths: 14.400 x 14.400 x 14.400 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 2 256s Linearized traditional PBE 256s Boundary conditions from focusing 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 78.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 7.121048606059E+02 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 4.87072 A 256s Current memory usage: 62.428 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 1.500 x 1.500 x 1.500 256s Grid lengths: 96.000 x 96.000 x 96.000 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 2 256s Linearized traditional PBE 256s Multiple Debye-Huckel sphere boundary conditions 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 2.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 6.751571424823E+01 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s CALCULATION #8 (dmso-ref-fine): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 4.87072 A 256s Current memory usage: 62.428 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 0.225 x 0.225 x 0.225 256s Grid lengths: 14.400 x 14.400 x 14.400 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 2 256s Linearized traditional PBE 256s Boundary conditions from focusing 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 2.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 7.339101343121E+02 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 30.4176 A 256s Current memory usage: 121.736 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 1.500 x 1.500 x 1.500 256s Grid lengths: 96.000 x 96.000 x 96.000 256s Grid center: (25.875, 18.349, 19.112) 256s Multigrid levels: 5 256s Molecule ID: 3 256s Linearized traditional PBE 256s Multiple Debye-Huckel sphere boundary conditions 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 78.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 1.058410584089E+04 kJ/mol 256s Calculating forces... 256s [focusFillBound()]: WARNING: 256s Unusually large potential values 256s detected on the focusing boundary! 256s Convergence not guaranteed for NPBE/NRPBE calculations! 256s 256s ---------------------------------------- 256s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 30.4176 A 256s Current memory usage: 121.736 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 0.225 x 0.225 x 0.225 256s Grid lengths: 14.400 x 14.400 x 14.400 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 3 256s Linearized traditional PBE 256s Boundary conditions from focusing 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 78.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 4.205385249581E+04 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s CALCULATION #11 (1d7h-ref-coarse): MULTIGRIDTesting computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 256s *** PASSED *** 256s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 256s *** PASSED *** 256s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 256s *** PASSED *** 256s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 256s *** PASSED *** 256s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 256s *** PASSED *** 256s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 256s *** PASSED *** 256s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 256s *** PASSED *** 256s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 256s *** PASSED *** 256s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 256s *** PASSED *** 256s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 256s *** PASSED *** 256s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 256s *** PASSED *** 256s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 256s *** PASSED *** 256s Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) 256s *** PASSED *** 256s Elapsed time: 7.939031 seconds 256s -------------------------------------------------------------------------------- 256s -------------------------------------------------------------------------------- 256s Testing input file 1d7h-dmso-smol.in 256s 256s 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 4.87072 A 256s Current memory usage: 121.736 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 1.500 x 1.500 x 1.500 256s Grid lengths: 96.000 x 96.000 x 96.000 256s Grid center: (25.875, 18.349, 19.112) 256s Multigrid levels: 5 256s Molecule ID: 3 256s Linearized traditional PBE 256s Multiple Debye-Huckel sphere boundary conditions 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 2.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 1.395961902233E+04 kJ/mol 256s Calculating forces... 256s [focusFillBound()]: WARNING: 256s Unusually large potential values 256s detected on the focusing boundary! 256s Convergence not guaranteed for NPBE/NRPBE calculations! 256s 256s ---------------------------------------- 256s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 256s Setting up problem... 256s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 256s Debye length: 4.87072 A 256s Current memory usage: 121.736 MB total, 221.696 MB high water 256s Using linear spline charge discretization. 256s Grid dimensions: 65 x 65 x 65 256s Grid spacings: 0.225 x 0.225 x 0.225 256s Grid lengths: 14.400 x 14.400 x 14.400 256s Grid center: (17.751, 17.770, 20.492) 256s Multigrid levels: 5 256s Molecule ID: 3 256s Linearized traditional PBE 256s Boundary conditions from focusing 256s 2 ion species (0.010 M ionic strength): 256s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 256s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 256s Solute dielectric: 2.000 256s Solvent dielectric: 2.000 256s Using "molecular" surface definition; no smoothing 256s Solvent probe radius: 0.000 A 256s Temperature: 300.000 K 256s Electrostatic energies will be calculated 256s Total electrostatic energy = 4.538248433997E+04 kJ/mol 256s Calculating forces... 256s ---------------------------------------- 256s PRINT STATEMENTS 256s 256s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 256s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 256s Global net ELEC energy = -3.335429017008E+03 kJ/mol 256s 256s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 256s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 256s Global net ELEC energy = -2.180527370616E+01 kJ/mol 256s 256s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 256s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 256s Global net ELEC energy = -3.328631844166E+03 kJ/mol 256s 256s 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 256s Local net energy (PE 0) = 1.500810086373E+01 kJ/mol 256s Global net ELEC energy = 1.500810086373E+01 kJ/mol 256s ---------------------------------------- 256s CLEANING UP AND SHUTTING DOWN... 256s Destroying force arrays. 256s No energy arrays to destroy. 256s Destroying multigrid structures. 256s Destroying finite element structures. 256s Destroying 3 molecules 256s Final memory usage: 0.001 MB total, 221.696 MB high water 256s 256s 256s Thanks for using APBS! 256s 264s Checking for intermediate energies in input file 1d7h-dmso-mol.out 264s EXPECTED COMPUTED: 16 264s EXPECTED EXPECTED: 16 264s 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] 264s 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'] 264s COMPUTED RESULT 10608.99690259 264s COMPUTED RESULT 42765.23673491 264s COMPUTED RESULT 13992.34956777 264s COMPUTED RESULT 46100.66575192 264s COMPUTED RESULT 39.61107503213 264s COMPUTED RESULT 712.1048606059 264s COMPUTED RESULT 67.51571424823 264s COMPUTED RESULT 733.9101343121 264s COMPUTED RESULT 10584.10584089 264s COMPUTED RESULT 42053.85249581 264s COMPUTED RESULT 13959.61902233 264s COMPUTED RESULT 45382.48433997 264s COMPUTED RESULT -3335.429017008 264s COMPUTED RESULT -21.80527370616 264s COMPUTED RESULT -3328.631844166 264s COMPUTED RESULT 15.00810086373 264s BINARY: /usr/bin/apbs 264s INPUT: 1d7h-dmso-smol.in 264s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 264s asc_getToken: Error occurred (bailing out). 264s Vio_scanf: Format problem with input. 264s 264s 264s ---------------------------------------------------------------------- 264s APBS -- Adaptive Poisson-Boltzmann Solver 264s Version APBS 3.4.1 264s 264s Nathan A. Baker (nathan.baker@pnnl.gov) 264s Pacific Northwest National Laboratory 264s 264s Additional contributing authors listed in the code documentation. 264s 264s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 264s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 264s Northwest Division for the U.S. Department of Energy. 264s 264s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 264s Portions Copyright (c) 2002-2020, Nathan A. Baker. 264s Portions Copyright (c) 1999-2002, The Regents of the University of California. 264s Portions Copyright (c) 1995, Michael Holst. 264s All rights reserved. 264s 264s Redistribution and use in source and binary forms, with or without 264s modification, are permitted provided that the following conditions are met: 264s 264s * Redistributions of source code must retain the above copyright notice, this 264s list of conditions and the following disclaimer. 264s 264s * Redistributions in binary form must reproduce the above copyright notice, 264s this list of conditions and the following disclaimer in the documentation 264s and/or other materials provided with the distribution. 264s 264s * Neither the name of the developer nor the names of its contributors may be 264s used to endorse or promote products derived from this software without 264s specific prior written permission. 264s 264s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 264s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 264s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 264s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 264s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 264s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 264s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 264s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 264s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 264s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 264s ---------------------------------------------------------------------- 264s APBS uses FETK (the Finite Element ToolKit) to solve the 264s Poisson-Boltzmann equation numerically. FETK is a portable collection 264s of finite element modeling class libraries developed by the Michael Holst 264s research group and written in an object-oriented form of C. FEtk is 264s designed to solve general coupled systems of nonlinear partial differential 264s equations using adaptive finite element methods, inexact Newton methods, 264s and algebraic multilevel methods. More information about FEtk may be found 264s at . 264s ---------------------------------------------------------------------- 264s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 264s Aqua is a modified form of the Holst group PMG library 264s which has been modified by Patrice Koehl 264s for improved efficiency and 264s memory usage when solving the Poisson-Boltzmann equation. 264s ---------------------------------------------------------------------- 264s Please cite your use of APBS as: 264s 264s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 264s nanosystems: application to microtubules and the ribosome. Proc. 264s Natl. Acad. Sci. USA 98, 10037-10041 2001. 264s 264s 264s This executable compiled on Jan 3 2025 at 11:01:42 264s 264s Parsing input file 1d7h-dmso-smol.in... 264s rank 0 size 1... 264s Parsed input file. 264s Got paths for 3 molecules 264s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 264s asc_getToken: Error occurred (bailing out). 264s Vio_scanf: Format problem with input. 264s 1673 atoms 264s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 264s Net charge 9.91e-01 e 264s Reading PQR-format atom data from dmso-min.pqr. 264s asc_getToken: Error occurred (bailing out). 264s Vio_scanf: Format problem with input. 264s 10 atoms 264s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 264s Net charge 2.78e-17 e 264s Reading PQR-format atom data from 1d7h-min.pqr. 264s 1663 atoms 264s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 264s Net charge 9.91e-01 e 264s Preparing to run 12 PBE calculations. 264s ---------------------------------------- 264s CALCULATION #1 (complex-solv-coarse): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 30.4176 A 264s Current memory usage: 122.059 MB total, 122.059 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 1.500 x 1.500 x 1.500 264s Grid lengths: 96.000 x 96.000 x 96.000 264s Grid center: (25.875, 18.349, 19.112) 264s Multigrid levels: 5 264s Molecule ID: 1 264s Linearized traditional PBE 264s Multiple Debye-Huckel sphere boundary conditions 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 78.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 1.074948704824E+04 kJ/mol 264s Calculating forces... 264s [focusFillBound()]: WARNING: 264s Unusually large potential values 264s detected on the focusing boundary! 264s Convergence not guaranteed for NPBE/NRPBE calculations! 264s 264s ---------------------------------------- 264s CALCULATION #2 (complex-solv-fine): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 30.4176 A 264s Current memory usage: 122.059 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 0.225 x 0.225 x 0.225 264s Grid lengths: 14.400 x 14.400 x 14.400 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 1 264s Linearized traditional PBE 264s Boundary conditions from focusing 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 78.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 4.289487256481E+04 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s CALCULATION #3 (complex-ref-coarse): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 4.87072 A 264s Current memory usage: 122.059 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 1.500 x 1.500 x 1.500 264s Grid lengths: 96.000 x 96.000 x 96.000 264s Grid center: (25.875, 18.349, 19.112) 264s Multigrid levels: 5 264s Molecule ID: 1 264s Linearized traditional PBE 264s Multiple Debye-Huckel sphere boundary conditions 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 2.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 1.399234956777E+04 kJ/mol 264s Calculating forces... 264s [focusFillBound()]: WARNING: 264s Unusually large potential values 264s detected on the focusing boundary! 264s Convergence not guaranteed for NPBE/NRPBE calculations! 264s 264s ---------------------------------------- 264s CALCULATION #4 (complex-ref-fine): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 4.87072 A 264s Current memory usage: 122.059 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 0.225 x 0.225 x 0.225 264s Grid lengths: 14.400 x 14.400 x 14.400 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 1 264s Linearized traditional PBE 264s Boundary conditions from focusing 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 2.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 4.610066575192E+04 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 30.4176 A 264s Current memory usage: 62.428 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 1.500 x 1.500 x 1.500 264s Grid lengths: 96.000 x 96.000 x 96.000 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 2 264s Linearized traditional PBE 264s Multiple Debye-Huckel sphere boundary conditions 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 78.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 3.719709905887E+01 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s CALCULATION #6 (dmso-solv-fine): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 30.4176 A 264s Current memory usage: 62.428 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 0.225 x 0.225 x 0.225 264s Grid lengths: 14.400 x 14.400 x 14.400 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 2 264s Linearized traditional PBE 264s Boundary conditions from focusing 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 78.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 7.125747080979E+02 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 4.87072 A 264s Current memory usage: 62.428 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 1.500 x 1.500 x 1.500 264s Grid lengths: 96.000 x 96.000 x 96.000 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 2 264s Linearized traditional PBE 264s Multiple Debye-Huckel sphere boundary conditions 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 2.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 6.751571424823E+01 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s CALCULATION #8 (dmso-ref-fine): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 4.87072 A 264s Current memory usage: 62.428 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 0.225 x 0.225 x 0.225 264s Grid lengths: 14.400 x 14.400 x 14.400 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 2 264s Linearized traditional PBE 264s Boundary conditions from focusing 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 2.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 7.339101343121E+02 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 30.4176 A 264s Current memory usage: 121.736 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 1.500 x 1.500 x 1.500 264s Grid lengths: 96.000 x 96.000 x 96.000 264s Grid center: (25.875, 18.349, 19.112) 264s Multigrid levels: 5 264s Molecule ID: 3 264s Linearized traditional PBE 264s Multiple Debye-Huckel sphere boundary conditions 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 78.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 1.071654753674E+04 kJ/mol 264s Calculating forces... 264s [focusFillBound()]: WARNING: 264s Unusually large potential values 264s detected on the focusing boundary! 264s Convergence not guaranteed for NPBE/NRPBE calculations! 264s 264s ---------------------------------------- 264s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 30.4176 A 264s Current memory usage: 121.736 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 0.225 x 0.225 x 0.225 264s Grid lengths: 14.400 x 14.400 x 14.400 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 3 264s Linearized traditional PBE 264s Boundary conditions from focusing 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 78.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 4.218178203716E+04 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 4.87072 A 264s Current memory usage: 121.736 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 1.500 x 1.500 x 1.500 264s Grid lengths: 96.000 x 96.000 x 96.000 264s Grid center: (25.875, 18.349, 19.112) 264s Multigrid levels: 5 264s Molecule ID: 3 264s Linearized traditional PBE 264s Multiple Debye-Huckel sphere boundary conditions 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 2.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 1.395961902233E+04 kJ/mol 264s Calculating forces... 264s [focusFillBound()]: WARNING: 264s Unusually large potential values 264s detected on the focusing boundary! 264s Convergence not guaranteed for NPBE/NRPBE calculations! 264s 264s ---------------------------------------- 264s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 264s Setting up problem... 264s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 264s Debye length: 4.87072 A 264s Current memory usage: 121.736 MB total, 221.696 MB high water 264s Using linear spline charge discretization. 264s Grid dimensions: 65 x 65 x 65 264s Grid spacings: 0.225 x 0.225 x 0.225 264s Grid lengths: 14.400 x 14.400 x 14.400 264s Grid center: (17.751, 17.770, 20.492) 264s Multigrid levels: 5 264s Molecule ID: 3 264s Linearized traditional PBE 264s Boundary conditions from focusing 264s 2 ion species (0.010 M ionic strength): 264s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 264s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 264s Solute dielectric: 2.000 264s Solvent dielectric: 2.000 264s Using "molecular" surface definition;harmonic average smoothing 264s Solvent probe radius: 0.000 A 264s Temperature: 300.000 K 264s Electrostatic energies will be calculated 264s Total electrostatic energy = 4.538248433997E+04 kJ/mol 264s Calculating forces... 264s ---------------------------------------- 264s PRINT STATEMENTS 264s 264s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 264s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 264s Global net ELEC energy = -3.205793187109E+03 kJ/mol 264s 264s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 264s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 264s Global net ELEC energy = -2.133542621421E+01 kJ/mol 264s 264s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 264s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 264s Global net ELEC energy = -3.200702302816E+03 kJ/mol 264s 264s 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 264s Local net energy (PE 0) = 1.624454192074E+01 kJ/mol 264s Global net ELEC energy = 1.624454192074E+01 kJ/mol 264s ---------------------------------------- 264s CLEANING UP AND SHUTTING DOWN... 264s Destroying force arrays. 264s No energy arrays to destroy. 264s Destroying multigrid structures. 264s Destroying finite element structures. 264s Destroying 3 molecules 264s Final memory usage: 0.001 MB total, 221.696 MB high water 264s 264s 264s Thanks for using APBS! 264s 264s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 264s *** PASSED *** 264s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 264s *** PASSED *** 264s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 264s *** PASSED *** 264s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 264s *** PASSED *** 264s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 264s *** PASSED *** 264s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 264s *** PASSED *** 264s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 264s *** PASSED *** 264s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 264s *** PASSED *** 264s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 264s *** PASSED *** 264s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 264s *** PASSED *** 264s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 264s *** PASSED *** 264s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 264s *** PASSED *** 264s Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) 264s *** PASSED *** 264s Elapsed time: 7.664988 seconds 264s -------------------------------------------------------------------------------- 264s -------------------------------------------------------------------------------- 264s Testing input file 1d7i-dss-mol.in 264s 271s Checking for intermediate energies in input file 1d7h-dmso-smol.out 271s EXPECTED COMPUTED: 16 271s EXPECTED EXPECTED: 16 271s 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] 271s 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'] 271s COMPUTED RESULT 10749.48704824 271s COMPUTED RESULT 42894.87256481 271s COMPUTED RESULT 13992.34956777 271s COMPUTED RESULT 46100.66575192 271s COMPUTED RESULT 37.19709905887 271s COMPUTED RESULT 712.5747080979 271s COMPUTED RESULT 67.51571424823 271s COMPUTED RESULT 733.9101343121 271s COMPUTED RESULT 10716.54753674 271s COMPUTED RESULT 42181.78203716 271s COMPUTED RESULT 13959.61902233 271s COMPUTED RESULT 45382.48433997 271s COMPUTED RESULT -3205.793187109 271s COMPUTED RESULT -21.33542621421 271s COMPUTED RESULT -3200.702302816 271s COMPUTED RESULT 16.24454192074 271s BINARY: /usr/bin/apbs 271s INPUT: 1d7i-dss-mol.in 271s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 272s asc_getToken: Error occurred (bailing out). 272s Vio_scanf: Format problem with input. 272s 272s 272s ---------------------------------------------------------------------- 272s APBS -- Adaptive Poisson-Boltzmann Solver 272s Version APBS 3.4.1 272s 272s Nathan A. Baker (nathan.baker@pnnl.gov) 272s Pacific Northwest National Laboratory 272s 272s Additional contributing authors listed in the code documentation. 272s 272s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 272s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 272s Northwest Division for the U.S. Department of Energy. 272s 272s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 272s Portions Copyright (c) 2002-2020, Nathan A. Baker. 272s Portions Copyright (c) 1999-2002, The Regents of the University of California. 272s Portions Copyright (c) 1995, Michael Holst. 272s All rights reserved. 272s 272s Redistribution and use in source and binary forms, with or without 272s modification, are permitted provided that the following conditions are met: 272s 272s * Redistributions of source code must retain the above copyright notice, this 272s list of conditions and the following disclaimer. 272s 272s * Redistributions in binary form must reproduce the above copyright notice, 272s this list of conditions and the following disclaimer in the documentation 272s and/or other materials provided with the distribution. 272s 272s * Neither the name of the developer nor the names of its contributors may be 272s used to endorse or promote products derived from this software without 272s specific prior written permission. 272s 272s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 272s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 272s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 272s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 272s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 272s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 272s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 272s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 272s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 272s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 272s ---------------------------------------------------------------------- 272s APBS uses FETK (the Finite Element ToolKit) to solve the 272s Poisson-Boltzmann equation numerically. FETK is a portable collection 272s of finite element modeling class libraries developed by the Michael Holst 272s research group and written in an object-oriented form of C. FEtk is 272s designed to solve general coupled systems of nonlinear partial differential 272s equations using adaptive finite element methods, inexact Newton methods, 272s and algebraic multilevel methods. More information about FEtk may be found 272s at . 272s ---------------------------------------------------------------------- 272s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 272s Aqua is a modified form of the Holst group PMG library 272s which has been modified by Patrice Koehl 272s for improved efficiency and 272s memory usage when solving the Poisson-Boltzmann equation. 272s ---------------------------------------------------------------------- 272s Please cite your use of APBS as: 272s 272s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 272s nanosystems: application to microtubules and the ribosome. Proc. 272s Natl. Acad. Sci. USA 98, 10037-10041 2001. 272s 272s 272s This executable compiled on Jan 3 2025 at 11:01:42 272s 272s Parsing input file 1d7i-dss-mol.in... 272s rank 0 size 1... 272s Parsed input file. 272s Got paths for 3 molecules 272s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 272s asc_getToken: Error occurred (bailing out). 272s Vio_scanf: Format problem with input. 272s 1677 atoms 272s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 272s Net charge 9.91e-01 e 272s Reading PQR-format atom data from dss-min.pqr. 272s asc_getToken: Error occurred (bailing out). 272s Vio_scanf: Format problem with input. 272s 14 atoms 272s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 272s Net charge -8.33e-17 e 272s Reading PQR-format atom data from 1d7i-min.pqr. 272s 1663 atoms 272s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 272s Net charge 9.91e-01 e 272s Preparing to run 12 PBE calculations. 272s ---------------------------------------- 272s CALCULATION #1 (complex-solv-coarse): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 30.4176 A 272s Current memory usage: 122.425 MB total, 122.425 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 1.500 x 1.500 x 1.500 272s Grid lengths: 96.000 x 96.000 x 96.000 272s Grid center: (25.264, 18.988, 19.122) 272s Multigrid levels: 5 272s Molecule ID: 1 272s Linearized traditional PBE 272s Multiple Debye-Huckel sphere boundary conditions 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 78.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 9.160578033846E+03 kJ/mol 272s Calculating forces... 272s [focusFillBound()]: WARNING: 272s Unusually large potential values 272s detected on the focusing boundary! 272s Convergence not guaranteed for NPBE/NRPBE calculations! 272s 272s ---------------------------------------- 272s CALCULATION #2 (complex-solv-fine): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 30.4176 A 272s Current memory usage: 122.425 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 0.225 x 0.225 x 0.225 272s Grid lengths: 14.400 x 14.400 x 14.400 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 1 272s Linearized traditional PBE 272s Boundary conditions from focusing 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 78.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 3.955701871716E+04 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s CALCULATION #3 (complex-ref-coarse): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 4.87072 A 272s Current memory usage: 122.425 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 1.500 x 1.500 x 1.500 272s Grid lengths: 96.000 x 96.000 x 96.000 272s Grid center: (25.264, 18.988, 19.122) 272s Multigrid levels: 5 272s Molecule ID: 1 272s Linearized traditional PBE 272s Multiple Debye-Huckel sphere boundary conditions 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 2.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 1.264965939588E+04 kJ/mol 272s Calculating forces... 272s [focusFillBound()]: WARNING: 272s Unusually large potential values 272s detected on the focusing boundary! 272s Convergence not guaranteed for NPBE/NRPBE calculations! 272s 272s ---------------------------------------- 272s CALCULATION #4 (complex-ref-fine): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 4.87072 A 272s Current memory usage: 122.425 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 0.225 x 0.225 x 0.225 272s Grid lengths: 14.400 x 14.400 x 14.400 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 1 272s Linearized traditional PBE 272s Boundary conditions from focusing 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 2.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 4.301801664829E+04 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s CALCULATION #5 (dss-solv-coarse): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 30.4176 A 272s Current memory usage: 62.528 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 1.500 x 1.500 x 1.500 272s Grid lengths: 96.000 x 96.000 x 96.000 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 2 272s Linearized traditional PBE 272s Multiple Debye-Huckel sphere boundary conditions 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 78.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 9.431133325426E+01 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s CALCULATION #6 (dss-solv-fine): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 30.4176 A 272s Current memory usage: 62.528 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 0.225 x 0.225 x 0.225 272s Grid lengths: 14.400 x 14.400 x 14.400 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 2 272s Linearized traditional PBE 272s Boundary conditions from focusing 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 78.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 1.677348113184E+03 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s CALCULATION #7 (dss-ref-coarse): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 4.87072 A 272s Current memory usage: 62.528 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 1.500 x 1.500 x 1.500 272s Grid lengths: 96.000 x 96.000 x 96.000 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 2 272s Linearized traditional PBE 272s Multiple Debye-Huckel sphere boundary conditions 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 2.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 1.171079106781E+02 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s CALCULATION #8 (dss-ref-fine): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 4.87072 A 272s Current memory usage: 62.528 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 0.225 x 0.225 x 0.225 272s Grid lengths: 14.400 x 14.400 x 14.400 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 2 272s Linearized traditional PBE 272s Boundary conditions from focusing 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 2.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 1.697869784185E+03 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 30.4176 A 272s Current memory usage: 121.977 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 1.500 x 1.500 x 1.500 272s Grid lengths: 96.000 x 96.000 x 96.000 272s Grid center: (25.264, 18.988, 19.122) 272s Multigrid levels: 5 272s Molecule ID: 3 272s Linearized traditional PBE 272s Multiple Debye-Huckel sphere boundary conditions 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 78.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 9.040108332204E+03 kJ/mol 272s Calculating forces... 272s [focusFillBound()]: WARNING: 272s Unusually large potential values 272s detected on the focusing boundary! 272s Convergence not guaranteed for NPBE/NRPBE calculations! 272s 272s ---------------------------------------- 272s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 30.4176 A 272s Current memory usage: 121.977 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 0.225 x 0.225 x 0.225 272s Grid lengths: 14.400 x 14.400 x 14.400 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 3 272s Linearized traditional PBE 272s Boundary conditions from focusing 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 78.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 3.787747796627E+04 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 4.87072 A 272s Current memory usage: 121.977 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 1.500 x 1.500 x 1.500 272s Grid lengths: 96.000 x 96.000 x 96.000 272s Grid center: (25.264, 18.988, 19.122) 272s Multigrid levels: 5 272s Molecule ID: 3 272s Linearized traditional PBE 272s Multiple Debye-Huckel sphere boundary conditions 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 2.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 1.252495566243E+04 kJ/mol 272s Calculating forces... 272s [focusFillBound()]: WARNING: 272s Unusually large potential values 272s detected on the focusing boundary! 272s Convergence not guaranteed for NPBE/NRPBE calculations! 272s 272s ---------------------------------------- 272s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 272s Setting up problem... 272s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 272s Debye length: 4.87072 A 272s Current memory usage: 121.977 MB total, 222.305 MB high water 272s Using linear spline charge discretization. 272s Grid dimensions: 65 x 65 x 65 272s Grid spacings: 0.225 x 0.225 x 0.225 272s Grid lengths: 14.400 x 14.400 x 14.400 272s Grid center: (17.340, 19.211, 20.503) 272s Multigrid levels: 5 272s Molecule ID: 3 272s Linearized traditional PBE 272s Boundary conditions from focusing 272s 2 ion species (0.010 M ionic strength): 272s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 272s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 272s Solute dielectric: 2.000 272s Solvent dielectric: 2.000 272s Using "molecular" surface definition; no smoothing 272s Solvent probe radius: 0.000 A 272s Temperature: 300.000 K 272s Electrostatic energies will be calculated 272s Total electrostatic energy = 4.133237922574E+04 kJ/mol 272s Calculating forces... 272s ---------------------------------------- 272s PRINT STATEMENTS 272s 272s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 272s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 272s Global net ELEC energy = -3.460997931137E+03 kJ/mol 272s 272s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 272s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 272s Global net ELEC energy = -2.052167100108E+01 kJ/mol 272s 272s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 272s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 272s Global net ELEC energy = -3.454901259473E+03 kJ/mol 272s 272s 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 272s Local net energy (PE 0) = 1.442499933664E+01 kJ/mol 272s Global net ELEC energy = 1.442499933664E+01 kJ/mol 272s ---------------------------------------- 272s CLEANING UP AND SHUTTING DOWN... 272s Destroying force arrays. 272s No energy arrays to destroy. 272s Destroying multigrid structures. 272s Destroying finite element structures. 272s Destroying 3 molecules 272s Final memory usage: 0.001 MB total, 222.305 MB high water 272s 272s 272s Thanks for using APBS! 272s 272s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 272s *** PASSED *** 272s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 272s *** PASSED *** 272s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 272s *** PASSED *** 272s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 272s *** PASSED *** 272s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 272s *** PASSED *** 272s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 272s *** PASSED *** 272s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 272s *** PASSED *** 272s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 272s *** PASSED *** 272s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 272s *** PASSED *** 272s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 272s *** PASSED *** 272s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 272s *** PASSED *** 272s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 272s *** PASSED *** 272s Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) 272s *** PASSED *** 272s Elapsed time: 7.823178 seconds 272s -------------------------------------------------------------------------------- 272s -------------------------------------------------------------------------------- 272s Testing input file 1d7i-dss-smol.in 272s 279s Checking for intermediate energies in input file 1d7i-dss-mol.out 279s EXPECTED COMPUTED: 16 279s EXPECTED EXPECTED: 16 279s 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] 279s 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'] 279s COMPUTED RESULT 9160.578033846 279s COMPUTED RESULT 39557.01871716 279s COMPUTED RESULT 12649.65939588 279s COMPUTED RESULT 43018.01664829 279s COMPUTED RESULT 94.31133325426 279s COMPUTED RESULT 1677.348113184 279s COMPUTED RESULT 117.1079106781 279s COMPUTED RESULT 1697.869784185 279s COMPUTED RESULT 9040.108332204 279s COMPUTED RESULT 37877.47796627 279s COMPUTED RESULT 12524.95566243 279s COMPUTED RESULT 41332.37922574 279s COMPUTED RESULT -3460.997931137 279s COMPUTED RESULT -20.52167100108 279s COMPUTED RESULT -3454.901259473 279s COMPUTED RESULT 14.42499933664 279s BINARY: /usr/bin/apbs 279s INPUT: 1d7i-dss-smol.in 279s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 279s asc_getToken: Error occurred (bailing out). 279s Vio_scanf: Format problem with input. 279s 279s 279s ---------------------------------------------------------------------- 279s APBS -- Adaptive Poisson-Boltzmann Solver 279s Version APBS 3.4.1 279s 279s Nathan A. Baker (nathan.baker@pnnl.gov) 279s Pacific Northwest National Laboratory 279s 279s Additional contributing authors listed in the code documentation. 279s 279s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 279s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 279s Northwest Division for the U.S. Department of Energy. 279s 279s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 279s Portions Copyright (c) 2002-2020, Nathan A. Baker. 279s Portions Copyright (c) 1999-2002, The Regents of the University of California. 279s Portions Copyright (c) 1995, Michael Holst. 279s All rights reserved. 279s 279s Redistribution and use in source and binary forms, with or without 279s modification, are permitted provided that the following conditions are met: 279s 279s * Redistributions of source code must retain the above copyright notice, this 279s list of conditions and the following disclaimer. 279s 279s * Redistributions in binary form must reproduce the above copyright notice, 279s this list of conditions and the following disclaimer in the documentation 279s and/or other materials provided with the distribution. 279s 279s * Neither the name of the developer nor the names of its contributors may be 279s used to endorse or promote products derived from this software without 279s specific prior written permission. 279s 279s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 279s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 279s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 279s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 279s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 279s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 279s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 279s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 279s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 279s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 279s ---------------------------------------------------------------------- 279s APBS uses FETK (the Finite Element ToolKit) to solve the 279s Poisson-Boltzmann equation numerically. FETK is a portable collection 279s of finite element modeling class libraries developed by the Michael Holst 279s research group and written in an object-oriented form of C. FEtk is 279s designed to solve general coupled systems of nonlinear partial differential 279s equations using adaptive finite element methods, inexact Newton methods, 279s and algebraic multilevel methods. More information about FEtk may be found 279s at . 279s ---------------------------------------------------------------------- 279s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 279s Aqua is a modified form of the Holst group PMG library 279s which has been modified by Patrice Koehl 279s for improved efficiency and 279s memory usage when solving the Poisson-Boltzmann equation. 279s ---------------------------------------------------------------------- 279s Please cite your use of APBS as: 279s 279s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 279s nanosystems: application to microtubules and the ribosome. Proc. 279s Natl. Acad. Sci. USA 98, 10037-10041 2001. 279s 279s 279s This executable compiled on Jan 3 2025 at 11:01:42 279s 279s Parsing input file 1d7i-dss-smol.in... 279s rank 0 size 1... 279s Parsed input file. 279s Got paths for 3 molecules 279s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 279s asc_getToken: Error occurred (bailing out). 279s Vio_scanf: Format problem with input. 279s 1677 atoms 279s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 279s Net charge 9.91e-01 e 279s Reading PQR-format atom data from dss-min.pqr. 279s asc_getToken: Error occurred (bailing out). 279s Vio_scanf: Format problem with input. 279s 14 atoms 279s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 279s Net charge -8.33e-17 e 279s Reading PQR-format atom data from 1d7i-min.pqr. 279s 1663 atoms 279s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 279s Net charge 9.91e-01 e 279s Preparing to run 12 PBE calculations. 279s ---------------------------------------- 279s CALCULATION #1 (complex-solv-coarse): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 30.4176 A 279s Current memory usage: 122.425 MB total, 122.425 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 1.500 x 1.500 x 1.500 279s Grid lengths: 96.000 x 96.000 x 96.000 279s Grid center: (25.264, 18.988, 19.122) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 78.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 9.634884642408E+03 kJ/mol 279s Calculating forces... 279s [focusFillBound()]: WARNING: 279s Unusually large potential values 279s detected on the focusing boundary! 279s Convergence not guaranteed for NPBE/NRPBE calculations! 279s 279s ---------------------------------------- 279s CALCULATION #2 (complex-solv-fine): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 30.4176 A 279s Current memory usage: 122.425 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.225 x 0.225 x 0.225 279s Grid lengths: 14.400 x 14.400 x 14.400 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 78.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 4.003177540425E+04 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #3 (complex-ref-coarse): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 4.87072 A 279s Current memory usage: 122.425 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 1.500 x 1.500 x 1.500 279s Grid lengths: 96.000 x 96.000 x 96.000 279s Grid center: (25.264, 18.988, 19.122) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 2.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 1.264965939588E+04 kJ/mol 279s Calculating forces... 279s [focusFillBound()]: WARNING: 279s Unusually large potential values 279s detected on the focusing boundary! 279s Convergence not guaranteed for NPBE/NRPBE calculations! 279s 279s ---------------------------------------- 279s CALCULATION #4 (complex-ref-fine): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 279s *** PASSED *** 279s 4.87072 A 279s Current memory usage: 122.425 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.225 x 0.225 x 0.225 279s Grid lengths: 14.400 x 14.400 x 14.400 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 1 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 2.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 4.301801664829E+04 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #5 (dss-solv-coarse): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 30.4176 A 279s Current memory usage: 62.528 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 1.500 x 1.500 x 1.500 279s Grid lengths: 96.000 x 96.000 x 96.000 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 2 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 78.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 7.942232645345E+01 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #6 (dss-solv-fine): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 30.4176 A 279s Current memory usage: 62.528 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.225 x 0.225 x 0.225 279s Grid lengths: 14.400 x 14.400 x 14.400 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 2 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 78.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 1.677798535473E+03 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #7 (dss-ref-coarse): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 4.87072 A 279s Current memory usage: 62.528 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 1.500 x 1.500 x 1.500 279s Grid lengths: 96.000 x 96.000 x 96.000 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 2 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 2.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 1.171079106781E+02 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #8 (dss-ref-fine): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 4.87072 A 279s Current memory usage: 62.528 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.225 x 0.225 x 0.225 279s Grid lengths: 14.400 x 14.400 x 14.400 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 2 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 2.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 1.697869784185E+03 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 30.4176 A 279s Current memory usage: 121.977 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 1.500 x 1.500 x 1.500 279s Grid lengths: 96.000 x 96.000 x 96.000 279s Grid center: (25.264, 18.988, 19.122) 279s Multigrid levels: 5 279s Molecule ID: 3 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 78.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 9.507068451372E+03 kJ/mol 279s Calculating forces... 279s [focusFillBound()]: WARNING: 279s Unusually large potential values 279s detected on the focusing boundary! 279s Convergence not guaranteed for NPBE/NRPBE calculations! 279s 279s ---------------------------------------- 279s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 30.4176 A 279s Current memory usage: 121.977 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.225 x 0.225 x 0.225 279s Grid lengths: 14.400 x 14.400 x 14.400 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 3 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 78.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 3.835075772299E+04 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 4.87072 A 279s Current memory usage: 121.977 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 1.500 x 1.500 x 1.500 279s Grid lengths: 96.000 x 96.000 x 96.000 279s Grid center: (25.264, 18.988, 19.122) 279s Multigrid levels: 5 279s Molecule ID: 3 279s Linearized traditional PBE 279s Multiple Debye-Huckel sphere boundary conditions 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 2.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 1.252495566243E+04 kJ/mol 279s Calculating forces... 279s [focusFillBound()]: WARNING: 279s Unusually large potential values 279s detected on the focusing boundary! 279s Convergence not guaranteed for NPBE/NRPBE calculations! 279s 279s ---------------------------------------- 279s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 279s Setting up problem... 279s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 279s Debye length: 4.87072 A 279s Current memory usage: 121.977 MB total, 222.305 MB high water 279s Using linear spline charge discretization. 279s Grid dimensions: 65 x 65 x 65 279s Grid spacings: 0.225 x 0.225 x 0.225 279s Grid lengths: 14.400 x 14.400 x 14.400 279s Grid center: (17.340, 19.211, 20.503) 279s Multigrid levels: 5 279s Molecule ID: 3 279s Linearized traditional PBE 279s Boundary conditions from focusing 279s 2 ion species (0.010 M ionic strength): 279s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 279s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 279s Solute dielectric: 2.000 279s Solvent dielectric: 2.000 279s Using "molecular" surface definition;harmonic average smoothing 279s Solvent probe radius: 0.000 A 279s Temperature: 300.000 K 279s Electrostatic energies will be calculated 279s Total electrostatic energy = 4.133237922574E+04 kJ/mol 279s Calculating forces... 279s ---------------------------------------- 279s PRINT STATEMENTS 279s 279s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 279s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 279s Global net ELEC energy = -2.986241244040E+03 kJ/mol 279s 279s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 279s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 279s Global net ELEC energy = -2.007124871262E+01 kJ/mol 279s 279s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 279s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 279s Global net ELEC energy = -2.981621502756E+03 kJ/mol 279s 279s 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 279s Local net energy (PE 0) = 1.545150742843E+01 kJ/mol 279s Global net ELEC energy = 1.545150742843E+01 kJ/mol 279s ---------------------------------------- 279s CLEANING UP AND SHUTTING DOWN... 279s Destroying force arrays. 279s No energy arrays to destroy. 279s Destroying multigrid structures. 279s Destroying finite element structures. 279s Destroying 3 molecules 279s Final memory usage: 0.001 MB total, 222.305 MB high water 279s 279s 279s Thanks for using APBS! 279s 279s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 279s *** PASSED *** 279s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 279s *** PASSED *** 279s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 279s *** PASSED *** 279s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 279s *** PASSED *** 279s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 279s *** PASSED *** 279s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 279s *** PASSED *** 279s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 279s *** PASSED *** 279s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 279s *** PASSED *** 279s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 279s *** PASSED *** 279s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 279s *** PASSED *** 279s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 279s *** PASSED *** 279s Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) 279s *** PASSED *** 279s Elapsed time: 7.612027 seconds 279s -------------------------------------------------------------------------------- 279s Total elapsed time: 31.039224 seconds 279s Test results have been logged 279s -------------------------------------------------------------------------------- 279s -------------------------------------------------------------------------------- 279s Testing input file apbs-mol.in 279s 286s Checking for intermediate energies in input file 1d7i-dss-smol.out 286s EXPECTED COMPUTED: 16 286s EXPECTED EXPECTED: 16 286s 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] 286s 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'] 286s COMPUTED RESULT 9634.884642408 286s COMPUTED RESULT 40031.77540425 286s COMPUTED RESULT 12649.65939588 286s COMPUTED RESULT 43018.01664829 286s COMPUTED RESULT 79.42232645345 286s COMPUTED RESULT 1677.798535473 286s COMPUTED RESULT 117.1079106781 286s COMPUTED RESULT 1697.869784185 286s COMPUTED RESULT 9507.068451372 286s COMPUTED RESULT 38350.75772299 286s COMPUTED RESULT 12524.95566243 286s COMPUTED RESULT 41332.37922574 286s COMPUTED RESULT -2986.24124404 286s COMPUTED RESULT -20.07124871262 286s COMPUTED RESULT -2981.621502756 286s COMPUTED RESULT 15.45150742843 286s Running tests for hca-bind section 286s BINARY: /usr/bin/apbs 286s INPUT: apbs-mol.in 286s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 286s asc_getToken: Error occurred (bailing out). 286s Vio_scanf: Format problem with input. 286s 286s 286s ---------------------------------------------------------------------- 286s APBS -- Adaptive Poisson-Boltzmann Solver 286s Version APBS 3.4.1 286s 286s Nathan A. Baker (nathan.baker@pnnl.gov) 286s Pacific Northwest National Laboratory 286s 286s Additional contributing authors listed in the code documentation. 286s 286s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 286s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 286s Northwest Division for the U.S. Department of Energy. 286s 286s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 286s Portions Copyright (c) 2002-2020, Nathan A. Baker. 286s Portions Copyright (c) 1999-2002, The Regents of the University of California. 286s Portions Copyright (c) 1995, Michael Holst. 286s All rights reserved. 286s 286s Redistribution and use in source and binary forms, with or without 286s modification, are permitted provided that the following conditions are met: 286s 286s * Redistributions of source code must retain the above copyright notice, this 286s list of conditions and the following disclaimer. 286s 286s * Redistributions in binary form must reproduce the above copyright notice, 286s this list of conditions and the following disclaimer in the documentation 286s and/or other materials provided with the distribution. 286s 286s * Neither the name of the developer nor the names of its contributors may be 286s used to endorse or promote products derived from this software without 286s specific prior written permission. 286s 286s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 286s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 286s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 286s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 286s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 286s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 286s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 286s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 286s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 286s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 286s ---------------------------------------------------------------------- 286s APBS uses FETK (the Finite Element ToolKit) to solve the 286s Poisson-Boltzmann equation numerically. FETK is a portable collection 286s of finite element modeling class libraries developed by the Michael Holst 286s research group and written in an object-oriented form of C. FEtk is 286s designed to solve general coupled systems of nonlinear partial differential 286s equations using adaptive finite element methods, inexact Newton methods, 286s and algebraic multilevel methods. More information about FEtk may be found 286s at . 286s ---------------------------------------------------------------------- 286s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 286s Aqua is a modified form of the Holst group PMG library 286s which has been modified by Patrice Koehl 286s for improved efficiency and 286s memory usage when solving the Poisson-Boltzmann equation. 286s ---------------------------------------------------------------------- 286s Please cite your use of APBS as: 286s 286s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 286s nanosystems: application to microtubules and the ribosome. Proc. 286s Natl. Acad. Sci. USA 98, 10037-10041 2001. 286s 286s 286s This executable compiled on Jan 3 2025 at 11:01:42 286s 286s Parsing input file apbs-mol.in... 286s rank 0 size 1... 286s Parsed input file. 286s Got paths for 3 molecules 286s Reading PQR-format atom data from acet.pqr. 286s asc_getToken: Error occurred (bailing out). 286s Vio_scanf: Format problem with input. 286s 18 atoms 286s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 286s Net charge -1.00e+00 e 286s Reading PQR-format atom data from hca.pqr. 286s asc_getToken: Error occurred (bailing out). 286s Vio_scanf: Format problem with input. 286s 2482 atoms 286s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 286s Net charge 1.00e+00 e 286s Reading PQR-format atom data from complex.pqr. 286s 2500 atoms 286s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 286s Net charge -1.02e-14 e 286s Preparing to run 9 PBE calculations. 286s ---------------------------------------- 286s CALCULATION #1 (acet): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 62.727 MB total, 62.727 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 1.500 x 1.500 x 1.500 286s Grid lengths: 96.000 x 96.000 x 96.000 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Single Debye-Huckel sphere boundary conditions 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 2.213600726771E+02 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #2 (acet): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 62.727 MB total, 123.701 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.581 x 0.581 x 0.581 286s Grid lengths: 37.181 x 37.181 x 37.181 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.825764811255E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #3 (acet): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 62.727 MB total, 123.701 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.225 x 0.225 x 0.225 286s Grid lengths: 14.400 x 14.400 x 14.400 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 1 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 6.458471211905E+03 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #4 (hca): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 146.516 MB total, 146.516 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 1.500 x 1.500 x 1.500 286s Grid lengths: 96.000 x 96.000 x 96.000 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 2 286s Linearized traditional PBE 286s Single Debye-Huckel sphere boundary conditions 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 2.093606095527E+04 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #5 (hca): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 146.516 MB total, 245.092 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.581 x 0.581 x 0.581 286s Grid lengths: 37.181 x 37.181 x 37.181 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 2 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.515433544464E+05 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #6 (hca): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 146.516 MB total, 245.092 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.225 x 0.225 x 0.225 286s Grid lengths: 14.400 x 14.400 x 14.400 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 2 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.786369323561E+05 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s CALCULATION #7 (complex): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 146.926 MB total, 245.092 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 1.500 x 1.500 x 1.500 286s Grid lengths: 96.000 x 96.000 x 96.000 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 3 286s Linearized traditional PBE 286s Single Debye-Huckel sphere boundary conditions 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 2.105322784838E+04 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #8 (complex): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 146.926 MB total, 245.725 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.581 x 0.581 x 0.581 286s Grid lengths: 37.181 x 37.181 x 37.181 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 3 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.533304996252E+05 kJ/mol 286s Calculating forces... 286s [focusFillBound()]: WARNING: 286s Unusually large potential values 286s detected on the focusing boundary! 286s Convergence not guaranteed for NPBE/NRPBE calculations! 286s 286s ---------------------------------------- 286s CALCULATION #9 (complex): MULTIGRID 286s Setting up problem... 286s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 286s Debye length: 0 A 286s Current memory usage: 146.926 MB total, 245.725 MB high water 286s Using linear spline charge discretization. 286s Grid dimensions: 65 x 65 x 65 286s Grid spacings: 0.225 x 0.225 x 0.225 286s Grid lengths: 14.400 x 14.400 x 14.400 286s Grid center: (-6.028, 3.898, 15.179) 286s Multigrid levels: 5 286s Molecule ID: 3 286s Linearized traditional PBE 286s Boundary conditions from focusing 286s 2 ion species (0.000 M ionic strength): 286s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 286s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 286s Solute dielectric: 2.000 286s Solvent dielectric: 78.540 286s Using "molecular" surface definition; no smoothing 286s Solvent probe radius: 0.000 A 286s Temperature: 298.150 K 286s Electrostatic energies will be calculated 286s Total electrostatic energy = 1.850429388099E+05 kJ/mol 286s Calculating forces... 286s ---------------------------------------- 286s PRINT STATEMENTS 286s 286s print energy 3 (complex) - 1 (acet) - 2 (hca) end 286s Local net energy (PE 0) = -5.246475812684E+01 kJ/mol 286s Global net ELEC energy = -5.246475812684E+01 kJ/mol 286s ---------------------------------------- 286s CLEANING UP AND SHUTTING DOWN... 286s Destroying force arrays. 286s No energy arrays to destroy. 286s Destroying multigrid structures. 286s Destroying finite element structures. 286s Destroying 3 molecules 286s Final memory usage: 0.001 MB total, 245.725 MB high water 286s 286s 286s Thanks for using APBS! 286s 286s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 286s *** PASSED *** 286s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 286s *** PASSED *** 286s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 286s *** PASSED *** 286s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 286s *** PASSED *** 286s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 286s *** PASSED *** 286s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 286s *** PASSED *** 286s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 286s *** PASSED *** 286s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 286s *** PASSED *** 286s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 286s *** PASSED *** 286s Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) 286s *** PASSED *** 286s Elapsed time: 6.940775 seconds 286s -------------------------------------------------------------------------------- 286s -------------------------------------------------------------------------------- 286s Testing input file apbs-smol.in 286s 292s Checking for intermediate energies in input file apbs-mol.out 292s EXPECTED COMPUTED: 10 292s EXPECTED EXPECTED: 10 292s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] 292s 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'] 292s COMPUTED RESULT 221.3600726771 292s COMPUTED RESULT 1825.764811255 292s COMPUTED RESULT 6458.471211905 292s COMPUTED RESULT 20936.06095527 292s COMPUTED RESULT 151543.3544464 292s COMPUTED RESULT 178636.9323561 292s COMPUTED RESULT 21053.22784838 292s COMPUTED RESULT 153330.4996252 292s COMPUTED RESULT 185042.9388099 292s COMPUTED RESULT -52.46475812684 292s BINARY: /usr/bin/apbs 292s INPUT: apbs-smol.in 292s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 292s asc_getToken: Error occurred (bailing out). 292s Vio_scanf: Format problem with input. 292s 292s 292s ---------------------------------------------------------------------- 292s APBS -- Adaptive Poisson-Boltzmann Solver 292s Version APBS 3.4.1 292s 292s Nathan A. Baker (nathan.baker@pnnl.gov) 292s Pacific Northwest National Laboratory 292s 292s Additional contributing authors listed in the code documentation. 292s 292s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 292s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 292s Northwest Division for the U.S. Department of Energy. 292s 292s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 292s Portions Copyright (c) 2002-2020, Nathan A. Baker. 292s Portions Copyright (c) 1999-2002, The Regents of the University of California. 292s Portions Copyright (c) 1995, Michael Holst. 292s All rights reserved. 292s 292s Redistribution and use in source and binary forms, with or without 292s modification, are permitted provided that the following conditions are met: 292s 292s * Redistributions of source code must retain the above copyright notice, this 292s list of conditions and the following disclaimer. 292s 292s * Redistributions in binary form must reproduce the above copyright notice, 292s this list of conditions and the following disclaimer in the documentation 292s and/or other materials provided with the distribution. 292s 292s * Neither the name of the developer nor the names of its contributors may be 292s used to endorse or promote products derived from this software without 292s specific prior written permission. 292s 292s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 292s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 292s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 292s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 292s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 292s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 292s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 292s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 292s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 292s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 292s ---------------------------------------------------------------------- 292s APBS uses FETK (the Finite Element ToolKit) to solve the 292s Poisson-Boltzmann equation numerically. FETK is a portable collection 292s of finite element modeling class libraries developed by the Michael Holst 292s research group and written in an object-oriented form of C. FEtk is 292s designed to solve general coupled systems of nonlinear partial differential 292s equations using adaptive finite element methods, inexact Newton methods, 292s and algebraic multilevel methods. More information about FEtk may be found 292s at . 292s ---------------------------------------------------------------------- 292s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 292s Aqua is a modified form of the Holst group PMG library 292s which has been modified by Patrice Koehl 292s for improved efficiency and 292s memory usage when solving the Poisson-Boltzmann equation. 292s ---------------------------------------------------------------------- 292s Please cite your use of APBS as: 292s 292s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 292s nanosystems: application to microtubules and the ribosome. Proc. 292s Natl. Acad. Sci. USA 98, 10037-10041 2001. 292s 292s 292s This executable compiled on Jan 3 2025 at 11:01:42 292s 292s Parsing input file apbs-smol.in... 292s rank 0 size 1... 292s Parsed input file. 292s Got paths for 3 molecules 292s Reading PQR-format atom data from acet.pqr. 292s asc_getToken: Error occurred (bailing out). 292s Vio_scanf: Format problem with input. 292s 18 atoms 292s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 292s Net charge -1.00e+00 e 292s Reading PQR-format atom data from hca.pqr. 292s asc_getToken: Error occurred (bailing out). 292s Vio_scanf: Format problem with input. 292s 2482 atoms 292s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 292s Net charge 1.00e+00 e 292s Reading PQR-format atom data from complex.pqr. 292s 2500 atoms 292s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 292s Net charge -1.02e-14 e 292s Preparing to run 9 PBE calculations. 292s ---------------------------------------- 292s CALCULATION #1 (acet): MULTIGRID 292s Setting up problem... 292s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 292s Debye length: 0 A 292s Current memory usage: 62.727 MB total, 62.727 MB high water 292s Using linear spline charge discretization. 292s Grid dimensions: 65 x 65 x 65 292s Grid spacings: 1.500 x 1.500 x 1.500 292s Grid lengths: 96.000 x 96.000 x 96.000 292s Grid center: (-6.028, 3.898, 15.179) 292s Multigrid levels: 5 292s Molecule ID: 1 292s Linearized traditional PBE 292s Single Debye-Huckel sphere boundary conditions 292s 2 ion species (0.000 M ionic strength): 292s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 292s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 292s Solute dielectric: 2.000 292s Solvent dielectric: 78.540 292s Using "molecular" surface definition;harmonic average smoothing 292s Solvent probe radius: 0.000 A 292s Temperature: 298.150 K 292s Electrostatic energies will be calculated 292s Total electrostatic energy = 1.884888131017E+02 kJ/mol 292s Calculating forces... 292s ---------------------------------------- 292s CALCULATION #2 (acet): MULTIGRID 292s Setting up problem... 292s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 292s Debye length: 0 A 292s Current memory usage: 62.727 MB total, 123.701 MB high water 292s Using linear spline charge discretization. 292s Grid dimensions: 65 x 65 x 65 292s Grid spacings: 0.581 x 0.581 x 0.581 292s Grid lengths: 37.181 x 37.181 x 37.181 292s Grid center: (-6.028, 3.898, 15.179) 292s Multigrid levels: 5 292s Molecule ID: 1 292s Linearized traditional PBE 292s Boundary conditions from focusing 292s 2 ion species (0.000 M ionic strength): 292s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 292s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 292s Solute dielectric: 2.000 292s Solvent dielectric: 78.540 292s Using "molecular" surface definition;harmonic average smoothing 292s Solvent probe radius: 0.000 A 292s Temperature: 298.150 K 292s Electrostatic energies will be calculated 292s Total electrostatic energy = 1.820045922544E+03 kJ/mol 292s Calculating forces... 292s ---------------------------------------- 292s CALCULATION #3 (acet): MULTIGRID 292s Setting up problem... 292s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 292s Debye length: 0 A 292s Current memory usage: 62.727 MB total, 123.701 MB high water 292s Using linear spline charge discretization. 292s Grid dimensions: 65 x 65 x 65 292s Grid spacings: 0.225 x 0.225 x 0.225 292s Grid lengths: 14.400 x 14.400 x 14.400 292s Grid center: (-6.028, 3.898, 15.179) 292s Multigrid levels: 5 292s Molecule ID: 1 292s Linearized traditional PBE 292s Boundary conditions from focusing 292s 2 ion species (0.000 M ionic strength): 292s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 292s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 6.460002606908E+03 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #4 (hca): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 146.516 MB total, 146.516 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: (-6.028, 3.898, 15.179) 293s Multigrid levels: 5 293s Molecule ID: 2 293s Linearized traditional PBE 293s Single Debye-Huckel sphere boundary conditions 293s 2 ion species (0.000 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 2.189161497021E+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 #5 (hca): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 146.516 MB total, 245.092 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.581 x 0.581 x 0.581 293s Grid lengths: 37.181 x 37.181 x 37.181 293s Grid center: (-6.028, 3.898, 15.179) 293s Multigrid levels: 5 293s Molecule ID: 2 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.000 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.520000494925E+05 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 #6 (hca): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 146.516 MB total, 245.092 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: (-6.028, 3.898, 15.179) 293s Multigrid levels: 5 293s Molecule ID: 2 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.000 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.790436191580E+05 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s CALCULATION #7 (complex): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 146.926 MB total, 245.092 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: (-6.028, 3.898, 15.179) 293s Multigrid levels: 5 293s Molecule ID: 3 293s Linearized traditional PBE 293s Single Debye-Huckel sphere boundary conditions 293s 2 ion species (0.000 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 2.195842512312E+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 #8 (complex): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 146.926 MB total, 245.725 MB high water 293s Using linear spline charge discretization. 293s Grid dimensions: 65 x 65 x 65 293s Grid spacings: 0.581 x 0.581 x 0.581 293s Grid lengths: 37.181 x 37.181 x 37.181 293s Grid center: (-6.028, 3.898, 15.179) 293s Multigrid levels: 5 293s Molecule ID: 3 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.000 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.537771604355E+05 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 #9 (complex): MULTIGRID 293s Setting up problem... 293s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 293s Debye length: 0 A 293s Current memory usage: 146.926 MB total, 245.725 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: (-6.028, 3.898, 15.179) 293s Multigrid levels: 5 293s Molecule ID: 3 293s Linearized traditional PBE 293s Boundary conditions from focusing 293s 2 ion species (0.000 M ionic strength): 293s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 293s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 293s Solute dielectric: 2.000 293s Solvent dielectric: 78.540 293s Using "molecular" surface definition;harmonic average smoothing 293s Solvent probe radius: 0.000 A 293s Temperature: 298.150 K 293s Electrostatic energies will be calculated 293s Total electrostatic energy = 1.854495619747E+05 kJ/mol 293s Calculating forces... 293s ---------------------------------------- 293s PRINT STATEMENTS 293s 293s print energy 3 (complex) - 1 (acet) - 2 (hca) end 293s Local net energy (PE 0) = -5.405979017059E+01 kJ/mol 293s Global net ELEC energy = -5.405979017059E+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, 245.725 MB high water 293s 293s 293s Thanks for using APBS! 293s 293s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 293s *** PASSED *** 293s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 293s *** PASSED *** 293s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 293s *** PASSED *** 293s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 293s *** PASSED *** 293s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 293s *** PASSED *** 293s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 293s *** PASSED *** 293s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 293s *** PASSED *** 293s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 293s *** PASSED *** 293s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 293s *** PASSED *** 293s Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) 293s *** PASSED *** 293s Elapsed time: 6.480403 seconds 293s -------------------------------------------------------------------------------- 293s Total elapsed time: 13.421178 seconds 293s Test results have been logged 293s -------------------------------------------------------------------------------- 293s -------------------------------------------------------------------------------- 293s Testing input file apbs-mol.in 293s 294s Checking for intermediate energies in input file apbs-smol.out 294s EXPECTED COMPUTED: 10 294s EXPECTED EXPECTED: 10 294s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] 294s 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'] 294s COMPUTED RESULT 188.4888131017 294s COMPUTED RESULT 1820.045922544 294s COMPUTED RESULT 6460.002606908 294s COMPUTED RESULT 21891.61497021 294s COMPUTED RESULT 152000.0494925 294s COMPUTED RESULT 179043.619158 294s COMPUTED RESULT 21958.42512312 294s COMPUTED RESULT 153777.1604355 294s COMPUTED RESULT 185449.5619747 294s COMPUTED RESULT -54.05979017059 294s Running tests for ionize section 294s BINARY: /usr/bin/apbs 294s INPUT: apbs-mol.in 294s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 294s asc_getToken: Error occurred (bailing out). 294s Vio_scanf: Format problem with input. 294s 294s 294s ---------------------------------------------------------------------- 294s APBS -- Adaptive Poisson-Boltzmann Solver 294s Version APBS 3.4.1 294s 294s Nathan A. Baker (nathan.baker@pnnl.gov) 294s Pacific Northwest National Laboratory 294s 294s Additional contributing authors listed in the code documentation. 294s 294s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 294s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 294s Northwest Division for the U.S. Department of Energy. 294s 294s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 294s Portions Copyright (c) 2002-2020, Nathan A. Baker. 294s Portions Copyright (c) 1999-2002, The Regents of the University of California. 294s Portions Copyright (c) 1995, Michael Holst. 294s All rights reserved. 294s 294s Redistribution and use in source and binary forms, with or without 294s modification, are permitted provided that the following conditions are met: 294s 294s * Redistributions of source code must retain the above copyright notice, this 294s list of conditions and the following disclaimer. 294s 294s * Redistributions in binary form must reproduce the above copyright notice, 294s this list of conditions and the following disclaimer in the documentation 294s and/or other materials provided with the distribution. 294s 294s * Neither the name of the developer nor the names of its contributors may be 294s used to endorse or promote products derived from this software without 294s specific prior written permission. 294s 294s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 294s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 294s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 294s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 294s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 294s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 294s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 294s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 294s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 294s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 294s ---------------------------------------------------------------------- 294s APBS uses FETK (the Finite Element ToolKit) to solve the 294s Poisson-Boltzmann equation numerically. FETK is a portable collection 294s of finite element modeling class libraries developed by the Michael Holst 294s research group and written in an object-oriented form of C. FEtk is 294s designed to solve general coupled systems of nonlinear partial differential 294s equations using adaptive finite element methods, inexact Newton methods, 294s and algebraic multilevel methods. More information about FEtk may be found 294s at . 294s ---------------------------------------------------------------------- 294s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 294s Aqua is a modified form of the Holst group PMG library 294s which has been modified by Patrice Koehl 294s for improved efficiency and 294s memory usage when solving the Poisson-Boltzmann equation. 294s ---------------------------------------------------------------------- 294s Please cite your use of APBS as: 294s 294s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 294s nanosystems: application to microtubules and the ribosome. Proc. 294s Natl. Acad. Sci. USA 98, 10037-10041 2001. 294s 294s 294s This executable compiled on Jan 3 2025 at 11:01:42 294s 294s Parsing input file apbs-mol.in... 294s rank 0 size 1... 294s Parsed input file. 294s Got paths for 3 molecules 294s Reading PQR-format atom data from acetic-acid.pqr. 294s asc_getToken: Error occurred (bailing out). 294s Vio_scanf: Format problem with input. 294s 8 atoms 294s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 294s Net charge -1.67e-16 e 294s Reading PQR-format atom data from acetate.pqr. 294s asc_getToken: Error occurred (bailing out). 294s Vio_scanf: Format problem with input. 294s 8 atoms 294s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 294s Net charge -1.00e+00 e 294s Reading PQR-format atom data from proton.pqr. 294s 1 atoms 294s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 294s Net charge 1.00e+00 e 294s Preparing to run 12 PBE calculations. 294s ---------------------------------------- 294s CALCULATION #1 (acetic-solv): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 7.76163 A 294s Current memory usage: 61.598 MB total, 61.598 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.188 x 0.188 x 0.188 294s Grid lengths: 12.000 x 12.000 x 12.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 1 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 2 ion species (0.150 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 78.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 5.823898055191E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #2 (acetic-solv): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 7.76163 A 294s Current memory usage: 61.598 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.094 x 0.094 x 0.094 294s Grid lengths: 6.000 x 6.000 x 6.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 1 294s Linearized traditional PBE 294s Boundary conditions from focusing 294s 2 ion species (0.150 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 78.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 9.793274462353E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #3 (acetic-ref): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.422 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.188 x 0.188 x 0.188 294s Grid lengths: 12.000 x 12.000 x 12.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 1 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 2 ion species (0.000 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 2.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 5.846917564309E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #4 (acetic-ref): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.422 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.094 x 0.094 x 0.094 294s Grid lengths: 6.000 x 6.000 x 6.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 1 294s Linearized traditional PBE 294s Boundary conditions from focusing 294s 2 ion species (0.000 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 2.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 9.815953282539E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #5 (acetate-solv): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 7.76163 A 294s Current memory usage: 61.598 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.188 x 0.188 x 0.188 294s Grid lengths: 12.000 x 12.000 x 12.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 2 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 2 ion species (0.150 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 78.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 8.219846763777E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #6 (acetate-solv): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 7.76163 A 294s Current memory usage: 61.598 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.094 x 0.094 x 0.094 294s Grid lengths: 6.000 x 6.000 x 6.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 2 294s Linearized traditional PBE 294s Boundary conditions from focusing 294s 2 ion species (0.150 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 78.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 1.392741988698E+04 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #7 (acetate-ref): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.422 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.188 x 0.188 x 0.188 294s Grid lengths: 12.000 x 12.000 x 12.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 2 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 2 ion species (0.000 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 2.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 8.420373979905E+03 kJ/mol 294s Calculating forces... 294s [focusFillBound()]: WARNING: 294s Unusually large potential values 294s detected on the focusing boundary! 294s Convergence not guaranteed for NPBE/NRPBE calculations! 294s 294s ---------------------------------------- 294s CALCULATION #8 (acetate-ref): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.422 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.094 x 0.094 x 0.094 294s Grid lengths: 6.000 x 6.000 x 6.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 2 294s Linearized traditional PBE 294s Boundary conditions from focusing 294s 2 ion species (0.000 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 2.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 1.412716615065E+04 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #9 (proton-solv): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 7.76163 A 294s Current memory usage: 61.412 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.188 x 0.188 x 0.188 294s Grid lengths: 12.000 x 12.000 x 12.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 3 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 2 ion species (0.150 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 78.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 3.862359524598E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #10 (proton-solv): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 7.76163 A 294s Current memory usage: 61.412 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.094 x 0.094 x 0.094 294s Grid lengths: 6.000 x 6.000 x 6.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 3 294s Linearized traditional PBE 294s Boundary conditions from focusing 294s 2 ion species (0.150 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 78.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 6.288156251610E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s CALCULATION #11 (proton-ref): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.373 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.188 x 0.188 x 0.188 294s Grid lengths: 12.000 x 12.000 x 12.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 3 294s Linearized traditional PBE 294s Multiple Debye-Huckel sphere boundary conditions 294s 2 ion species (0.000 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 2.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 4.162533113906E+03 kJ/mol 294s Calculating forces... 294s [focusFillBound()]: WARNING: 294s Unusually large potential values 294s detected on the focusing boundary! 294s Convergence not guaranteed for NPBE/NRPBE calculations! 294s 294s ---------------------------------------- 294s CALCULATION #12 (proton-ref): MULTIGRID 294s Setting up problem... 294s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 294s Debye length: 0 A 294s Current memory usage: 61.373 MB total, 122.404 MB high water 294s Using linear spline charge discretization. 294s Grid dimensions: 65 x 65 x 65 294s Grid spacings: 0.094 x 0.094 x 0.094 294s Grid lengths: 6.000 x 6.000 x 6.000 294s Grid center: (0.000, -0.154, 1.287) 294s Multigrid levels: 5 294s Molecule ID: 3 294s Linearized traditional PBE 294s Boundary conditions from focusing 294s 2 ion species (0.000 M ionic strength): 294s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 294s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 294s Solute dielectric: 2.000 294s Solvent dielectric: 2.000 294s Using "molecular" surface definition; no smoothing 294s Solvent probe radius: 0.000 A 294s Temperature: 293.000 K 294s Electrostatic energies will be calculated 294s Total electrostatic energy = 6.585616091973E+03 kJ/mol 294s Calculating forces... 294s ---------------------------------------- 294s PRINT STATEMENTS 294s 294s print energy 1 (acetic-solv) - 2 (acetic-ref) end 294s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 294s Global net ELEC energy = -2.267882018629E+01 kJ/mol 294s 294s print energy 3 (acetate-solv) - 4 (acetate-ref) end 294s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 294s Global net ELEC energy = -1.997462636633E+02 kJ/mol 294s 294s print energy 5 (proton-solv) - 6 (proton-ref) end 294s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 294s Global net ELEC energy = -2.974598403628E+02 kJ/mol 294s 294s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 294s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 294s Global net ELEC energy = -4.745272838398E+02 kJ/mol 294s ---------------------------------------- 294s CLEANING UP AND SHUTTING DOWN... 294s Destroying force arrays. 294s No energy arrays to destroy. 294s Destroying multigrid structures. 294s Destroying finite element structures. 294s Destroying 3 molecules 294s Final memory usage: 0.001 MB total, 122.404 MB high water 294s 294s 294s Thanks for using APBS! 294s 294s Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 294s *** PASSED *** 294s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 294s *** PASSED *** 294s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 294s *** PASSED *** 294s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 294s *** PASSED *** 294s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 294s *** PASSED *** 294s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 294s *** PASSED *** 294s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 294s *** PASSED *** 294s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 294s *** PASSED *** 294s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 294s *** PASSED *** 294s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 294s *** PASSED *** 294s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 294s *** PASSED *** 294s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 294s *** PASSED *** 294s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 294s *** PASSED *** 294s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 294s *** PASSED *** 294s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 294s *** PASSED *** 294s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 294s *** PASSED *** 294s Elapsed time: 1.837852 seconds 294s -------------------------------------------------------------------------------- 294s -------------------------------------------------------------------------------- 294s Testing input file apbs-smol.in 294s 296s Checking for intermediate energies in input file apbs-mol.out 296s EXPECTED COMPUTED: 16 296s EXPECTED EXPECTED: 16 296s 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] 296s 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'] 296s COMPUTED RESULT 5823.898055191 296s COMPUTED RESULT 9793.274462353 296s COMPUTED RESULT 5846.917564309 296s COMPUTED RESULT 9815.953282539 296s COMPUTED RESULT 8219.846763777 296s COMPUTED RESULT 13927.41988698 296s COMPUTED RESULT 8420.373979905 296s COMPUTED RESULT 14127.16615065 296s COMPUTED RESULT 3862.359524598 296s COMPUTED RESULT 6288.15625161 296s COMPUTED RESULT 4162.533113906 296s COMPUTED RESULT 6585.616091973 296s COMPUTED RESULT -22.67882018629 296s COMPUTED RESULT -199.7462636633 296s COMPUTED RESULT -297.4598403628 296s COMPUTED RESULT -474.5272838398 296s BINARY: /usr/bin/apbs 296s INPUT: apbs-smol.in 296s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 296s asc_getToken: Error occurred (bailing out). 296s Vio_scanf: Format problem with input. 296s 296s 296s ---------------------------------------------------------------------- 296s APBS -- Adaptive Poisson-Boltzmann Solver 296s Version APBS 3.4.1 296s 296s Nathan A. Baker (nathan.baker@pnnl.gov) 296s Pacific Northwest National Laboratory 296s 296s Additional contributing authors listed in the code documentation. 296s 296s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 296s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 296s Northwest Division for the U.S. Department of Energy. 296s 296s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 296s Portions Copyright (c) 2002-2020, Nathan A. Baker. 296s Portions Copyright (c) 1999-2002, The Regents of the University of California. 296s Portions Copyright (c) 1995, Michael Holst. 296s All rights reserved. 296s 296s Redistribution and use in source and binary forms, with or without 296s modification, are permitted provided that the following conditions are met: 296s 296s * Redistributions of source code must retain the above copyright notice, this 296s list of conditions and the following disclaimer. 296s 296s * Redistributions in binary form must reproduce the above copyright notice, 296s this list of conditions and the following disclaimer in the documentation 296s and/or other materials provided with the distribution. 296s 296s * Neither the name of the developer nor the names of its contributors may be 296s used to endorse or promote products derived from this software without 296s specific prior written permission. 296s 296s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 296s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 296s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 296s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 296s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 296s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 296s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 296s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 296s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 296s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 296s ---------------------------------------------------------------------- 296s APBS uses FETK (the Finite Element ToolKit) to solve the 296s Poisson-Boltzmann equation numerically. FETK is a portable collection 296s of finite element modeling class libraries developed by the Michael Holst 296s research group and written in an object-oriented form of C. FEtk is 296s designed to solve general coupled systems of nonlinear partial differential 296s equations using adaptive finite element methods, inexact Newton methods, 296s and algebraic multilevel methods. More information about FEtk may be found 296s at . 296s ---------------------------------------------------------------------- 296s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 296s Aqua is a modified form of the Holst group PMG library 296s which has been modified by Patrice Koehl 296s for improved efficiency and 296s memory usage when solving the Poisson-Boltzmann equation. 296s ---------------------------------------------------------------------- 296s Please cite your use of APBS as: 296s 296s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 296s nanosystems: application to microtubules and the ribosome. Proc. 296s Natl. Acad. Sci. USA 98, 10037-10041 2001. 296s 296s 296s This executable compiled on Jan 3 2025 at 11:01:42 296s 296s Parsing input file apbs-smol.in... 296s rank 0 size 1... 296s Parsed input file. 296s Got paths for 3 molecules 296s Reading PQR-format atom data from acetic-acid.pqr. 296s asc_getToken: Error occurred (bailing out). 296s Vio_scanf: Format problem with input. 296s 8 atoms 296s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 296s Net charge -1.67e-16 e 296s Reading PQR-format atom data from acetate.pqr. 296s asc_getToken: Error occurred (bailing out). 296s Vio_scanf: Format problem with input. 296s 8 atoms 296s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 296s Net charge -1.00e+00 e 296s Reading PQR-format atom data from proton.pqr. 296s 1 atoms 296s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 296s Net charge 1.00e+00 e 296s Preparing to run 12 PBE calculations. 296s ---------------------------------------- 296s CALCULATION #1 (acetic-solv): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 7.76163 A 296s Current memory usage: 61.598 MB total, 61.598 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.188 x 0.188 x 0.188 296s Grid lengths: 12.000 x 12.000 x 12.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 1 296s Linearized traditional PBE 296s Multiple Debye-Huckel sphere boundary conditions 296s 2 ion species (0.150 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 78.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 5.824172730822E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #2 (acetic-solv): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 7.76163 A 296s Current memory usage: 61.598 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.094 x 0.094 x 0.094 296s Grid lengths: 6.000 x 6.000 x 6.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 1 296s Linearized traditional PBE 296s Boundary conditions from focusing 296s 2 ion species (0.150 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 78.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 9.793622759239E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #3 (acetic-ref): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 0 A 296s Current memory usage: 61.422 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.188 x 0.188 x 0.188 296s Grid lengths: 12.000 x 12.000 x 12.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 1 296s Linearized traditional PBE 296s Multiple Debye-Huckel sphere boundary conditions 296s 2 ion species (0.000 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 2.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 5.846917564309E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #4 (acetic-ref): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 0 A 296s Current memory usage: 61.422 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.094 x 0.094 x 0.094 296s Grid lengths: 6.000 x 6.000 x 6.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 1 296s Linearized traditional PBE 296s Boundary conditions from focusing 296s 2 ion species (0.000 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 2.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 9.815953282539E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #5 (acetate-solv): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 7.76163 A 296s Current memory usage: 61.598 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.188 x 0.188 x 0.188 296s Grid lengths: 12.000 x 12.000 x 12.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 2 296s Linearized traditional PBE 296s Multiple Debye-Huckel sphere boundary conditions 296s 2 ion species (0.150 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 78.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 8.221328580569E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #6 (acetate-solv): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 7.76163 A 296s Current memory usage: 61.598 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.094 x 0.094 x 0.094 296s Grid lengths: 6.000 x 6.000 x 6.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 2 296s Linearized traditional PBE 296s Boundary conditions from focusing 296s 2 ion species (0.150 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 78.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 1.392867783119E+04 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #7 (acetate-ref): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 0 A 296s Current memory usage: 61.422 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.188 x 0.188 x 0.188 296s Grid lengths: 12.000 x 12.000 x 12.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 2 296s Linearized traditional PBE 296s Multiple Debye-Huckel sphere boundary conditions 296s 2 ion species (0.000 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 2.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 8.420373979905E+03 kJ/mol 296s Calculating forces... 296s [focusFillBound()]: WARNING: 296s Unusually large potential values 296s detected on the focusing boundary! 296s Convergence not guaranteed for NPBE/NRPBE calculations! 296s 296s ---------------------------------------- 296s CALCULATION #8 (acetate-ref): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 0 A 296s Current memory usage: 61.422 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.094 x 0.094 x 0.094 296s Grid lengths: 6.000 x 6.000 x 6.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 2 296s Linearized traditional PBE 296s Boundary conditions from focusing 296s 2 ion species (0.000 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 2.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 1.412716615065E+04 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #9 (proton-solv): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 7.76163 A 296s Current memory usage: 61.412 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.188 x 0.188 x 0.188 296s Grid lengths: 12.000 x 12.000 x 12.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 3 296s Linearized traditional PBE 296s Multiple Debye-Huckel sphere boundary conditions 296s 2 ion species (0.150 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 78.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 3.863066835285E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #10 (proton-solv): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 7.76163 A 296s Current memory usage: 61.412 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.094 x 0.094 x 0.094 296s Grid lengths: 6.000 x 6.000 x 6.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 3 296s Linearized traditional PBE 296s Boundary conditions from focusing 296s 2 ion species (0.150 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 78.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 6.289649216644E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s CALCULATION #11 (proton-ref): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 0 A 296s Current memory usage: 61.373 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.188 x 0.188 x 0.188 296s Grid lengths: 12.000 x 12.000 x 12.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 3 296s Linearized traditional PBE 296s Multiple Debye-Huckel sphere boundary conditions 296s 2 ion species (0.000 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 2.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 4.162533113906E+03 kJ/mol 296s Calculating forces... 296s [focusFillBound()]: WARNING: 296s Unusually large potential values 296s detected on the focusing boundary! 296s Convergence not guaranteed for NPBE/NRPBE calculations! 296s 296s ---------------------------------------- 296s CALCULATION #12 (proton-ref): MULTIGRID 296s Setting up problem... 296s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 296s Debye length: 0 A 296s Current memory usage: 61.373 MB total, 122.404 MB high water 296s Using linear spline charge discretization. 296s Grid dimensions: 65 x 65 x 65 296s Grid spacings: 0.094 x 0.094 x 0.094 296s Grid lengths: 6.000 x 6.000 x 6.000 296s Grid center: (0.000, -0.154, 1.287) 296s Multigrid levels: 5 296s Molecule ID: 3 296s Linearized traditional PBE 296s Boundary conditions from focusing 296s 2 ion species (0.000 M ionic strength): 296s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 296s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 296s Solute dielectric: 2.000 296s Solvent dielectric: 2.000 296s Using "molecular" surface definition;harmonic average smoothing 296s Solvent probe radius: 0.000 A 296s Temperature: 293.000 K 296s Electrostatic energies will be calculated 296s Total electrostatic energy = 6.585616091973E+03 kJ/mol 296s Calculating forces... 296s ---------------------------------------- 296s PRINT STATEMENTS 296s 296s print energy 1 (acetic-solv) - 2 (acetic-ref) end 296s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 296s Global net ELEC energy = -2.233052329981E+01 kJ/mol 296s 296s print energy 3 (acetate-solv) - 4 (acetate-ref) end 296s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 296s Global net ELEC energy = -1.984883194538E+02 kJ/mol 296s 296s print energy 5 (proton-solv) - 6 (proton-ref) end 296s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 296s Global net ELEC energy = -2.959668753288E+02 kJ/mol 296s 296s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 296s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 296s Global net ELEC energy = -4.721246714828E+02 kJ/mol 296s ---------------------------------------- 296s CLEANING UP AND SHUTTING DOWN... 296s Destroying force arrays. 296s No energy arrays to destroy. 296s Destroying multigrid structures. 296s Destroying finite element structures. 296s Destroying 3 molecules 296s Final memory usage: 0.001 MB total, 122.404 MB high water 296s 296s 296s Thanks for using APBS! 296s 296s Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 296s *** PASSED *** 296s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 296s *** PASSED *** 296s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 296s *** PASSED *** 296s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 296s *** PASSED *** 296s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 296s *** PASSED *** 296s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 296s *** PASSED *** 296s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 296s *** PASSED *** 296s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 296s *** PASSED *** 296s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 296s *** PASSED *** 296s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 296s *** PASSED *** 296s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 296s *** PASSED *** 296s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 296s *** PASSED *** 296s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 296s *** PASSED *** 296s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 296s *** PASSED *** 296s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 296s *** PASSED *** 296s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 296s *** PASSED *** 296s Elapsed time: 1.620441 seconds 296s -------------------------------------------------------------------------------- 296s Total elapsed time: 3.458293 seconds 296s Test results have been logged 296s -------------------------------------------------------------------------------- 296s -------------------------------------------------------------------------------- 296s Testing input file ion-pmf.in 296s 303s Checking for intermediate energies in input file apbs-smol.out 303s EXPECTED COMPUTED: 16 303s EXPECTED EXPECTED: 16 303s 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] 303s 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'] 303s COMPUTED RESULT 5824.172730822 303s COMPUTED RESULT 9793.622759239 303s COMPUTED RESULT 5846.917564309 303s COMPUTED RESULT 9815.953282539 303s COMPUTED RESULT 8221.328580569 303s COMPUTED RESULT 13928.67783119 303s COMPUTED RESULT 8420.373979905 303s COMPUTED RESULT 14127.16615065 303s COMPUTED RESULT 3863.066835285 303s COMPUTED RESULT 6289.649216644 303s COMPUTED RESULT 4162.533113906 303s COMPUTED RESULT 6585.616091973 303s COMPUTED RESULT -22.33052329981 303s COMPUTED RESULT -198.4883194538 303s COMPUTED RESULT -295.9668753288 303s COMPUTED RESULT -472.1246714828 303s Running tests for ion-pmf section 303s BINARY: /usr/bin/apbs 303s INPUT: ion-pmf.in 303s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 303s asc_getToken: Error occurred (bailing out). 303s Vio_scanf: Format problem with input. 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 ion-pmf.in... 303s rank 0 size 1... 303s Parsed input file. 303s Reading parameter data from parm.dat. 303s Got paths for 1 molecules 303s Reading PDB-format atom data from ion-pmf.pdb. 303s Vpmg_ibForce: No force for zero ionic strength! 303s Vpmg_ibForce: No force for zero ionic strength! 303s 2 atoms 303s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 303s Net charge 2.00e+00 e 303s Preparing to run 3 PBE calculations. 303s ---------------------------------------- 303s CALCULATION #1 (solv): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 303s Debye length: 0 A 303s Current memory usage: 61.106 MB total, 61.106 MB high water 303s Using cubic spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.210 x 0.210 x 0.210 303s Grid lengths: 13.440 x 13.440 x 13.440 303s Grid center: (0.000, 0.000, 0.000) 303s Multigrid levels: 5 303s Molecule ID: 1 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 0 ion species (0.000 M ionic strength): 303s Solute dielectric: 1.000 303s Solvent dielectric: 78.540 303s Using spline-based surface definition;window = 0.300 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s All-atom solvent forces will be calculated 303s Total electrostatic energy = 7.839535983197E+03 kJ/mol 303s Calculating forces... 303s Printing per-atom forces for molecule 1 (kJ/mol/A) 303s Legend: 303s tot n -- total force for atom n 303s qf n -- fixed charge force for atom n 303s db n -- dielectric boundary force for atom n 303s ib n -- ionic boundary force for atom n 303s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 303s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 303s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 303s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 303s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 303s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 303s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 303s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 303s Vpmg_ibForce: No force for zero ionic strength! 303s Vpmg_ibForce: No force for zero ionic strength! 303s ---------------------------------------- 303s CALCULATION #2 (ref): MULTIGRID 303s Setting up problem... 303s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 303s Debye length: 0 A 303s Current memory usage: 61.106 MB total, 61.155 MB high water 303s Using cubic spline charge discretization. 303s Grid dimensions: 65 x 65 x 65 303s Grid spacings: 0.210 x 0.210 x 0.210 303s Grid lengths: 13.440 x 13.440 x 13.440 303s Grid center: (0.000, 0.000, 0.000) 303s Multigrid levels: 5 303s Molecule ID: 1 303s Linearized traditional PBE 303s Multiple Debye-Huckel sphere boundary conditions 303s 0 ion species (0.000 M ionic strength): 303s Solute dielectric: 1.000 303s Solvent dielectric: 1.000 303s Using spline-based surface definition;window = 0.300 303s Temperature: 298.150 K 303s Electrostatic energies will be calculated 303s All-atom solvent forces will be calculated 303s Total electrostatic energy = 8.964727588811E+03 kJ/mol 303s Calculating forces... 303s Printing per-atom forces for molecule 1 (kJ/mol/A) 303s Legend: 303s tot n -- total force for atom n 303s qf n -- fixed charge force for atom n 303s db n -- dielectric boundary force for atom n 303s ib n -- ionic boundary force for atom n 303s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 303s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 303s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 303s mgF db 0 0.000e+00 0.000e+00 0.000e+00 303s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 303s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 303s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 303s mgF db 1 0.000e+00 0.000e+00 0.000e+00 303s ---------------------------------------- 303s CALCULATION #3 (asolv): APOLAR 303s Printing per atom forces (kJ/mol/A) 303s Legend: 303s tot n -- Total force for atom n 303s sasa n -- SASA force for atom n 303s sav n -- SAV force for atom n 303s wca n -- WCA force for atom n 303s 303s gamma 0.000720 303s pressure 0.000000 303s bconc 0.033000 303s 303s tot 0 2.715e-02 9.130e-07 9.128e-07 303s sasa 0 -1.100e+01 0.000e+00 0.000e+00 303s sav 0 0.000e+00 0.000e+00 0.000e+00 303s wca 0 -5.827e-01 -2.767e-05 -2.766e-05 303s tot 1 -2.723e-02 9.131e-07 9.134e-07 303s sasa 1 1.112e+01 0.000e+00 0.000e+00 303s sav 1 0.000e+00 0.000e+00 0.000e+00 303s wca 1 5.827e-01 -2.767e-05 -2.768e-05 303s 303s 303s Solvent Accessible Surface Area (SASA) for each atom: 303s SASA for atom 0: 1.153275282828E+02 303s SASA for atom 1:Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 303s *** PASSED *** 303s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 303s *** PASSED *** 303s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 303s *** PASSED *** 303s Elapsed time: 6.833382 seconds 303s -------------------------------------------------------------------------------- 303s Total elapsed time: 6.833382 seconds 303s Test results have been logged 303s -------------------------------------------------------------------------------- 303s -------------------------------------------------------------------------------- 303s Testing input file apbs-mol-vdw.in 303s 303s 1.153114143344E+02 303s 303s Total solvent accessible surface area: 230.639 A^2 303s 303s Surface tension*area energies (gamma * SASA) for each atom: 303s Surface tension*area energy for atom 0: 8.303582036361E-02 303s Surface tension*area energy for atom 1: 8.302421832080E-02 303s 303s Total surface tension energy: 0.16606 kJ/mol 303s 303s Total solvent accessible volume: 0 A^3 303s 303s Total pressure*volume energy: 0 kJ/mol 303s 303s WCA dispersion Energies for each atom: 303s WCA energy for atom 0: -6.909718345777E+00 303s WCA energy for atom 1: -6.909411348230E+00 303s 303s Total WCA energy: -13.8191 kJ/mol 303s 303s Total non-polar energy = -1.365306965532E+01 kJ/mol 303s ---------------------------------------- 303s PRINT STATEMENTS 303s 303s print energy 1 (solv) - 2 (ref) end 303s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 303s Global net ELEC energy = -1.125191605614E+03 kJ/mol 303s print force 1 (solv) - 2 (ref) end 303s Printing per-atom forces (kJ/mol/A). 303s Legend: 303s tot n -- Total force for atom n 303s qf n -- Fixed charge force for atom n 303s db n -- Dielectric boundary force for atom n 303s ib n -- Ionic boundary force for atom n 303s tot all -- Total force for system 303s qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 303s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 303s db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 303s tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 303s qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 303s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 303s db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 303s tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 303s tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 303s 303s print APOL energy 1 (asolv) end 303s Global net APOL energy = -1.365306965532E+01 kJ/mol 303s 303s print APOL force 1 (asolv) end 303s Printing per atom forces (kJ/mol/A) 303s Legend: 303s tot n -- Total force for atom n 303s sasa n -- SASA force for atom n 303s sav n -- SAV force for atom n 303s wca n -- WCA force for atom n 303s tot all -- Total force for system 303s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 303s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 303s wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 303s tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 303s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 303s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 303s wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 303s tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 303s tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 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 1 molecules 303s Final memory usage: 60.711 MB total, 62.250 MB high water 303s 303s 303s Thanks for using APBS! 303s 312s Checking for intermediate energies in input file ion-pmf.out 312s EXPECTED COMPUTED: 4 312s EXPECTED EXPECTED: 4 312s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] 312s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 312s COMPUTED RESULT 7839.535983197 312s COMPUTED RESULT 8964.727588811 312s COMPUTED RESULT -1125.191605614 312s COMPUTED RESULT -13.65306965532 312s Running tests for pka-lig section 312s BINARY: /usr/bin/apbs 312s INPUT: apbs-mol-vdw.in 312s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 312s asc_getToken: Error occurred (bailing out). 312s Vio_scanf: Format problem with input. 312s 312s 312s ---------------------------------------------------------------------- 312s APBS -- Adaptive Poisson-Boltzmann Solver 312s Version APBS 3.4.1 312s 312s Nathan A. Baker (nathan.baker@pnnl.gov) 312s Pacific Northwest National Laboratory 312s 312s Additional contributing authors listed in the code documentation. 312s 312s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 312s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 312s Northwest Division for the U.S. Department of Energy. 312s 312s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 312s Portions Copyright (c) 2002-2020, Nathan A. Baker. 312s Portions Copyright (c) 1999-2002, The Regents of the University of California. 312s Portions Copyright (c) 1995, Michael Holst. 312s All rights reserved. 312s 312s Redistribution and use in source and binary forms, with or without 312s modification, are permitted provided that the following conditions are met: 312s 312s * Redistributions of source code must retain the above copyright notice, this 312s list of conditions and the following disclaimer. 312s 312s * Redistributions in binary form must reproduce the above copyright notice, 312s this list of conditions and the following disclaimer in the documentation 312s and/or other materials provided with the distribution. 312s 312s * Neither the name of the developer nor the names of its contributors may be 312s used to endorse or promote products derived from this software without 312s specific prior written permission. 312s 312s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 312s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 312s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 312s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 312s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 312s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 312s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 312s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 312s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 312s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 312s ---------------------------------------------------------------------- 312s APBS uses FETK (the Finite Element ToolKit) to solve the 312s Poisson-Boltzmann equation numerically. FETK is a portable collection 312s of finite element modeling class libraries developed by the Michael Holst 312s research group and written in an object-oriented form of C. FEtk is 312s designed to solve general coupled systems of nonlinear partial differential 312s equations using adaptive finite element methods, inexact Newton methods, 312s and algebraic multilevel methods. More information about FEtk may be found 312s at . 312s ---------------------------------------------------------------------- 312s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 312s Aqua is a modified form of the Holst group PMG library 312s which has been modified by Patrice Koehl 312s for improved efficiency and 312s memory usage when solving the Poisson-Boltzmann equation. 312s ---------------------------------------------------------------------- 312s Please cite your use of APBS as: 312s 312s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 312s nanosystems: application to microtubules and the ribosome. Proc. 312s Natl. Acad. Sci. USA 98, 10037-10041 2001. 312s 312s 312s This executable compiled on Jan 3 2025 at 11:01:42 312s 312s Parsing input file apbs-mol-vdw.in... 312s rank 0 size 1... 312s Parsed input file. 312s Got paths for 3 molecules 312s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 312s asc_getToken: Error occurred (bailing out). 312s Vio_scanf: Format problem with input. 312s 47 atoms 312s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 312s Net charge 1.11e-16 e 312s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 312s asc_getToken: Error occurred (bailing out). 312s Vio_scanf: Format problem with input. 312s 3423 atoms 312s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 312s Net charge 1.00e+00 e 312s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 312s 3470 atoms 312s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 312s Net charge 1.00e+00 e 312s Preparing to run 6 PBE calculations. 312s ---------------------------------------- 312s CALCULATION #1 (lig-coarse): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 204.292 MB total, 204.292 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.729 x 0.729 x 0.729 312s Grid lengths: 70.000 x 70.000 x 70.000 312s Grid center: (28.969, -32.507, 27.022) 312s Multigrid levels: 4 312s Molecule ID: 1 312s Linearized traditional PBE 312s Single Debye-Huckel sphere boundary conditions 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition; no smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 2.224988750664E+03 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s CALCULATION #2 (lig-fine): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 204.292 MB total, 406.001 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.250 x 0.250 x 0.250 312s Grid lengths: 24.000 x 24.000 x 24.000 312s Grid center: (24.822, -33.153, 21.545) 312s Multigrid levels: 4 312s Molecule ID: 1 312s Linearized traditional PBE 312s Boundary conditions from focusing 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition; no smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 1.049695084686E+04 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s CALCULATION #3 (pka-coarse): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 291.151 MB total, 406.001 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.729 x 0.729 x 0.729 312s Grid lengths: 70.000 x 70.000 x 70.000 312s Grid center: (28.969, -32.507, 27.022) 312s Multigrid levels: 4 312s Molecule ID: 2 312s Linearized traditional PBE 312s Single Debye-Huckel sphere boundary conditions 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition; no smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 1.818450789522E+05 kJ/mol 312s Calculating forces... 312s [focusFillBound()]: WARNING: 312s Unusually large potential values 312s detected on the focusing boundary! 312s Convergence not guaranteed for NPBE/NRPBE calculations! 312s 312s ---------------------------------------- 312s CALCULATION #4 (pka-fine): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 291.151 MB total, 533.426 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.250 x 0.250 x 0.250 312s Grid lengths: 24.000 x 24.000 x 24.000 312s Grid center: (24.822, -33.153, 21.545) 312s Multigrid levels: 4 312s Molecule ID: 2 312s Linearized traditional PBE 312s Boundary conditions from focusing 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition; no smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 3.008254338259E+05 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s CALCULATION #5 (complex-coarse): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 292.063 MB total, 533.426 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.729 x 0.729 x 0.729 312s Grid lengths: 70.000 x 70.000 x 70.000 312s Grid center: (28.969, -32.507, 27.022) 312s Multigrid levels: 4 312s Molecule ID: 3 312s Linearized traditional PBE 312s Single Debye-Huckel sphere boundary conditions 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition; no smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 1.840918409896E+05 kJ/mol 312s Calculating forces... 312s [focusFillBound()]: WARNING: 312s Unusually large potential values 312s detected on the focusing boundary! 312s Convergence not guaranteed for NPBE/NRPBE calculations! 312s 312s ---------------------------------------- 312s CALCULATION #6 (complex-fine): MULTIGRID 312s Setting up problem... 312s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 312s Debye length: 0 A 312s Current memory usage: 292.063 MB total, 534.806 MB high water 312s Using linear spline charge discretization. 312s Grid dimensions: 97 x 97 x 97 312s Grid spacings: 0.250 x 0.250 x 0.250 312s Grid lengths: 24.000 x 24.000 x 24.000 312s Grid center: (24.822, -33.153, 21.545) 312s Multigrid levels: 4 312s Molecule ID: 3 312s Linearized traditional PBE 312s Boundary conditions from focusing 312s 2 ion species (0.000 M ionic strength): 312s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 312s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 312s Solute dielectric: 2.000 312s Solvent dielectric: 78.000 312s Using "molecular" surface definition; no smoothing 312s Solvent probe radius: 0.000 A 312s Temperature: 298.150 K 312s Electrostatic energies will be calculated 312s Total electrostatic energy = 3.113304681884E+05 kJ/mol 312s Calculating forces... 312s ---------------------------------------- 312s PRINT STATEMENTS 312s 312s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 312s Local net energy (PE 0) = 8.083515648803E+00 kJ/mol 312s Global net ELEC energy = 8.083515648803E+00 kJ/mol 312s ---------------------------------------- 312s CLEANING UP AND SHUTTING DOWN... 312s Destroying force arrays. 312s No energy arrays to destroy. 312s Destroying multigrid structures. 312s Destroying finite element structures. 312s Destroying 3 molecules 312s Final memory usage: 0.001 MB total, 534.806 MB high water 312s 312s 312s Thanks for using APBS! 312s 312s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 312s *** PASSED *** 312s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 312s *** PASSED *** 312s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 312s *** PASSED *** 312s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 312s *** PASSED *** 312s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 312s *** PASSED *** 312s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 312s *** PASSED *** 312s Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) 312s *** PASSED *** 312s Elapsed time: 8.921424 seconds 312s -------------------------------------------------------------------------------- 312s -------------------------------------------------------------------------------- 312s Testing input file apbs-smol-vdw.in 312s 320s Checking for intermediate energies in input file apbs-mol-vdw.out 320s EXPECTED COMPUTED: 7 320s EXPECTED EXPECTED: 7 320s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] 320s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 320s COMPUTED RESULT 2224.988750664 320s COMPUTED RESULT 10496.95084686 320s COMPUTED RESULT 181845.0789522 320s COMPUTED RESULT 300825.4338259 320s COMPUTED RESULT 184091.8409896 320s COMPUTED RESULT 311330.4681884 320s COMPUTED RESULT 8.083515648803 320s BINARY: /usr/bin/apbs 320s INPUT: apbs-smol-vdw.in 320s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 320s asc_getToken: Error occurred (bailing out). 320s Vio_scanf: Format problem with input. 320s 320s 320s ---------------------------------------------------------------------- 320s APBS -- Adaptive Poisson-Boltzmann Solver 320s Version APBS 3.4.1 320s 320s Nathan A. Baker (nathan.baker@pnnl.gov) 320s Pacific Northwest National Laboratory 320s 320s Additional contributing authors listed in the code documentation. 320s 320s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 320s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 320s Northwest Division for the U.S. Department of Energy. 320s 320s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 320s Portions Copyright (c) 2002-2020, Nathan A. Baker. 320s Portions Copyright (c) 1999-2002, The Regents of the University of California. 320s Portions Copyright (c) 1995, Michael Holst. 320s All rights reserved. 320s 320s Redistribution and use in source and binary forms, with or without 320s modification, are permitted provided that the following conditions are met: 320s 320s * Redistributions of source code must retain the above copyright notice, this 320s list of conditions and the following disclaimer. 320s 320s * Redistributions in binary form must reproduce the above copyright notice, 320s this list of conditions and the following disclaimer in the documentation 320s and/or other materials provided with the distribution. 320s 320s * Neither the name of the developer nor the names of its contributors may be 320s used to endorse or promote products derived from this software without 320s specific prior written permission. 320s 320s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 320s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 320s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 320s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 320s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 320s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 320s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 320s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 320s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 320s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 320s ---------------------------------------------------------------------- 320s APBS uses FETK (the Finite Element ToolKit) to solve the 320s Poisson-Boltzmann equation numerically. FETK is a portable collection 320s of finite element modeling class libraries developed by the Michael Holst 320s research group and written in an object-oriented form of C. FEtk is 320s designed to solve general coupled systems of nonlinear partial differential 320s equations using adaptive finite element methods, inexact Newton methods, 320s and algebraic multilevel methods. More information about FEtk may be found 320s at . 320s ---------------------------------------------------------------------- 320s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 320s Aqua is a modified form of the Holst group PMG library 320s which has been modified by Patrice Koehl 320s for improved efficiency and 320s memory usage when solving the Poisson-Boltzmann equation. 320s ---------------------------------------------------------------------- 320s Please cite your use of APBS as: 320s 320s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 320s nanosystems: application to microtubules and the ribosome. Proc. 320s Natl. Acad. Sci. USA 98, 10037-10041 2001. 320s 320s 320s This executable compiled on Jan 3 2025 at 11:01:42 320s 320s Parsing input file apbs-smol-vdw.in... 320s rank 0 size 1... 320s Parsed input file. 320s Got paths for 3 molecules 320s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 320s asc_getToken: Error occurred (bailing out). 320s Vio_scanf: Format problem with input. 320s 47 atoms 320s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 320s Net charge 1.11e-16 e 320s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 320s asc_getToken: Error occurred (bailing out). 320s Vio_scanf: Format problem with input. 320s 3423 atoms 320s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 320s Net charge 1.00e+00 e 320s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 320s 3470 atoms 320s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 320s Net charge 1.00e+00 e 320s Preparing to run 6 PBE calculations. 320s ---------------------------------------- 320s CALCULATION #1 (lig-coarse): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 204.292 MB total, 204.292 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.729 x 0.729 x 0.729 320s Grid lengths: 70.000 x 70.000 x 70.000 320s Grid center: (28.969, -32.507, 27.022) 320s Multigrid levels: 4 320s Molecule ID: 1 320s Linearized traditional PBE 320s Single Debye-Huckel sphere boundary conditions 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition;harmonic average smoothing 320s Solvent probe radius: 0.000 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 2.226793167046E+03 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s CALCULATION #2 (lig-fine): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 204.292 MB total, 406.001 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.250 x 0.250 x 0.250 320s Grid lengths: 24.000 x 24.000 x 24.000 320s Grid center: (24.822, -33.153, 21.545) 320s Multigrid levels: 4 320s Molecule ID: 1 320s Linearized traditional PBE 320s Boundary conditions from focusing 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition;harmonic average smoothing 320s Solvent probe radius: 0.000 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 1.050504485887E+04 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s CALCULATION #3 (pka-coarse): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 291.151 MB total, 406.001 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.729 x 0.729 x 0.729 320s Grid lengths: 70.000 x 70.000 x 70.000 320s Grid center: (28.969, -32.507, 27.022) 320s Multigrid levels: 4 320s Molecule ID: 2 320s Linearized traditional PBE 320s Single Debye-Huckel sphere boundary conditions 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition;harmonic average smoothing 320s Solvent probe radius: 0.000 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 1.827976621645E+05 kJ/mol 320s Calculating forces... 320s [focusFillBound()]: WARNING: 320s Unusually large potential values 320s detected on the focusing boundary! 320s Convergence not guaranteed for NPBE/NRPBE calculations! 320s 320s ---------------------------------------- 320s CALCULATION #4 (pka-fine): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 291.151 MB total, 533.426 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.250 x 0.250 x 0.250 320s Grid lengths: 24.000 x 24.000 x 24.000 320s Grid center: (24.822, -33.153, 21.545) 320s Multigrid levels: 4 320s Molecule ID: 2 320s Linearized traditional PBE 320s Boundary conditions from focusing 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition;harmonic average smoothing 320s Solvent probe radius: 0.000 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 3.017228546773E+05 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s CALCULATION #5 (complex-coarse): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 292.063 MB total, 533.426 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.729 x 0.729 x 0.729 320s Grid lengths: 70.000 x 70.000 x 70.000 320s Grid center: (28.969, -32.507, 27.022) 320s Multigrid levels: 4 320s Molecule ID: 3 320s Linearized traditional PBE 320s Single Debye-Huckel sphere boundary conditions 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition;harmonic average smoothing 320s Solvent probe radius: 0.000 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 1.850819075387E+05 kJ/mol 320s Calculating forces... 320s [focusFillBound()]: WARNING: 320s Unusually large potential values 320s detected on the focusing boundary! 320s Convergence not guaranteed for NPBE/NRPBE calculations! 320s 320s ---------------------------------------- 320s CALCULATION #6 (complex-fine): MULTIGRID 320s Setting up problem... 320s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 320s Debye length: 0 A 320s Current memory usage: 292.063 MB total, 534.806 MB high water 320s Using linear spline charge discretization. 320s Grid dimensions: 97 x 97 x 97 320s Grid spacings: 0.250 x 0.250 x 0.250 320s Grid lengths: 24.000 x 24.000 x 24.000 320s Grid center: (24.822, -33.153, 21.545) 320s Multigrid levels: 4 320s Molecule ID: 3 320s Linearized traditional PBE 320s Boundary conditions from focusing 320s 2 ion species (0.000 M ionic strength): 320s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 320s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 320s Solute dielectric: 2.000 320s Solvent dielectric: 78.000 320s Using "molecular" surface definition;harmonic average smoothing 320s Solvent probe radius: 0.000 A 320s Temperature: 298.150 K 320s Electrostatic energies will be calculated 320s Total electrostatic energy = 3.122488625388E+05 kJ/mol 320s Calculating forces... 320s ---------------------------------------- 320s PRINT STATEMENTS 320s 320s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 320s Local net energy (PE 0) = 2.096300255720E+01 kJ/mol 320s Global net ELEC energy = 2.096300255720E+01 kJ/mol 320s ---------------------------------------- 320s CLEANING UP AND SHUTTING DOWN... 320s Destroying force arrays. 320s No energy arrays to destroy. 320s Destroying multigrid structures. 320s Destroying finite element structures. 320s Destroying 3 molecules 320s Final memory usage: 0.001 MB total, 534.806 MB high water 320s 320s 320s Thanks for using APBS! 320s 320s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 320s *** PASSED *** 320s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 320s *** PASSED *** 320s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 320s *** PASSED *** 320s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 320s *** PASSED *** 320s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 320s *** PASSED *** 320s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 320s *** PASSED *** 320s Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) 320s *** PASSED *** 320s Elapsed time: 7.890546 seconds 320s -------------------------------------------------------------------------------- 320s -------------------------------------------------------------------------------- 320s Testing input file apbs-mol-surf.in 320s 328s Checking for intermediate energies in input file apbs-smol-vdw.out 328s EXPECTED COMPUTED: 7 328s EXPECTED EXPECTED: 7 328s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] 328s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 328s COMPUTED RESULT 2226.793167046 328s COMPUTED RESULT 10505.04485887 328s COMPUTED RESULT 182797.6621645 328s COMPUTED RESULT 301722.8546773 328s COMPUTED RESULT 185081.9075387 328s COMPUTED RESULT 312248.8625388 328s COMPUTED RESULT 20.9630025572 328s BINARY: /usr/bin/apbs 328s INPUT: apbs-mol-surf.in 328s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 328s 328s ---------------------------------------------------------------------- 328s APBS -- Adaptive Poisson-Boltzmann Solver 328s Version APBS 3.4.1 328s 328s Nathan A. Baker (nathan.baker@pnnl.gov) 328s Pacific Northwest National Laboratory 328s 328s Additional contributing authors listed in the code documentation. 328s 328s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 328s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 328s Northwest Division for the U.S. Department of Energy. 328s 328s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 328s Portions Copyright (c) 2002-2020, Nathan A. Baker. 328s Portions Copyright (c) 1999-2002, The Regents of the University of California. 328s Portions Copyright (c) 1995, Michael Holst. 328s All rights reserved. 328s 328s Redistribution and use in source and binary forms, with or without 328s modification, are permitted provided that the following conditions are met: 328s 328s * Redistributions of source code must retain the above copyright notice, this 328s list of conditions and the following disclaimer. 328s 328s * Redistributions in binary form must reproduce the above copyright notice, 328s this list of conditions and the following disclaimer in the documentation 328s and/or other materials provided with the distribution. 328s 328s * Neither the name of the developer nor the names of its contributors may be 328s used to endorse or promote products derived from this software without 328s specific prior written permission. 328s 328s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 328s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 328s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 328s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 328s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 328s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 328s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 328s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 328s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 328s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 328s ---------------------------------------------------------------------- 328s APBS uses FETK (the Finite Element ToolKit) to solve the 328s Poisson-Boltzmann equation numerically. FETK is a portable collection 328s of finite element modeling class libraries developed by the Michael Holst 328s research group and written in an object-oriented form of C. FEtk is 328s designed to solve general coupled systems of nonlinear partial differential 328s equations using adaptive finite element methods, inexact Newton methods, 328s and algebraic multilevel methods. More information about FEtk may be found 328s at . 328s ---------------------------------------------------------------------- 328s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 328s Aqua is a modified form of the Holst group PMG library 328s which has been modified by Patrice Koehl 328s for improved efficiency and 328s memory usage when solving the Poisson-Boltzmann equation. 328s ---------------------------------------------------------------------- 328s Please cite your use of APBS as: 328s 328s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 328s nanosystems: application to microtubules and the ribosome. Proc. 328s Natl. Acad. Sci. USA 98, 10037-10041 2001. 328s 328s 328s This executable compiled on Jan 3 2025 at 11:01:42 328s 328s Parsing input file apbs-mol-surf.in... 328s rank 0 size 1... 328s Parsed input file. 328s Got paths for 3 molecules 328s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 47 atoms 328s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 328s Net charge 1.11e-16 e 328s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 328s asc_getToken: Error occurred (bailing out). 328s Vio_scanf: Format problem with input. 328s 3423 atoms 328s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 328s Net charge 1.00e+00 e 328s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 328s 3470 atoms 328s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 328s Net charge 1.00e+00 e 328s Preparing to run 6 PBE calculations. 328s ---------------------------------------- 328s CALCULATION #1 (lig-coarse): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 203.877 MB total, 203.877 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.729 x 0.729 x 0.729 328s Grid lengths: 70.000 x 70.000 x 70.000 328s Grid center: (28.969, -32.507, 27.022) 328s Multigrid levels: 4 328s Molecule ID: 1 328s Linearized traditional PBE 328s Single Debye-Huckel sphere boundary conditions 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition; no smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 2.244350164274E+03 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #2 (lig-fine): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 203.877 MB total, 405.586 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.250 x 0.250 x 0.250 328s Grid lengths: 24.000 x 24.000 x 24.000 328s Grid center: (24.822, -33.153, 21.545) 328s Multigrid levels: 4 328s Molecule ID: 1 328s Linearized traditional PBE 328s Boundary conditions from focusing 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition; no smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 1.052149475373E+04 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #3 (pka-coarse): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.521 MB total, 405.586 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.729 x 0.729 x 0.729 328s Grid lengths: 70.000 x 70.000 x 70.000 328s Grid center: (28.969, -32.507, 27.022) 328s Multigrid levels: 4 328s Molecule ID: 2 328s Linearized traditional PBE 328s Single Debye-Huckel sphere boundary conditions 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition; no smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 1.862615690066E+05 kJ/mol 328s Calculating forces... 328s [focusFillBound()]: WARNING: 328s Unusually large potential values 328s detected on the focusing boundary! 328s Convergence not guaranteed for NPBE/NRPBE calculations! 328s 328s ---------------------------------------- 328s CALCULATION #4 (pka-fine): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.521 MB total, 493.795 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.250 x 0.250 x 0.250 328s Grid lengths: 24.000 x 24.000 x 24.000 328s Grid center: (24.822, -33.153, 21.545) 328s Multigrid levels: 4 328s Molecule ID: 2 328s Linearized traditional PBE 328s Boundary conditions from focusing 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition; no smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 3.051810884053E+05 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s CALCULATION #5 (complex-coarse): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.858 MB total, 493.795 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.729 x 0.729 x 0.729 328s Grid lengths: 70.000 x 70.000 x 70.000 328s Grid center: (28.969, -32.507, 27.022) 328s Multigrid levels: 4 328s Molecule ID: 3 328s Linearized traditional PBE 328s Single Debye-Huckel sphere boundary conditions 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition; no smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 1.886625455219E+05 kJ/mol 328s Calculating forces... 328s [focusFillBound()]: WARNING: 328s Unusually large potential values 328s detected on the focusing boundary! 328s Convergence not guaranteed for NPBE/NRPBE calculations! 328s 328s ---------------------------------------- 328s CALCULATION #6 (complex-fine): MULTIGRID 328s Setting up problem... 328s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 328s Debye length: 0 A 328s Current memory usage: 251.858 MB total, 494.601 MB high water 328s Using linear spline charge discretization. 328s Grid dimensions: 97 x 97 x 97 328s Grid spacings: 0.250 x 0.250 x 0.250 328s Grid lengths: 24.000 x 24.000 x 24.000 328s Grid center: (24.822, -33.153, 21.545) 328s Multigrid levels: 4 328s Molecule ID: 3 328s Linearized traditional PBE 328s Boundary conditions from focusing 328s 2 ion species (0.000 M ionic strength): 328s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 328s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 328s Solute dielectric: 2.000 328s Solvent dielectric: 78.000 328s Using "molecular" surface definition; no smoothing 328s Solvent probe radius: 1.400 A 328s Temperature: 298.150 K 328s Electrostatic energies will be calculated 328s Total electrostatic energy = 3.158218439277E+05 kJ/mol 328s Calculating forces... 328s ---------------------------------------- 328s PRINT STATEMENTS 328s 328s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 328s Local net energy (PE 0) = 1.192607686582E+02 kJ/mol 328s Global net ELEC energy = 1.192607686582E+02 kJ/mol 328s ---------------------------------------- 328s CLEANING UP AND SHUTTING DOWN... 328s Destroying force arrays. 328s No energy arrays to destroy. 328s Destroying multigrid structures. 328s Destroying finite element structures. 328s Destroying 3 molecules 328s Final memory usage: 0.001 MB total, 494.601 MB high water 328s 328s 328s Thanks for using APBS! 328s 328s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 328s *** PASSED *** 328s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 328s *** PASSED *** 328s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 328s *** PASSED *** 328s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 328s *** PASSED *** 328s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 328s *** PASSED *** 328s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 328s *** PASSED *** 328s Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) 328s *** PASSED *** 328s Elapsed time: 8.046228 seconds 328s -------------------------------------------------------------------------------- 328s -------------------------------------------------------------------------------- 328s Testing input file apbs-smol-surf.in 328s 335s Checking for intermediate energies in input file apbs-mol-surf.out 335s EXPECTED COMPUTED: 7 335s EXPECTED EXPECTED: 7 335s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] 335s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 335s COMPUTED RESULT 2244.350164274 335s COMPUTED RESULT 10521.49475373 335s COMPUTED RESULT 186261.5690066 335s COMPUTED RESULT 305181.0884053 335s COMPUTED RESULT 188662.5455219 335s COMPUTED RESULT 315821.8439277 335s COMPUTED RESULT 119.2607686582 335s BINARY: /usr/bin/apbs 335s INPUT: apbs-smol-surf.in 335s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 335s asc_getToken: Error occurred (bailing out). 335s Vio_scanf: Format problem with input. 335s 335s 335s ---------------------------------------------------------------------- 335s APBS -- Adaptive Poisson-Boltzmann Solver 335s Version APBS 3.4.1 335s 335s Nathan A. Baker (nathan.baker@pnnl.gov) 335s Pacific Northwest National Laboratory 335s 335s Additional contributing authors listed in the code documentation. 335s 335s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 335s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 335s Northwest Division for the U.S. Department of Energy. 335s 335s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 335s Portions Copyright (c) 2002-2020, Nathan A. Baker. 335s Portions Copyright (c) 1999-2002, The Regents of the University of California. 335s Portions Copyright (c) 1995, Michael Holst. 335s All rights reserved. 335s 335s Redistribution and use in source and binary forms, with or without 335s modification, are permitted provided that the following conditions are met: 335s 335s * Redistributions of source code must retain the above copyright notice, this 335s list of conditions and the following disclaimer. 335s 335s * Redistributions in binary form must reproduce the above copyright notice, 335s this list of conditions and the following disclaimer in the documentation 335s and/or other materials provided with the distribution. 335s 335s * Neither the name of the developer nor the names of its contributors may be 335s used to endorse or promote products derived from this software without 335s specific prior written permission. 335s 335s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 335s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 335s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 335s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 335s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 335s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 335s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 335s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 335s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 335s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 335s ---------------------------------------------------------------------- 335s APBS uses FETK (the Finite Element ToolKit) to solve the 335s Poisson-Boltzmann equation numerically. FETK is a portable collection 335s of finite element modeling class libraries developed by the Michael Holst 335s research group and written in an object-oriented form of C. FEtk is 335s designed to solve general coupled systems of nonlinear partial differential 335s equations using adaptive finite element methods, inexact Newton methods, 335s and algebraic multilevel methods. More information about FEtk may be found 335s at . 335s ---------------------------------------------------------------------- 335s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 335s Aqua is a modified form of the Holst group PMG library 335s which has been modified by Patrice Koehl 335s for improved efficiency and 335s memory usage when solving the Poisson-Boltzmann equation. 335s ---------------------------------------------------------------------- 335s Please cite your use of APBS as: 335s 335s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 335s nanosystems: application to microtubules and the ribosome. Proc. 335s Natl. Acad. Sci. USA 98, 10037-10041 2001. 335s 335s 335s This executable compiled on Jan 3 2025 at 11:01:42 335s 335s Parsing input file apbs-smol-surf.in... 335s rank 0 size 1... 335s Parsed input file. 335s Got paths for 3 molecules 335s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 335s asc_getToken: Error occurred (bailing out). 335s Vio_scanf: Format problem with input. 335s 47 atoms 335s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 335s Net charge 1.11e-16 e 335s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 335s asc_getToken: Error occurred (bailing out). 335s Vio_scanf: Format problem with input. 335s 3423 atoms 335s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 335s Net charge 1.00e+00 e 335s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 335s 3470 atoms 335s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 335s Net charge 1.00e+00 e 335s Preparing to run 6 PBE calculations. 335s ---------------------------------------- 335s CALCULATION #1 (lig-coarse): MULTIGRID 335s Setting up problem... 335s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 335s Debye length: 0 A 335s Current memory usage: 203.877 MB total, 203.877 MB high water 335s Using linear spline charge discretization. 335s Grid dimensions: 97 x 97 x 97 335s Grid spacings: 0.729 x 0.729 x 0.729 335s Grid lengths: 70.000 x 70.000 x 70.000 335s Grid center: (28.969, -32.507, 27.022) 335s Multigrid levels: 4 335s Molecule ID: 1 335s Linearized traditional PBE 335s Single Debye-Huckel sphere boundary conditions 335s 2 ion species (0.000 M ionic strength): 335s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 335s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 335s Solute dielectric: 2.000 335s Solvent dielectric: 78.000 335s Using "molecular" surface definition;harmonic average smoothing 335s Solvent probe radius: 1.400 A 335s Temperature: 298.150 K 335s Electrostatic energies will be calculated 335s Total electrostatic energy = 2.251466789420E+03 kJ/mol 335s Calculating forces... 335s ---------------------------------------- 335s CALCULATION #2 (lig-fine): MULTIGRID 335s Setting up problem... 335s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 335s Debye length: 0 A 335s Current memory usage: 203.877 MB total, 405.586 MB high water 335s Using linear spline charge discretization. 335s Grid dimensions: 97 x 97 x 97 335s Grid spacings: 0.250 x 0.250 x 0.250 335s Grid lengths: 24.000 x 24.000 x 24.000 335s Grid center: (24.822, -33.153, 21.545) 335s Multigrid levels: 4 335s Molecule ID: 1 335s Linearized traditional PBE 335s Boundary conditions from focusing 335s 2 ion species (0.000 M ionic strength): 335s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 335s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 335s Solute dielectric: 2.000 335s Solvent dielectric: 78.000 335s Using "molecular" surface definition;harmonic average smoothing 335s Solvent probe radius: 1.400 A 335s Temperature: 298.150 K 335s Electrostatic energies will be calculated 335s Total electrostatic energy = 1.052814502873E+04 kJ/mol 335s Calculating forces... 335s ---------------------------------------- 335s CALCULATION #3 (pka-coarse): MULTIGRID 335s Setting up problem... 335s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 335s Debye length: 0 A 335s Current memory usage: 251.521 MB total, 405.586 MB high water 335s Using linear spline charge discretization. 335s Grid dimensions: 97 x 97 x 97 335s Grid spacings: 0.729 x 0.729 x 0.729 335s Grid lengths: 70.000 x 70.000 x 70.000 335s Grid center: (28.969, -32.507, 27.022) 335s Multigrid levels: 4 335s Molecule ID: 2 335s Linearized traditional PBE 335s Single Debye-Huckel sphere boundary conditions 335s 2 ion species (0.000 M ionic strength): 335s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 335s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 335s Solute dielectric: 2.000 335s Solvent dielectric: 78.000 335s Using "molecular" surface definition;harmonic average smoothing 335s Solvent probe radius: 1.400 A 335s Temperature: 298.150 K 335s Electrostatic energies will be calculated 335s Total electrostatic energy = 1.864071689626E+05 kJ/mol 335s Calculating forces... 335s [focusFillBound()]: WARNING: 335s Unusually large potential values 335s detected on the focusing boundary! 335s Convergence not guaranteed for NPBE/NRPBE calculations! 335s 335s ---------------------------------------- 335s CALCULATION #4 (pka-fine): MULTIGRID 335s Setting up problem... 335s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 335s Debye length: 0 A 335s Current memory usage: 251.521 MB total, 493.795 MB high water 335s Using linear spline charge discretization. 335s Grid dimensions: 97 x 97 x 97 335s Grid spacings: 0.250 x 0.250 x 0.250 335s Grid lengths: 24.000 x 24.000 x 24.000 335s Grid center: (24.822, -33.153, 21.545) 335s Multigrid levels: 4 335s Molecule ID: 2 335s Linearized traditional PBE 335s Boundary conditions from focusing 335s 2 ion species (0.000 M ionic strength): 335s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 335s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 335s Solute dielectric: 2.000 335s Solvent dielectric: 78.000 335s Using "molecular" surface definition;harmonic average smoothing 335s Solvent probe radius: 1.400 A 335s Temperature: 298.150 K 335s Electrostatic energies will be calculated 335s Total electrostatic energy = 3.053319953673E+05 kJ/mol 335s Calculating forces... 335s ---------------------------------------- 335s CALCULATION #5 (complex-coarse): MULTIGRID 335s Setting up problem... 335s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 335s Debye length: 0 A 335s Current memory usage: 251.858 MB total, 493.795 MB high water 335s Using linear spline charge discretization. 335s Grid dimensions: 97 x 97 x 97 335s Grid spacings: 0.729 x 0.729 x 0.729 335s Grid lengths: 70.000 x 70.000 x 70.000 335s Grid center: (28.969, -32.507, 27.022) 335s Multigrid levels: 4 335s Molecule ID: 3 335s Linearized traditional PBE 335s Single Debye-Huckel sphere boundary conditions 335s 2 ion species (0.000 M ionic strength): 335s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 335s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 335s Solute dielectric: 2.000 335s Solvent dielectric: 78.000 335s Using "molecular" surface definition;harmonic average smoothing 335s Solvent probe radius: 1.400 A 335s Temperature: 298.150 K 335s Electrostatic energies will be calculated 335s Total electrostatic energy = 1.888027142979E+05 kJ/mol 335s Calculating forces... 335s [focusFillBound()]: WARNING: 335s Unusually large potential values 335s detected on the focusing boundary! 335s Convergence not guaranteed for NPBE/NRPBE calculations! 335s 335s ---------------------------------------- 335s CALCULATION #6 (complex-fine): MULTIGRID 335s Setting up problem... 335s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 335s Debye length: 0 A 335s Current memory usage: 251.858 MB total, 494.601 MB high water 335s Using linear spline charge discretization. 335s Grid dimensions: 97 x 97 x 97 335s Grid spacings: 0.250 x 0.250 x 0.250 335s Grid lengths: 24.000 x 24.000 x 24.000 335s Grid center: (24.822, -33.153, 21.545) 335s Multigrid levels: 4 335s Molecule ID: 3 335s Linearized traditional PBE 335s Boundary conditions from focusing 335s 2 ion species (0.000 M ionic strength): 335s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 335s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 335s Solute dielectric: 2.000 335s Solvent dielectric: 78.000 335s Using "molecular" surface definition;harmonic average smoothing 335s Solvent probe radius: 1.400 A 335s Temperature: 298.150 K 335s Electrostatic energies will be calculated 335s Total electrostatic energy = 3.159690177241E+05 kJ/mol 335s Calculating forces... 335s ---------------------------------------- 335s PRINT STATEMENTS 335s 335s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 335s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 335s Global net ELEC energy = 1.088773280806E+02 kJ/mol 335s ---------------------------------------- 335s CLEANING UP AND SHUTTING DOWN... 335s Destroying force arrays. 335s No energy arrays to destroy. 335s Destroying multigrid structures. 335s Destroying finite element structures. 335s Destroying 3 molecules 335s Final memory usage: 0.001 MB total, 494.601 MB high water 335s 335s 335s Thanks for using APBS! 335s 335s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 335s *** PASSED *** 335s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 335s *** PASSED *** 335s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 335s *** PASSED *** 335s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 335s *** PASSED *** 335s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 335s *** PASSED *** 335s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 335s *** PASSED *** 335s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 335s *** PASSED *** 335s Elapsed time: 7.677863 seconds 335s -------------------------------------------------------------------------------- 335s Total elapsed time: 32.536061 seconds 335s Test results have been logged 335s -------------------------------------------------------------------------------- 335s -------------------------------------------------------------------------------- 335s Testing input file complex-0_1.in 335s 336s Checking for intermediate energies in input file apbs-smol-surf.out 336s EXPECTED COMPUTED: 7 336s EXPECTED EXPECTED: 7 336s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 336s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 336s COMPUTED RESULT 2251.46678942 336s COMPUTED RESULT 10528.14502873 336s COMPUTED RESULT 186407.1689626 336s COMPUTED RESULT 305331.9953673 336s COMPUTED RESULT 188802.7142979 336s COMPUTED RESULT 315969.0177241 336s COMPUTED RESULT 108.8773280806 336s Running tests for point-pmf section 336s BINARY: /usr/bin/apbs 336s INPUT: complex-0_1.in 336s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 336s 336s ---------------------------------------------------------------------- 336s APBS -- Adaptive Poisson-Boltzmann Solver 336s Version APBS 3.4.1 336s 336s Nathan A. Baker (nathan.baker@pnnl.gov) 336s Pacific Northwest National Laboratory 336s 336s Additional contributing authors listed in the code documentation. 336s 336s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 336s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 336s Northwest Division for the U.S. Department of Energy. 336s 336s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 336s Portions Copyright (c) 2002-2020, Nathan A. Baker. 336s Portions Copyright (c) 1999-2002, The Regents of the University of California. 336s Portions Copyright (c) 1995, Michael Holst. 336s All rights reserved. 336s 336s Redistribution and use in source and binary forms, with or without 336s modification, are permitted provided that the following conditions are met: 336s 336s * Redistributions of source code must retain the above copyright notice, this 336s list of conditions and the following disclaimer. 336s 336s * Redistributions in binary form must reproduce the above copyright notice, 336s this list of conditions and the following disclaimer in the documentation 336s and/or other materials provided with the distribution. 336s 336s * Neither the name of the developer nor the names of its contributors may be 336s used to endorse or promote products derived from this software without 336s specific prior written permission. 336s 336s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 336s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 336s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 336s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 336s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 336s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 336s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 336s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 336s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 336s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 336s ---------------------------------------------------------------------- 336s APBS uses FETK (the Finite Element ToolKit) to solve the 336s Poisson-Boltzmann equation numerically. FETK is a portable collection 336s of finite element modeling class libraries developed by the Michael Holst 336s research group and written in an object-oriented form of C. FEtk is 336s designed to solve general coupled systems of nonlinear partial differential 336s equations using adaptive finite element methods, inexact Newton methods, 336s and algebraic multilevel methods. More information about FEtk may be found 336s at . 336s ---------------------------------------------------------------------- 336s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 336s Aqua is a modified form of the Holst group PMG library 336s which has been modified by Patrice Koehl 336s for improved efficiency and 336s memory usage when solving the Poisson-Boltzmann equation. 336s ---------------------------------------------------------------------- 336s Please cite your use of APBS as: 336s 336s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 336s nanosystems: application to microtubules and the ribosome. Proc. 336s Natl. Acad. Sci. USA 98, 10037-10041 2001. 336s 336s 336s This executable compiled on Jan 3 2025 at 11:01:42 336s 336s Parsing input file complex-0_1.in... 336s rank 0 size 1... 336s Parsed input file. 336s Got paths for 3 molecules 336s Reading PQR-format atom data from mol0.pqr. 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 1 atoms 336s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 336s Net charge 1.00e+00 e 336s Reading PQR-format atom data from mol1.pqr. 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 1 atoms 336s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 336s Net charge 1.00e+00 e 336s Reading PQR-format atom data from complex-0_1.pqr. 336s 2 atoms 336s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 336s Net charge 2.00e+00 e 336s Preparing to run 3 PBE calculations. 336s ---------------------------------------- 336s CALCULATION #1 (point1): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.060 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 1 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 9.776035707281E+01 kJ/mol 336s Fixed charge energy = 97.7604 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 96.5336 kJ/mol 336s Per-atom energies: 336s Atom 0: 9.776035707281E+01 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s CALCULATION #2 (point2): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.067 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 2 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 8.975920687031E+01 kJ/mol 336s Fixed charge energy = 89.7592 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 88.6151 kJ/mol 336s Per-atom energies: 336s Atom 0: 8.975920687031E+01 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s CALCULATION #3 (complex): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.067 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 3 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 2.058277719334E+02 kJ/mol 336s Fixed charge energy = 205.828 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 201.106 kJ/mol 336s Per-atom energies: 336s Atom 0: 1.069144350786E+02 kJ/mol 336s Atom 1: 9.891333685475E+01 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s PRINT STATEMENTS 336s 336s print energy 3 (complex) - 1 (point1) - 2 (point2) end 336s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 336s Global net ELEC energy = 1.830820799027E+01 kJ/mol 336s ---------------------------------------- 336s CLEANING UP AND SHUTTING DOWN... 336s Destroying force arrays. 336s No energy arrays to destroy. 336s Destroying multigrid structures. 336s Destroying finite element structures. 336s Destroying 3 molecules 336s Final memory usage: 0.001 MB total, 61.067 MB high water 336s 336s 336s Thanks for using APBS! 336s 336s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 336s *** PASSED *** 336s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 336s *** PASSED *** 336s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 336s *** PASSED *** 336s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 336s *** PASSED *** 336s Elapsed time: 0.351582 seconds 336s -------------------------------------------------------------------------------- 336s -------------------------------------------------------------------------------- 336s Testing input file complex-0_2.in 336s 336s Checking for intermediate energies in input file complex-0_1.out 336s EXPECTED COMPUTED: 13 336s EXPECTED EXPECTED: 13 336s 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] 336s 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'] 336s COMPUTED RESULT 97.76035707281 336s COMPUTED RESULT 89.75920687031 336s COMPUTED RESULT 205.8277719334 336s COMPUTED RESULT 0.0 336s COMPUTED RESULT 0.0 336s COMPUTED RESULT 0.0 336s COMPUTED RESULT 97.7604 336s COMPUTED RESULT 89.7592 336s COMPUTED RESULT 205.828 336s COMPUTED RESULT 96.5336 336s COMPUTED RESULT 88.6151 336s COMPUTED RESULT 201.106 336s COMPUTED RESULT 18.30820799027 336s BINARY: /usr/bin/apbs 336s INPUT: complex-0_2.in 336s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 336s 336s ---------------------------------------------------------------------- 336s APBS -- Adaptive Poisson-Boltzmann Solver 336s Version APBS 3.4.1 336s 336s Nathan A. Baker (nathan.baker@pnnl.gov) 336s Pacific Northwest National Laboratory 336s 336s Additional contributing authors listed in the code documentation. 336s 336s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 336s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 336s Northwest Division for the U.S. Department of Energy. 336s 336s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 336s Portions Copyright (c) 2002-2020, Nathan A. Baker. 336s Portions Copyright (c) 1999-2002, The Regents of the University of California. 336s Portions Copyright (c) 1995, Michael Holst. 336s All rights reserved. 336s 336s Redistribution and use in source and binary forms, with or without 336s modification, are permitted provided that the following conditions are met: 336s 336s * Redistributions of source code must retain the above copyright notice, this 336s list of conditions and the following disclaimer. 336s 336s * Redistributions in binary form must reproduce the above copyright notice, 336s this list of conditions and the following disclaimer in the documentation 336s and/or other materials provided with the distribution. 336s 336s * Neither the name of the developer nor the names of its contributors may be 336s used to endorse or promote products derived from this software without 336s specific prior written permission. 336s 336s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 336s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 336s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 336s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 336s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 336s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 336s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 336s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 336s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 336s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 336s ---------------------------------------------------------------------- 336s APBS uses FETK (the Finite Element ToolKit) to solve the 336s Poisson-Boltzmann equation numerically. FETK is a portable collection 336s of finite element modeling class libraries developed by the Michael Holst 336s research group and written in an object-oriented form of C. FEtk is 336s designed to solve general coupled systems of nonlinear partial differential 336s equations using adaptive finite element methods, inexact Newton methods, 336s and algebraic multilevel methods. More information about FEtk may be found 336s at . 336s ---------------------------------------------------------------------- 336s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 336s Aqua is a modified form of the Holst group PMG library 336s which has been modified by Patrice Koehl 336s for improved efficiency and 336s memory usage when solving the Poisson-Boltzmann equation. 336s ---------------------------------------------------------------------- 336s Please cite your use of APBS as: 336s 336s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 336s nanosystems: application to microtubules and the ribosome. Proc. 336s Natl. Acad. Sci. USA 98, 10037-10041 2001. 336s 336s 336s This executable compiled on Jan 3 2025 at 11:01:42 336s 336s Parsing input file complex-0_2.in... 336s rank 0 size 1... 336s Parsed input file. 336s Got paths for 3 molecules 336s Reading PQR-format atom data from mol0.pqr. 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 1 atoms 336s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 336s Net charge 1.00e+00 e 336s Reading PQR-format atom data from mol2.pqr. 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 1 atoms 336s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 336s Net charge 1.00e+00 e 336s Reading PQR-format atom data from complex-0_2.pqr. 336s 2 atoms 336s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 336s Net charge 2.00e+00 e 336s Preparing to run 3 PBE calculations. 336s ---------------------------------------- 336s CALCULATION #1 (point1): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.060 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 1 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 9.776035707281E+01 kJ/mol 336s Fixed charge energy = 97.7604 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 96.5336 kJ/mol 336s Per-atom energies: 336s Atom 0: 9.776035707281E+01 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s CALCULATION #2 (point2): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.067 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 2 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 1.017611498797E+02 kJ/mol 336s Fixed charge energy = 101.761 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 100.656 kJ/mol 336s Per-atom energies: 336s Atom 0: 1.017611498797E+02 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s CALCULATION #3 (complex): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.068 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 3 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 2.084282010393E+02 kJ/mol 336s Fixed charge energy = 208.428 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 203.83 kJ/mol 336s Per-atom energies: 336s Atom 0: 1.022136878480E+02 kJ/mol 336s Atom 1: 1.062145131913E+02 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s PRINT STATEMENTS 336s 336s print energy 3 (complex) - 1 (point1) - 2 (point2) end 336s Local net energy (PE 0) = 8.906694086751E+00 kJ/mol 336s Global net ELEC energy = 8.906694086751E+00 kJ/mol 336s ---------------------------------------- 336s CLEANING UP AND SHUTTING DOWN... 336s Destroying force arrays. 336s No energy arrays to destroy. 336s Destroying multigrid structures. 336s Destroying finite element structures. 336s Destroying 3 molecules 336s Final memory usage: 0.001 MB total, 61.068 MB high water 336s 336s 336s Thanks for using APBS! 336s 336s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 336s *** PASSED *** 336s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 336s *** PASSED *** 336s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 336s *** PASSED *** 336s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) 336s *** PASSED *** 336s Elapsed time: 0.344981 seconds 336s -------------------------------------------------------------------------------- 336s -------------------------------------------------------------------------------- 336s Testing input file complex-0_3.in 336s 336s Checking for intermediate energies in input file complex-0_2.out 336s EXPECTED COMPUTED: 13 336s EXPECTED EXPECTED: 13 336s 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] 336s 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'] 336s COMPUTED RESULT 97.76035707281 336s COMPUTED RESULT 101.7611498797 336s COMPUTED RESULT 208.4282010393 336s COMPUTED RESULT 0.0 336s COMPUTED RESULT 0.0 336s COMPUTED RESULT 0.0 336s COMPUTED RESULT 97.7604 336s COMPUTED RESULT 101.761 336s COMPUTED RESULT 208.428 336s COMPUTED RESULT 96.5336 336s COMPUTED RESULT 100.656 336s COMPUTED RESULT 203.83 336s COMPUTED RESULT 8.906694086751 336s BINARY: /usr/bin/apbs 336s INPUT: complex-0_3.in 336s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 336s 336s ---------------------------------------------------------------------- 336s APBS -- Adaptive Poisson-Boltzmann Solver 336s Version APBS 3.4.1 336s 336s Nathan A. Baker (nathan.baker@pnnl.gov) 336s Pacific Northwest National Laboratory 336s 336s Additional contributing authors listed in the code documentation. 336s 336s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 336s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 336s Northwest Division for the U.S. Department of Energy. 336s 336s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 336s Portions Copyright (c) 2002-2020, Nathan A. Baker. 336s Portions Copyright (c) 1999-2002, The Regents of the University of California. 336s Portions Copyright (c) 1995, Michael Holst. 336s All rights reserved. 336s 336s Redistribution and use in source and binary forms, with or without 336s modification, are permitted provided that the following conditions are met: 336s 336s * Redistributions of source code must retain the above copyright notice, this 336s list of conditions and the following disclaimer. 336s 336s * Redistributions in binary form must reproduce the above copyright notice, 336s this list of conditions and the following disclaimer in the documentation 336s and/or other materials provided with the distribution. 336s 336s * Neither the name of the developer nor the names of its contributors may be 336s used to endorse or promote products derived from this software without 336s specific prior written permission. 336s 336s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 336s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 336s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 336s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 336s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 336s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 336s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 336s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 336s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 336s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 336s ---------------------------------------------------------------------- 336s APBS uses FETK (the Finite Element ToolKit) to solve the 336s Poisson-Boltzmann equation numerically. FETK is a portable collection 336s of finite element modeling class libraries developed by the Michael Holst 336s research group and written in an object-oriented form of C. FEtk is 336s designed to solve general coupled systems of nonlinear partial differential 336s equations using adaptive finite element methods, inexact Newton methods, 336s and algebraic multilevel methods. More information about FEtk may be found 336s at . 336s ---------------------------------------------------------------------- 336s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 336s Aqua is a modified form of the Holst group PMG library 336s which has been modified by Patrice Koehl 336s for improved efficiency and 336s memory usage when solving the Poisson-Boltzmann equation. 336s ---------------------------------------------------------------------- 336s Please cite your use of APBS as: 336s 336s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 336s nanosystems: application to microtubules and the ribosome. Proc. 336s Natl. Acad. Sci. USA 98, 10037-10041 2001. 336s 336s 336s This executable compiled on Jan 3 2025 at 11:01:42 336s 336s Parsing input file complex-0_3.in... 336s rank 0 size 1... 336s Parsed input file. 336s Got paths for 3 molecules 336s Reading PQR-format atom data from mol0.pqr. 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 1 atoms 336s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 336s Net charge 1.00e+00 e 336s Reading PQR-format atom data from mol3.pqr. 336s asc_getToken: Error occurred (bailing out). 336s Vio_scanf: Format problem with input. 336s 1 atoms 336s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 336s Net charge 1.00e+00 e 336s Reading PQR-format atom data from complex-0_3.pqr. 336s 2 atoms 336s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 336s Net charge 2.00e+00 e 336s Preparing to run 3 PBE calculations. 336s ---------------------------------------- 336s CALCULATION #1 (point1): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.060 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 1 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 9.776035707281E+01 kJ/mol 336s Fixed charge energy = 97.7604 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 96.5336 kJ/mol 336s Per-atom energies: 336s Atom 0: 9.776035707281E+01 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s CALCULATION #2 (point2): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.067 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 2 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 1.337661883222E+02 kJ/mol 336s Fixed charge energy = 133.766 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 132.672 kJ/mol 336s Per-atom energies: 336s Atom 0: 1.337661883222E+02 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s CALCULATION #3 (complex): MULTIGRID 336s Setting up problem... 336s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 336s Debye length: 0 A 336s Current memory usage: 61.060 MB total, 61.068 MB high water 336s Using linear spline charge discretization. 336s Grid dimensions: 65 x 65 x 65 336s Grid spacings: 0.210 x 0.210 x 0.210 336s Grid lengths: 13.440 x 13.440 x 13.440 336s Grid center: (0.000, 0.000, 0.000) 336s Multigrid levels: 5 336s Molecule ID: 3 336s Linearized traditional PBE 336s Multiple Debye-Huckel sphere boundary conditions 336s 0 ion species (0.000 M ionic strength): 336s Solute dielectric: 78.540 336s Solvent dielectric: 78.540 336s Using spline-based surface definition;window = 0.300 336s Temperature: 298.150 K 336s Electrostatic energies will be calculated 336s Total electrostatic energy = 2.374361452120E+02 kJ/mol 336s Fixed charge energy = 237.436 kJ/mol 336s Mobile charge energy = 0 kJ/mol 336s Dielectric energy = 232.924 kJ/mol 336s Per-atom energies: 336s Atom 0: 1.007151570480E+02 kJ/mol 336s Atom 1: 1.367209881640E+02 kJ/mol 336s Calculating forces... 336s ---------------------------------------- 336s PRINT STATEMENTS 336s 336s print energy 3 (complex) - 1 (point1) - 2 (point2) end 336s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 336s Global net ELEC energy = 5.909599816984E+00 kJ/mol 336s ---------------------------------------- 336s CLEANING UP AND SHUTTING DOWN... 336s Destroying force arrays. 336s No energy arrays to destroy. 336s Destroying multigrid structures. 336s Destroying finite element structures. 336s Destroying 3 molecules 336s Final memory usage: 0.001 MB total, 61.068 MB high water 336s 336s 336s Thanks for using APBS! 336s 336s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 336s *** PASSED *** 336s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 336s *** PASSED *** 336s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 336s *** PASSED *** 336s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 336s *** PASSED *** 336s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 336s *** PASSED *** 336s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 336s *** PASSED *** 336s Elapsed time: 0.347319 seconds 336s -------------------------------------------------------------------------------- 336s -------------------------------------------------------------------------------- 336s Testing input file complex-0_4.in 336s 337s Checking for intermediate energies in input file complex-0_3.out 337s EXPECTED COMPUTED: 13 337s EXPECTED EXPECTED: 13 337s 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] 337s 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'] 337s COMPUTED RESULT 97.76035707281 337s COMPUTED RESULT 133.7661883222 337s COMPUTED RESULT 237.436145212 337s COMPUTED RESULT 0.0 337s COMPUTED RESULT 0.0 337s COMPUTED RESULT 0.0 337s COMPUTED RESULT 97.7604 337s COMPUTED RESULT 133.766 337s COMPUTED RESULT 237.436 337s COMPUTED RESULT 96.5336 337s COMPUTED RESULT 132.672 337s COMPUTED RESULT 232.924 337s COMPUTED RESULT 5.909599816984 337s BINARY: /usr/bin/apbs 337s INPUT: complex-0_4.in 337s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 337s 337s ---------------------------------------------------------------------- 337s APBS -- Adaptive Poisson-Boltzmann Solver 337s Version APBS 3.4.1 337s 337s Nathan A. Baker (nathan.baker@pnnl.gov) 337s Pacific Northwest National Laboratory 337s 337s Additional contributing authors listed in the code documentation. 337s 337s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 337s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 337s Northwest Division for the U.S. Department of Energy. 337s 337s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 337s Portions Copyright (c) 2002-2020, Nathan A. Baker. 337s Portions Copyright (c) 1999-2002, The Regents of the University of California. 337s Portions Copyright (c) 1995, Michael Holst. 337s All rights reserved. 337s 337s Redistribution and use in source and binary forms, with or without 337s modification, are permitted provided that the following conditions are met: 337s 337s * Redistributions of source code must retain the above copyright notice, this 337s list of conditions and the following disclaimer. 337s 337s * Redistributions in binary form must reproduce the above copyright notice, 337s this list of conditions and the following disclaimer in the documentation 337s and/or other materials provided with the distribution. 337s 337s * Neither the name of the developer nor the names of its contributors may be 337s used to endorse or promote products derived from this software without 337s specific prior written permission. 337s 337s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 337s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 337s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 337s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 337s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 337s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 337s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 337s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 337s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 337s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 337s ---------------------------------------------------------------------- 337s APBS uses FETK (the Finite Element ToolKit) to solve the 337s Poisson-Boltzmann equation numerically. FETK is a portable collection 337s of finite element modeling class libraries developed by the Michael Holst 337s research group and written in an object-oriented form of C. FEtk is 337s designed to solve general coupled systems of nonlinear partial differential 337s equations using adaptive finite element methods, inexact Newton methods, 337s and algebraic multilevel methods. More information about FEtk may be found 337s at . 337s ---------------------------------------------------------------------- 337s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 337s Aqua is a modified form of the Holst group PMG library 337s which has been modified by Patrice Koehl 337s for improved efficiency and 337s memory usage when solving the Poisson-Boltzmann equation. 337s ---------------------------------------------------------------------- 337s Please cite your use of APBS as: 337s 337s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 337s nanosystems: application to microtubules and the ribosome. Proc. 337s Natl. Acad. Sci. USA 98, 10037-10041 2001. 337s 337s 337s This executable compiled on Jan 3 2025 at 11:01:42 337s 337s Parsing input file complex-0_4.in... 337s rank 0 size 1... 337s Parsed input file. 337s Got paths for 3 molecules 337s Reading PQR-format atom data from mol0.pqr. 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 1 atoms 337s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 337s Net charge 1.00e+00 e 337s Reading PQR-format atom data from mol4.pqr. 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 1 atoms 337s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 337s Net charge 1.00e+00 e 337s Reading PQR-format atom data from complex-0_4.pqr. 337s 2 atoms 337s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 337s Net charge 2.00e+00 e 337s Preparing to run 3 PBE calculations. 337s ---------------------------------------- 337s CALCULATION #1 (point1): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 337s Debye length: 0 A 337s Current memory usage: 61.060 MB total, 61.060 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.210 x 0.210 x 0.210 337s Grid lengths: 13.440 x 13.440 x 13.440 337s Grid center: (0.000, 0.000, 0.000) 337s Multigrid levels: 5 337s Molecule ID: 1 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 0 ion species (0.000 M ionic strength): 337s Solute dielectric: 78.540 337s Solvent dielectric: 78.540 337s Using spline-based surface definition;window = 0.300 337s Temperature: 298.150 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 9.776035707281E+01 kJ/mol 337s Fixed charge energy = 97.7604 kJ/mol 337s Mobile charge energy = 0 kJ/mol 337s Dielectric energy = 96.5336 kJ/mol 337s Per-atom energies: 337s Atom 0: 9.776035707281E+01 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #2 (point2): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 337s Debye length: 0 A 337s Current memory usage: 61.060 MB total, 61.067 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.210 x 0.210 x 0.210 337s Grid lengths: 13.440 x 13.440 x 13.440 337s Grid center: (0.000, 0.000, 0.000) 337s Multigrid levels: 5 337s Molecule ID: 2 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 0 ion species (0.000 M ionic strength): 337s Solute dielectric: 78.540 337s Solvent dielectric: 78.540 337s Using spline-based surface definition;window = 0.300 337s Temperature: 298.150 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 1.017611498797E+02 kJ/mol 337s Fixed charge energy = 101.761 kJ/mol 337s Mobile charge energy = 0 kJ/mol 337s Dielectric energy = 100.654 kJ/mol 337s Per-atom energies: 337s Atom 0: 1.017611498797E+02 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #3 (complex): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 337s Debye length: 0 A 337s Current memory usage: 61.061 MB total, 61.068 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.210 x 0.210 x 0.210 337s Grid lengths: 13.440 x 13.440 x 13.440 337s Grid center: (0.000, 0.000, 0.000) 337s Multigrid levels: 5 337s Molecule ID: 3 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 0 ion species (0.000 M ionic strength): 337s Solute dielectric: 78.540 337s Solvent dielectric: 78.540 337s Using spline-based surface definition;window = 0.300 337s Temperature: 298.150 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 2.039516519000E+02 kJ/mol 337s Fixed charge energy = 203.952 kJ/mol 337s Mobile charge energy = 0 kJ/mol 337s Dielectric energy = 199.493 kJ/mol 337s Per-atom energies: 337s Atom 0: 9.997541697022E+01 kJ/mol 337s Atom 1: 1.039762349297E+02 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s PRINT STATEMENTS 337s 337s print energy 3 (complex) - 1 (point1) - 2 (point2) end 337s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 337s Global net ELEC energy = 4.430144947418E+00 kJ/mol 337s ---------------------------------------- 337s CLEANING UP AND SHUTTING DOWN... 337s Destroying force arrays. 337s No energy arrays to destroy. 337s Destroying multigrid structures. 337s Destroying finite element structures. 337s Destroying 3 molecules 337s Final memory usage: 0.001 MB total, 61.068 MB high water 337s 337s 337s Thanks for using APBS! 337s 337s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 337s *** PASSED *** 337s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 337s *** PASSED *** 337s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 337s *** PASSED *** 337s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 337s *** PASSED *** 337s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 337s *** PASSED *** 337s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 337s *** PASSED *** 337s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 337s *** PASSED *** 337s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 337s *** PASSED *** 337s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 337s *** PASSED *** 337s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 337s *** PASSED *** 337s Elapsed time: 0.337231 seconds 337s -------------------------------------------------------------------------------- 337s Total elapsed time: 1.381113 seconds 337s Test results have been logged 337s -------------------------------------------------------------------------------- 337s -------------------------------------------------------------------------------- 337s Testing input file apbs-mol.in 337s 337s Checking for intermediate energies in input file complex-0_4.out 337s EXPECTED COMPUTED: 13 337s EXPECTED EXPECTED: 13 337s 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] 337s 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'] 337s COMPUTED RESULT 97.76035707281 337s COMPUTED RESULT 101.7611498797 337s COMPUTED RESULT 203.9516519 337s COMPUTED RESULT 0.0 337s COMPUTED RESULT 0.0 337s COMPUTED RESULT 0.0 337s COMPUTED RESULT 97.7604 337s COMPUTED RESULT 101.761 337s COMPUTED RESULT 203.952 337s COMPUTED RESULT 96.5336 337s COMPUTED RESULT 100.654 337s COMPUTED RESULT 199.493 337s COMPUTED RESULT 4.430144947418 337s Running tests for solv section 337s BINARY: /usr/bin/apbs 337s INPUT: apbs-mol.in 337s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 337s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 337s *** PASSED *** 337s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 337s 337s ---------------------------------------------------------------------- 337s APBS -- Adaptive Poisson-Boltzmann Solver 337s Version APBS 3.4.1 337s 337s Nathan A. Baker (nathan.baker@pnnl.gov) 337s Pacific Northwest National Laboratory 337s 337s Additional contributing authors listed in the code documentation. 337s 337s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 337s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 337s Northwest Division for the U.S. Department of Energy. 337s 337s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 337s Portions Copyright (c) 2002-2020, Nathan A. Baker. 337s Portions Copyright (c) 1999-2002, The Regents of the University of California. 337s Portions Copyright (c) 1995, Michael Holst. 337s All rights reserved. 337s 337s Redistribution and use in source and binary forms, with or without 337s modification, are permitted provided that the following conditions are met: 337s 337s * Redistributions of source code must retain the above copyright notice, this 337s list of conditions and the following disclaimer. 337s 337s * Redistributions in binary form must reproduce the above copyright notice, 337s this list of conditions and the following disclaimer in the documentation 337s and/or other materials provided with the distribution. 337s 337s * Neither the name of the developer nor the names of its contributors may be 337s used to endorse or promote products derived from this software without 337s specific prior written permission. 337s 337s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 337s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 337s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 337s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 337s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 337s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 337s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 337s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 337s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 337s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 337s ---------------------------------------------------------------------- 337s APBS uses FETK (the Finite Element ToolKit) to solve the 337s Poisson-Boltzmann equation numerically. FETK is a portable collection 337s of finite element modeling class libraries developed by the Michael Holst 337s research group and written in an object-oriented form of C. FEtk is 337s designed to solve general coupled systems of nonlinear partial differential 337s equations using adaptive finite element methods, inexact Newton methods, 337s and algebraic multilevel methods. More information about FEtk may be found 337s at . 337s ---------------------------------------------------------------------- 337s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 337s Aqua is a modified form of the Holst group PMG library 337s which has been modified by Patrice Koehl 337s for improved efficiency and 337s memory usage when solving the Poisson-Boltzmann equation. 337s ---------------------------------------------------------------------- 337s Please cite your use of APBS as: 337s 337s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 337s nanosystems: application to microtubules and the ribosome. Proc. 337s Natl. Acad. Sci. USA 98, 10037-10041 2001. 337s 337s 337s This executable compiled on Jan 3 2025 at 11:01:42 337s 337s Parsing input file apbs-mol.in... 337s rank 0 size 1... 337s Parsed input file. 337s Got paths for 2 molecules 337s Reading PQR-format atom data from methanol.pqr. 337s asc_getToken: Error occurred (bailing out). 337s Vio_scanf: Format problem with input. 337s 3 atoms 337s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 337s Net charge 5.55e-17 e 337s Reading PQR-format atom data from methoxide.pqr. 337s 2 atoms 337s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 337s Net charge -1.00e+00 e 337s Preparing to run 4 PBE calculations. 337s ---------------------------------------- 337s CALCULATION #1 (methanol-solv): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 0 A 337s Current memory usage: 61.253 MB total, 61.253 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.250 x 0.250 x 0.250 337s Grid lengths: 16.000 x 16.000 x 16.000 337s Grid center: (0.309, 0.000, -0.242) 337s Multigrid levels: 5 337s Molecule ID: 1 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.000 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 1.847663548071E+03 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #2 (methanol-ref): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 0 A 337s Current memory usage: 61.253 MB total, 61.328 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.250 x 0.250 x 0.250 337s Grid lengths: 16.000 x 16.000 x 16.000 337s Grid center: (0.309, 0.000, -0.242) 337s Multigrid levels: 5 337s Molecule ID: 1 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.000 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 1.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 1.883912182952E+03 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #3 (methoxide-solv): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 0 A 337s Current memory usage: 61.250 MB total, 61.328 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.250 x 0.250 x 0.250 337s Grid lengths: 16.000 x 16.000 x 16.000 337s Grid center: (0.000, 0.000, -0.128) 337s Multigrid levels: 5 337s Molecule ID: 2 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.000 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 78.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 2.732623683321E+03 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s CALCULATION #4 (methoxide-ref): MULTIGRID 337s Setting up problem... 337s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 337s Debye length: 0 A 337s Current memory usage: 61.250 MB total, 61.328 MB high water 337s Using linear spline charge discretization. 337s Grid dimensions: 65 x 65 x 65 337s Grid spacings: 0.250 x 0.250 x 0.250 337s Grid lengths: 16.000 x 16.000 x 16.000 337s Grid center: (0.000, 0.000, -0.128) 337s Multigrid levels: 5 337s Molecule ID: 2 337s Linearized traditional PBE 337s Multiple Debye-Huckel sphere boundary conditions 337s 2 ion species (0.000 M ionic strength): 337s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 337s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 337s Solute dielectric: 2.000 337s Solvent dielectric: 1.000 337s Using "molecular" surface definition; no smoothing 337s Solvent probe radius: 0.000 A 337s Temperature: 300.000 K 337s Electrostatic energies will be calculated 337s Total electrostatic energy = 3.123035854133E+03 kJ/mol 337s Calculating forces... 337s ---------------------------------------- 337s PRINT STATEMENTS 337s 337s print energy 1 (methanol-solv) - 2 (methanol-ref) end 337s Local net energy (PE 0) = -3.624863488075E+01 kJ/mol 337s Global net ELEC energy = -3.624863488075E+01 kJ/mol 337s 337s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 337s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 337s Global net ELEC energy = -3.904121708125E+02 kJ/mol 337s 337s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 337s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 337s Global net ELEC energy = -3.541635359318E+02 kJ/mol 337s ---------------------------------------- 337s CLEANING UP AND SHUTTING DOWN... 337s Destroying force arrays. 337s No energy arrays to destroy. 337s Destroying multigrid structures. 337s Destroying finite element structures. 337s Destroying 2 molecules 337s Final memory usage: 0.001 MB total, 61.328 MB high water 337s 337s 337s Thanks for using APBS! 337s 337s *** PASSED *** 337s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 337s *** PASSED *** 337s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 337s *** PASSED *** 337s Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) 337s *** PASSED *** 337s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 337s *** PASSED *** 337s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 337s *** PASSED *** 337s Elapsed time: 0.509824 seconds 337s -------------------------------------------------------------------------------- 337s -------------------------------------------------------------------------------- 337s Testing input file apbs-smol.in 337s 338s Checking for intermediate energies in input file apbs-mol.out 338s EXPECTED COMPUTED: 7 338s EXPECTED EXPECTED: 7 338s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] 338s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 338s COMPUTED RESULT 1847.663548071 338s COMPUTED RESULT 1883.912182952 338s COMPUTED RESULT 2732.623683321 338s COMPUTED RESULT 3123.035854133 338s COMPUTED RESULT -36.24863488075 338s COMPUTED RESULT -390.4121708125 338s COMPUTED RESULT -354.1635359318 338s BINARY: /usr/bin/apbs 338s INPUT: apbs-smol.in 338s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 338s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 338s *** PASSED *** 338s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 338s *** PASSED *** 338s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 338s *** PASSED *** 338s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 338s *** PASSED *** 338s Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) 338s *** PASSED *** 338s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 338s *** PASSED *** 338s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 338s *** PASSED *** 338s Elapsed time: 0.534825 seconds 338s -------------------------------------------------------------------------------- 338s Total elapsed time: 1.044649 seconds 338s Test results have been logged 338s -------------------------------------------------------------------------------- 338s asc_getToken: Error occurred (bailing out). 338s Vio_scanf: Format problem with input. 338s 338s 338s ---------------------------------------------------------------------- 338s APBS -- Adaptive Poisson-Boltzmann Solver 338s Version APBS 3.4.1 338s 338s Nathan A. Baker (nathan.baker@pnnl.gov) 338s Pacific Northwest National Laboratory 338s 338s Additional contributing authors listed in the code documentation. 338s 338s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 338s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 338s Northwest Division for the U.S. Department of Energy. 338s 338s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 338s Portions Copyright (c) 2002-2020, Nathan A. Baker. 338s Portions Copyright (c) 1999-2002, The Regents of the University of California. 338s Portions Copyright (c) 1995, Michael Holst. 338s All rights reserved. 338s 338s Redistribution and use in source and binary forms, with or without 338s modification, are permitted provided that the following conditions are met: 338s 338s * Redistributions of source code must retain the above copyright notice, this 338s list of conditions and the following disclaimer. 338s 338s * Redistributions in binary form must reproduce the above copyright notice, 338s this list of conditions and the following disclaimer in the documentation 338s and/or other materials provided with the distribution. 338s 338s * Neither the name of the developer nor the names of its contributors may be 338s used to endorse or promote products derived from this software without 338s specific prior written permission. 338s 338s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 338s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 338s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 338s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 338s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 338s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 338s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 338s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 338s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 338s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 338s ---------------------------------------------------------------------- 338s APBS uses FETK (the Finite Element ToolKit) to solve the 338s Poisson-Boltzmann equation numerically. FETK is a portable collection 338s of finite element modeling class libraries developed by the Michael Holst 338s research group and written in an object-oriented form of C. FEtk is 338s designed to solve general coupled systems of nonlinear partial differential 338s equations using adaptive finite element methods, inexact Newton methods, 338s and algebraic multilevel methods. More information about FEtk may be found 338s at . 338s ---------------------------------------------------------------------- 338s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 338s Aqua is a modified form of the Holst group PMG library 338s which has been modified by Patrice Koehl 338s for improved efficiency and 338s memory usage when solving the Poisson-Boltzmann equation. 338s ---------------------------------------------------------------------- 338s Please cite your use of APBS as: 338s 338s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 338s nanosystems: application to microtubules and the ribosome. Proc. 338s Natl. Acad. Sci. USA 98, 10037-10041 2001. 338s 338s 338s This executable compiled on Jan 3 2025 at 11:01:42 338s 338s Parsing input file apbs-smol.in... 338s rank 0 size 1... 338s Parsed input file. 338s Got paths for 2 molecules 338s Reading PQR-format atom data from methanol.pqr. 338s asc_getToken: Error occurred (bailing out). 338s Vio_scanf: Format problem with input. 338s 3 atoms 338s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 338s Net charge 5.55e-17 e 338s Reading PQR-format atom data from methoxide.pqr. 338s 2 atoms 338s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 338s Net charge -1.00e+00 e 338s Preparing to run 4 PBE calculations. 338s ---------------------------------------- 338s CALCULATION #1 (methanol-solv): MULTIGRID 338s Setting up problem... 338s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 338s Debye length: 0 A 338s Current memory usage: 61.253 MB total, 61.253 MB high water 338s Using linear spline charge discretization. 338s Grid dimensions: 65 x 65 x 65 338s Grid spacings: 0.250 x 0.250 x 0.250 338s Grid lengths: 16.000 x 16.000 x 16.000 338s Grid center: (0.309, 0.000, -0.242) 338s Multigrid levels: 5 338s Molecule ID: 1 338s Linearized traditional PBE 338s Multiple Debye-Huckel sphere boundary conditions 338s 2 ion species (0.000 M ionic strength): 338s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 338s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 338s Solute dielectric: 2.000 338s Solvent dielectric: 78.000 338s Using "molecular" surface definition;harmonic average smoothing 338s Solvent probe radius: 0.000 A 338s Temperature: 300.000 K 338s Electrostatic energies will be calculated 338s Total electrostatic energy = 1.847860440020E+03 kJ/mol 338s Calculating forces... 338s ---------------------------------------- 338s CALCULATION #2 (methanol-ref): MULTIGRID 338s Setting up problem... 338s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 338s Debye length: 0 A 338s Current memory usage: 61.253 MB total, 61.328 MB high water 338s Using linear spline charge discretization. 338s Grid dimensions: 65 x 65 x 65 338s Grid spacings: 0.250 x 0.250 x 0.250 338s Grid lengths: 16.000 x 16.000 x 16.000 338s Grid center: (0.309, 0.000, -0.242) 338s Multigrid levels: 5 338s Molecule ID: 1 338s Linearized traditional PBE 338s Multiple Debye-Huckel sphere boundary conditions 338s 2 ion species (0.000 M ionic strength): 338s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 338s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 338s Solute dielectric: 2.000 338s Solvent dielectric: 1.000 338s Using "molecular" surface definition;harmonic average smoothing 338s Solvent probe radius: 0.000 A 338s Temperature: 300.000 K 338s Electrostatic energies will be calculated 338s Total electrostatic energy = 1.885436377745E+03 kJ/mol 338s Calculating forces... 338s ---------------------------------------- 338s CALCULATION #3 (methoxide-solv): MULTIGRID 338s Setting up problem... 338s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 338s Debye length: 0 A 338s Current memory usage: 61.250 MB total, 61.328 MB high water 338s Using linear spline charge discretization. 338s Grid dimensions: 65 x 65 x 65 338s Grid spacings: 0.250 x 0.250 x 0.250 338s Grid lengths: 16.000 x 16.000 x 16.000 338s Grid center: (0.000, 0.000, -0.128) 338s Multigrid levels: 5 338s Molecule ID: 2 338s Linearized traditional PBE 338s Multiple Debye-Huckel sphere boundary conditions 338s 2 ion species (0.000 M ionic strength): 338s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 338s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 338s Solute dielectric: 2.000 338s Solvent dielectric: 78.000 338s Using "molecular" surface definition;harmonic average smoothing 338s Solvent probe radius: 0.000 A 338s Temperature: 300.000 K 338s Electrostatic energies will be calculated 338s Total electrostatic energy = 2.734040568569E+03 kJ/mol 338s Calculating forces... 338s ---------------------------------------- 338s CALCULATION #4 (methoxide-ref): MULTIGRID 338s Setting up problem... 338s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 338s Debye length: 0 A 338s Current memory usage: 61.250 MB total, 61.328 MB high water 338s Using linear spline charge discretization. 338s Grid dimensions: 65 x 65 x 65 338s Grid spacings: 0.250 x 0.250 x 0.250 338s Grid lengths: 16.000 x 16.000 x 16.000 338s Grid center: (0.000, 0.000, -0.128) 338s Multigrid levels: 5 338s Molecule ID: 2 338s Linearized traditional PBE 338s Multiple Debye-Huckel sphere boundary conditions 338s 2 ion species (0.000 M ionic strength): 338s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 338s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 338s Solute dielectric: 2.000 338s Solvent dielectric: 1.000 338s Using "molecular" surface definition;harmonic average smoothing 338s Solvent probe radius: 0.000 A 338s Temperature: 300.000 K 338s Electrostatic energies will be calculated 338s Total electrostatic energy = 3.125279428954E+03 kJ/mol 338s Calculating forces... 338s ---------------------------------------- 338s PRINT STATEMENTS 338s 338s print energy 1 (methanol-solv) - 2 (methanol-ref) end 338s Local net energy (PE 0) = -3.757593772492E+01 kJ/mol 338s Global net ELEC energy = -3.757593772492E+01 kJ/mol 338s 338s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 338s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 338s Global net ELEC energy = -3.912388603848E+02 kJ/mol 338s 338s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 338s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 338s Global net ELEC energy = -3.536629226599E+02 kJ/mol 338s ---------------------------------------- 338s CLEANING UP AND SHUTTING DOWN... 338s Destroying force arrays. 338s No energy arrays to destroy. 338s Destroying multigrid structures. 338s Destroying finite element structures. 338s Destroying 2 molecules 338s Final memory usage: 0.001 MB total, 61.328 MB high water 338s 338s 338s Thanks for using APBS! 338s 338s Checking for intermediate energies in input file apbs-smol.out 338s EXPECTED COMPUTED: 7 338s EXPECTED EXPECTED: 7 338s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] 338s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 338s COMPUTED RESULT 1847.86044002 338s COMPUTED RESULT 1885.436377745 338s COMPUTED RESULT 2734.040568569 338s COMPUTED RESULT 3125.279428954 338s COMPUTED RESULT -37.57593772492 338s COMPUTED RESULT -391.2388603848 338s COMPUTED RESULT -353.6629226599 338s autopkgtest [16:14:56]: test test-apbs: -----------------------] 339s test-apbs PASS 339s autopkgtest [16:14:57]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 339s autopkgtest [16:14:57]: @@@@@@@@@@@@@@@@@@@@ summary 339s test-apbs PASS